|
1
|
Jurburg SD. Short Read Lengths Recover Ecological Patterns in 16S rRNA Gene Amplicon Data. Mol Ecol Resour 2025:e14102. [PMID: 40079420 DOI: 10.1111/1755-0998.14102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 02/19/2025] [Accepted: 03/05/2025] [Indexed: 03/15/2025]
Abstract
16S rRNA gene metabarcoding, the study of amplicon sequences of the 16S rRNA gene from mixed environmental samples, is an increasingly popular and accessible method for assessing bacterial communities across a wide range of environments. As metabarcoding sequence data archives continue to grow, data reuse will likely become an important source of novel insights into the ecology of microbes. While recent work has demonstrated the benefits of longer read lengths for the study of microbial communities from 16S rRNA gene segments, no studies have explored the use of shorter (< 200 bp) read lengths in the context of data reuse. Nevertheless, this information is essential to improve the reuse and comparability of metabarcoding data across existing datasets. This study reanalyzed nine 16S rRNA datasets targeting aquatic, animal-associated and soil microbiomes, and evaluated how processing the sequence data across a range of read lengths affected the resulting taxonomic assignments, biodiversity metrics and differential (i.e., before-after treatment) analyses. Short read lengths successfully recovered ecological patterns and allowed for the use of more sequences. Limited increases in resolution were observed beyond 150 bp reads across environments. Furthermore, abundance-weighted diversity metrics (e.g., Inverse Simpson index, Morisita-Horn dissimilarities or weighted Unifrac distances) were more robust to variation in read lengths. Read lengths alone contributed to consistent increases in the total number of ASVs detected, highlighting the need to consider metabarcoding-derived diversity estimates within the context of the bioinformatics parameters selected. This study provides evidence-based guidelines for the processing of short reads.
Collapse
Affiliation(s)
- Stephanie D Jurburg
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| |
Collapse
|
|
2
|
Turton-Hughes S, Holmes G, Hassall C. The diversity of ignorance and the ignorance of diversity: origins and implications of "shadow diversity" for conservation biology and extinction. CAMBRIDGE PRISMS. EXTINCTION 2024; 2:e18. [PMID: 40078810 PMCID: PMC11895729 DOI: 10.1017/ext.2024.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 05/05/2024] [Accepted: 06/19/2024] [Indexed: 03/14/2025]
Abstract
Biodiversity shortfalls and taxonomic bias can lead to inaccurate assessment of conservation priorities. Previous literature has begun to explore practical reasons why some species are discovered sooner or are better researched than others. However, the deeper socio-cultural causes for undiscovered and neglected biodiversity, and the value of collectively analysing species at risk of unrecorded, or "dark", extinction, are yet to be fully examined. Here, we argue that a new label (we propose "shadow diversity") is needed to shift our perspective from biodiversity shortfalls to living, albeit unknown, species. We suggest this linguistic shift imparts intrinsic value to these species, beyond scientific gaze and cultural systems. We review research on undiscovered, undetected and hidden biodiversity in the fields of conservation biology, macroecology and genetics. Drawing on philosophy, geography, history and sociology, we demonstrate that a range of socio-cultural factors (funding, education and historical bias) combine with traditional, practical impediments to limit species discovery and detection. We propose using a spectrum of shadow diversity which enables a complex, non-binary and comprehensive approach to biodiversity unknowns. Shadow diversity holds exciting potential as a tool to increase awareness, appreciation and support for the conservation of traditionally less studied wildlife species and sites, from soil microbes to less charismatic habitat fragments. We advocate for a shift in how the conservation community and wider public see biodiversity and an increase in popular support for conserving a wider range of life forms. Most importantly, shadow diversity provides appropriate language and conceptual frameworks to discuss species absent from conservation assessment and at potential risk of dark extinction.
Collapse
Affiliation(s)
- Serena Turton-Hughes
- School of Earth and Environment, Faculty of Environment, University of Leeds, Leeds, UK
| | - George Holmes
- School of Earth and Environment, Faculty of Environment, University of Leeds, Leeds, UK
| | - Christopher Hassall
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| |
Collapse
|
|
3
|
Lin X, Waring K, Ghezzi H, Tropini C, Tyson J, Ziels RM. High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the Nanopore platform. PNAS NEXUS 2024; 3:pgae411. [PMID: 39386005 PMCID: PMC11462149 DOI: 10.1093/pnasnexus/pgae411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 09/05/2024] [Indexed: 10/12/2024]
Abstract
Small subunit (SSU) ribosomal RNA (rRNA) gene amplicon sequencing is a foundational method in microbial ecology. Currently, short-read platforms are commonly employed for high-throughput applications of SSU rRNA amplicon sequencing, but at the cost of poor taxonomic classification due to limited fragment lengths. The Oxford Nanopore Technologies (ONT) platform can sequence full-length SSU rRNA genes, but its lower raw-read accuracy has so-far limited accurate taxonomic classification and de novo feature generation. Here, we present a sequencing workflow, termed ssUMI, that combines unique molecular identifier (UMI)-based error correction with newer (R10.4+) ONT chemistry and sample barcoding to enable high throughput near full-length SSU rRNA (e.g. 16S rRNA) amplicon sequencing. The ssUMI workflow generated near full-length 16S rRNA consensus sequences with 99.99% mean accuracy using a minimum subread coverage of 3×, surpassing the accuracy of Illumina short reads. The consensus sequences generated with ssUMI were used to produce error-free de novo sequence features with no false positives with two microbial community standards. In contrast, Nanopore raw reads produced erroneous de novo sequence features, indicating that UMI-based error correction is currently necessary for high-accuracy microbial profiling with R10.4+ ONT sequencing chemistries. We showcase the cost-competitive scalability of the ssUMI workflow by sequencing 87 time-series wastewater samples and 27 human gut samples, obtaining quantitative ecological insights that were missed by short-read amplicon sequencing. ssUMI, therefore, enables accurate and low-cost full-length 16S rRNA amplicon sequencing on Nanopore, improving accessibility to high-resolution microbiome science.
Collapse
Affiliation(s)
- Xuan Lin
- Civil Engineering, The University of British Columbia, 6250 Applied Science Ln #2002, Vancouver, BC, CanadaV6T 1Z4
| | - Katherine Waring
- Civil Engineering, The University of British Columbia, 6250 Applied Science Ln #2002, Vancouver, BC, CanadaV6T 1Z4
| | - Hans Ghezzi
- Graduate Program in Bioinformatics, The University of British Columbia, Vancouver, BC, CanadaV5Z 4S6
| | - Carolina Tropini
- Graduate Program in Bioinformatics, The University of British Columbia, Vancouver, BC, CanadaV5Z 4S6
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, CanadaV6T 1Z3
- School of Biomedical Engineering, The University of British Columbia, Vancouver, BC, CanadaV6T 2B9
- Humans and the Microbiome Program, Canadian Institute for Advanced Research (CIFAR), Toronto, ON, CanadaM5G 1M1
| | - John Tyson
- British Columbia Center for Disease Control Public Health Laboratory, Vancouver, BC, CanadaV5Z 4R4
- Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, CanadaV6T 1Z7
| | - Ryan M Ziels
- Civil Engineering, The University of British Columbia, 6250 Applied Science Ln #2002, Vancouver, BC, CanadaV6T 1Z4
| |
Collapse
|
|
4
|
Baker BJ, Hyde E, Leão P. Nature should be the model for microbial sciences. J Bacteriol 2024; 206:e0022824. [PMID: 39158294 PMCID: PMC11411942 DOI: 10.1128/jb.00228-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024] Open
Abstract
Until recently, microbiologists have relied on cultures to understand the microbial world. As a result, model organisms have been the focus of research into understanding Bacteria and Archaea at a molecular level. Diversity surveys and metagenomic sequencing have revealed that these model species are often present in low abundance in the environment; instead, there are microbial taxa that are cosmopolitan in nature. Due to the numerical dominance of these microorganisms and the size of their habitats, these lineages comprise mind-boggling population sizes upward of 1028 cells on the planet. Many of these dominant groups have cultured representatives and have been shown to be involved in mediating key processes in nature. Given their importance and the increasing need to understand changes due to climate change, we propose that members of Nitrosophaerota (Nitrosopumilus maritimus), SAR11 (Pelagibacter ubique), Hadesarchaeia, Bathyarchaeia, and others become models in the future. Abundance should not be the only measure of a good model system; there are other organisms that are well suited to advance our understanding of ecology and evolution. For example, the most well-studied symbiotic bacteria, like Buchnera, Aliivibrio, and Rhizobium, should be models for understanding host-associations. Also, there are organisms that hold new insights into major transitions in the evolution of life on the planet like the Asgard Archaea (Heimdallarchaeia). Innovations in a variety of in situ techniques have enabled us to circumvent culturing when studying everything from genetics to physiology. Our deepest understanding of microbiology and its impact on the planet will come from studying these microbes in nature. Laboratory-based studies must be grounded in nature, not the other way around.
Collapse
Affiliation(s)
- Brett J Baker
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, Texas, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Emily Hyde
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Pedro Leão
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, Texas, USA
- Department of Microbiology-RIBES, Radboud University, Nijmegen, the Netherlands
| |
Collapse
|
|
5
|
Behrenfeld MJ, Bisson KM. Neutral Theory and Plankton Biodiversity. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:283-305. [PMID: 37368954 DOI: 10.1146/annurev-marine-112122-105229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
The biodiversity of the plankton has been interpreted largely through the monocle of competition. The spatial distancing of phytoplankton in nature is so large that cell boundary layers rarely overlap, undermining opportunities for resource-based competitive exclusion. Neutral theory accounts for biodiversity patterns based purely on random birth, death, immigration, and speciation events and has commonly served as a null hypothesis in terrestrial ecology but has received comparatively little attention in aquatic ecology. This review summarizes basic elements of neutral theory and explores its stand-alone utility for understanding phytoplankton diversity. A theoretical framework is described entailing a very nonneutral trophic exclusion principle melded with the concept of ecologically defined neutral niches. This perspective permits all phytoplankton size classes to coexist at any limiting resource level, predicts greater diversity than anticipated from readily identifiable environmental niches but less diversity than expected from pure neutral theory, and functions effectively in populations of distantly spaced individuals.
Collapse
Affiliation(s)
- Michael J Behrenfeld
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA; ,
| | - Kelsey M Bisson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA; ,
| |
Collapse
|
|
6
|
Arahal D, Bisgaard M, Christensen H, Clermont D, Dijkshoorn L, Duim B, Emler S, Figge M, Göker M, Moore ERB, Nemec A, Nørskov-Lauritsen N, Nübel U, On SLW, Vandamme P, Ventosa A. The best of both worlds: a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2024; 74. [PMID: 38180015 DOI: 10.1099/ijsem.0.006188] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Abstract
The naming of prokaryotes is governed by the International Code of Nomenclature of Prokaryotes (ICNP) and partially by the International Code of Nomenclature for Algae, Fungi and Plants (ICN). Such codes must be able to determine names of taxa in a universal and unambiguous manner, thus serving as a common language across different fields and activities. This unity is undermined when a new code of nomenclature emerges that overlaps in scope with an established, time-tested code and uses the same format of names but assigns different nomenclatural status values to the names. The resulting nomenclatural confusion is not beneficial to the wider scientific community. Such ambiguity is expected to result from the establishment of the 'Code of Nomenclature of Prokaryotes Described from DNA Sequence Data' ('SeqCode'), which is in general and specific conflict with the ICNP and the ICN. Shortcomings in the interpretation of the ICNP may have exacerbated the incompatibility between the codes. It is reiterated as to why proposals to accept sequences as nomenclatural types of species and subspecies with validly published names, now implemented in the SeqCode, have not been implemented by the International Committee on Systematics of Prokaryotes (ICSP), which oversees the ICNP. The absence of certain regulations from the ICNP for the naming of as yet uncultivated prokaryotes is an acceptable scientific argument, although it does not justify the establishment of a separate code. Moreover, the proposals rejected by the ICSP are unnecessary to adequately regulate the naming of uncultivated prokaryotes. To provide a better service to the wider scientific community, an alternative proposal to emend the ICNP is presented, which would result in Candidatus names being regulated analogously to validly published names. This proposal is fully consistent with previous ICSP decisions, preserves the essential unity of nomenclature and avoids the expected nomenclatural confusion.
Collapse
Affiliation(s)
- David Arahal
- Departamento de Microbiología y Ecología, Universitat de València, Valencia, Spain
| | | | - Henrik Christensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Dominique Clermont
- Institut Pasteur, Université Paris Cité, CRBIP, CIP-Collection of Institut Pasteur, F-75015 Paris, France
| | - Lenie Dijkshoorn
- Department of Infectious Diseases, Leiden University Medical Center, Albinusdreef 2, Leiden / Torensteelaan 68, 3281 MA Numansdorp, Netherlands
| | - Birgitta Duim
- Department Biomolecular Health Sciences, Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CS Utrecht, Netherlands
| | - Stefan Emler
- SmartGene Services SARL, EPFL Innovation Park, PSE-C, CH-1015 Lausanne, Switzerland
| | - Marian Figge
- Westerdijk Fungal Biodiversity Institute Uppsalalaan 8 3584 CT, Utrecht, Netherlands
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - Edward R B Moore
- Department of Infectious Disease and Culture Collection University of Gothenburg (CCUG), Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-402 34 Gothenburg, Sweden
| | - Alexandr Nemec
- Laboratory of Bacterial Genetics, National Institute of Public Health, Srobarova 48, 100 00 Prague 10, Czech Republic
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, V Úvalu 84, 150 06 Prague 5, Czechia
| | | | - Ulrich Nübel
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
- Technical University Braunschweig, Institute of Microbiology, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany
| | - Stephen L W On
- Department of Wine, Food and Molecular Biosciences, Faculty of Agricultural Science, Lincoln University, Lincoln 7647, Christchurch, New Zealand
| | - Peter Vandamme
- BCCM/LMG, Laboratorium voor Microbiologie, Universiteit Gent (UGent) K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, C/. Prof. Garcia Gonzalez 2, ES-41012 Sevilla, Spain
| |
Collapse
|
|
7
|
Liu L, Zhong KX, Chen Q, Wang Y, Zhang T, Jiao N, Zheng Q. Selective cell lysis pressure on rare and abundant prokaryotic taxa across a shelf-to-slope continuum in the Northern South China Sea. Appl Environ Microbiol 2023; 89:e0139323. [PMID: 38014961 PMCID: PMC10734510 DOI: 10.1128/aem.01393-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 10/19/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Virus-induced host lysis contributes up to 40% of total prokaryotic mortality and plays crucial roles in shaping microbial composition and diversity in the ocean. Nonetheless, what taxon-specific cell lysis is caused by viruses remains to be studied. The present study, therefore, examined the taxon-specific cell lysis and estimated its contribution to the variations in the rare and abundant microbial taxa. The results demonstrate that taxon-specific mortality differed in surface and bottom of the coastal environment. In addition, active rare taxa are more susceptible to heightened lytic pressure and suggested the importance of viral lysis in regulating the microbial community composition. These results improve our understanding of bottom-up (abiotic environmental variables) and top-down (viral lysis) controls contributing to microbial community assembly in the ocean.
Collapse
Affiliation(s)
- Lu Liu
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Kevin Xu Zhong
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | - Qi Chen
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Yu Wang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Ting Zhang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Qiang Zheng
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| |
Collapse
|
|
8
|
He XY, Liu NH, Liu JQ, Peng M, Teng ZJ, Gu TJ, Chen XL, Chen Y, Wang P, Li CY, Todd JD, Zhang YZ, Zhang XY. SAR92 clade bacteria are potentially important DMSP degraders and sources of climate-active gases in marine environments. mBio 2023; 14:e0146723. [PMID: 37948335 PMCID: PMC10746254 DOI: 10.1128/mbio.01467-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/25/2023] [Indexed: 11/12/2023] Open
Abstract
IMPORTANCE Catabolism of dimethylsulfoniopropionate (DMSP) by marine bacteria has important impacts on the global sulfur cycle and climate. However, whether and how members of most oligotrophic bacterial groups participate in DMSP metabolism in marine environments remains largely unknown. In this study, by characterizing culturable strains, we have revealed that bacteria of the SAR92 clade, an abundant oligotrophic group of Gammaproteobacteria in coastal seawater, can catabolize DMSP through the DMSP lyase DddD-mediated cleavage pathway and/or the DMSP demethylase DmdA-mediated demethylation pathway to produce climate-active gases dimethylsulfide and methanethiol. Additionally, we found that SAR92 clade bacteria capable of catabolizing DMSP are widely distributed in global oceans. These results indicate that SAR92 clade bacteria are potentially important DMSP degraders and sources of climate-active gases in marine environments that have been overlooked, contributing to a better understanding of the roles and mechanisms of the oligotrophic bacteria in oceanic DMSP degradation.
Collapse
Affiliation(s)
- Xiao-Yan He
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
| | - Ning-Hua Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
| | - Ji-Qing Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ming Peng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Zhao-Jie Teng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Tie-Ji Gu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
| | - Yin Chen
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Peng Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
| | - Chun-Yang Li
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
| | - Jonathan D. Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Yu-Zhong Zhang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
| |
Collapse
|
|
9
|
Villavicencio-Tejo F, Olesen MA, Navarro L, Calisto N, Iribarren C, García K, Corsini G, Quintanilla RA. Gut-Brain Axis Deregulation and Its Possible Contribution to Neurodegenerative Disorders. Neurotox Res 2023; 42:4. [PMID: 38103074 DOI: 10.1007/s12640-023-00681-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 11/10/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023]
Abstract
The gut-brain axis is an essential communication pathway between the central nervous system (CNS) and the gastrointestinal tract. The human microbiota is composed of a diverse and abundant microbial community that compasses more than 100 trillion microorganisms that participate in relevant physiological functions such as host nutrient metabolism, structural integrity, maintenance of the gut mucosal barrier, and immunomodulation. Recent evidence in animal models has been instrumental in demonstrating the possible role of the microbiota in neurodevelopment, neuroinflammation, and behavior. Furthermore, clinical studies suggested that adverse changes in the microbiota can be considered a susceptibility factor for neurological disorders (NDs), such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS). In this review, we will discuss evidence describing the role of gut microbes in health and disease as a relevant risk factor in the pathogenesis of neurodegenerative disorders, including AD, PD, HD, and ALS.
Collapse
Affiliation(s)
- Francisca Villavicencio-Tejo
- Laboratory of Neurodegenerative Diseases, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, El Llano Subercaseaux 2801, 5to Piso, San Miguel 8910060, Santiago, Chile
| | - Margrethe A Olesen
- Laboratory of Neurodegenerative Diseases, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, El Llano Subercaseaux 2801, 5to Piso, San Miguel 8910060, Santiago, Chile
| | - Laura Navarro
- Laboratorio de Microbiología Molecular y Compuestos Bioactivos, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Nancy Calisto
- Laboratorio de Microbiología Molecular y Compuestos Bioactivos, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Cristian Iribarren
- Laboratorio de Patógenos Gastrointestinales, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Katherine García
- Laboratorio de Patógenos Gastrointestinales, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Gino Corsini
- Laboratorio de Microbiología Molecular y Compuestos Bioactivos, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Rodrigo A Quintanilla
- Laboratory of Neurodegenerative Diseases, Facultad de Ciencias de La Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, El Llano Subercaseaux 2801, 5to Piso, San Miguel 8910060, Santiago, Chile.
| |
Collapse
|
|
10
|
Mendoza-Cano F, Encinas-García T, Muhlia-Almazán A, Porchas-Cornejo M, de la Re-Vega E, Sánchez-Paz A. Development and validation of a real-time PCR assay protocol for the specific detection and quantification of pelagiphages in seawater samples. MARINE ENVIRONMENTAL RESEARCH 2023; 191:106168. [PMID: 37708616 DOI: 10.1016/j.marenvres.2023.106168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/31/2023] [Accepted: 09/02/2023] [Indexed: 09/16/2023]
Abstract
Earth is inhabited by numerous adaptations of cellular forms shaped by the persistent scrutiny of natural selection. Thus, as natural selection has fixed beneficial adaptations of functional traits, cellular life has conquered almost all environmental niches on our planet. However, cellular life succumbs in number and genetic diversity to viruses. Among all viruses, phages are highly prevalent in diverse environments, and due to their vast genetic diversity and abundance, their relevant role as significant players in several ecological processes is now fully recognized. Pelagiphages, bacteriophages infecting bacteria of the SAR11 clade, are the most abundant viruses in the oceans. However, the ecological contribution of pelagiphages on populations of Pelagibacterales remains largely underestimated. An essential aspect of estimating the impact of bacteriophages is their absolute and precise quantification, which provides relevant information about the host-virus interactions and the structure of viral assemblages. Consequently, due to its abundance and claimed influence in the biogeochemical cycling of elements, the accurate quantification of pelagiphages results in an essential task. This study describes the development and validation of a sensitive, specific, accurate and reproducible qPCR platform targeting pelagiphages. Moreover, this method allowed the detection and quantification of pelagiphages in the Gulf of California for the first time.
Collapse
Affiliation(s)
- F Mendoza-Cano
- Laboratorio de Virología, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), S.C. (Campus Hermosillo), Calle Hermosa 101, Fraccionamiento Los Ángeles, Hermosillo, Sonora, C.P. 83206, México
| | - T Encinas-García
- Laboratorio de Virología, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), S.C. (Campus Hermosillo), Calle Hermosa 101, Fraccionamiento Los Ángeles, Hermosillo, Sonora, C.P. 83206, México; Departamento de Investigaciones Científicas y Tecnológicas (DICTUS), Universidad de Sonora, Hermosillo, Sonora, 83000, México
| | - A Muhlia-Almazán
- Bioenergetics and Molecular Genetics Lab, Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C. Carretera Gustavo Enrique Astiazarán Rosas, No. 46, Col. La Victoria, Hermosillo, Sonora, 83304, México
| | - M Porchas-Cornejo
- Centro de Investigaciones Biológicas del Noroeste, S.C. Km 2.35 Carretera a Las Tinajas, S/N Colonia Tinajas, Guaymas, Sonora, C.P. 85460, México
| | - E de la Re-Vega
- Departamento de Investigaciones Científicas y Tecnológicas (DICTUS), Universidad de Sonora, Hermosillo, Sonora, 83000, México
| | - A Sánchez-Paz
- Laboratorio de Virología, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), S.C. (Campus Hermosillo), Calle Hermosa 101, Fraccionamiento Los Ángeles, Hermosillo, Sonora, C.P. 83206, México.
| |
Collapse
|
|
11
|
Mandhata CP, Bishoyi AK, Sahoo CR, Maharana S, Padhy RN. Insight to biotechnological utility of phycochemicals from cyanobacterium Anabaena sp.: An overview. Fitoterapia 2023; 169:105594. [PMID: 37343687 DOI: 10.1016/j.fitote.2023.105594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/12/2023] [Accepted: 06/17/2023] [Indexed: 06/23/2023]
Abstract
Cyanobacteria (blue-green algae) are well-known for the ability to excrete extra-cellular products, as a variety of cyanochemicals (phycocompounds) of curio with several extensive therapeutic applications. Among these phycocompound, the cyanotoxins from certain water-bloom forming taxa are toxic to biota, including crocodiles. Failure of current non-renewable source compounds in producing sustainable and non-toxic therapeutics led the urgency of discovering products from natural sources. Particularly, compounds of the filamentous N2-fixing Anabaena sp. have effective antibacterial, antifungal, antioxidant, and anticancer properties. Today, such newer compounds are the potential targets for the possible novel chemical scaffolds, suitable for mainstream-drug development cascades. Bioactive compounds of Anabaena sp. such as, anatoxins, hassallidins and phycobiliproteins have proven their inherent antibacterial, antifungal, and antineoplastic activities, respectively. Herein, the available details of the biomass production and the inherent phyco-constituents namely, alkaloids, lipids, phenols, peptides, proteins, polysaccharides, terpenoids and cyanotoxins are considered, along with geographical distributions and morphological characteristics of the cyanobacterium. The acquisitions of cyanochemicals in recent years have newly addressed several pharmaceutical aliments, and the understanding of the associated molecular interactions of phycochemicals have been considered, for plausible use in drug developments in future.
Collapse
Affiliation(s)
- Chinmayee Priyadarsani Mandhata
- Central Research Laboratory, Institute of Medical Science & SUM Hospital, Siksha O Anusandhan Deemed to be University, Bhubaneswar, 751003, Odisha, India
| | - Ajit Kumar Bishoyi
- Central Research Laboratory, Institute of Medical Science & SUM Hospital, Siksha O Anusandhan Deemed to be University, Bhubaneswar, 751003, Odisha, India
| | - Chita Ranjan Sahoo
- Central Research Laboratory, Institute of Medical Science & SUM Hospital, Siksha O Anusandhan Deemed to be University, Bhubaneswar, 751003, Odisha, India.
| | | | - Rabindra Nath Padhy
- Central Research Laboratory, Institute of Medical Science & SUM Hospital, Siksha O Anusandhan Deemed to be University, Bhubaneswar, 751003, Odisha, India.
| |
Collapse
|
|
12
|
Thompson LR, Thielen P. Decoding dissolved information: environmental DNA sequencing at global scale to monitor a changing ocean. Curr Opin Biotechnol 2023; 81:102936. [PMID: 37060640 DOI: 10.1016/j.copbio.2023.102936] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/03/2023] [Accepted: 03/13/2023] [Indexed: 04/17/2023]
Abstract
The use of environmental DNA (eDNA) technology for environmental monitoring is rapidly expanding, with applications for fisheries, coral reefs, harmful algal blooms, invasive and endangered species, and biodiversity monitoring. By enabling detection of species over space and time, eDNA fulfills a fundamental need of environmental surveys. Traditional surveys are expensive, require significant capital expenditure, and can be destructive; eDNA offers promise for cheaper, less invasive, and higher-resolution (i.e. genetic) assessments of environments and stocks. However, challenges in quantification, detection limits, biobanking capacity, reference databases, and data management and integration remain significant hurdles to efficient eDNA monitoring at global and decadal scale. Here, we consider the current state of eDNA technology and its suitability for the problems for which it is being used. We explore the current best practices, the logistical and social challenges that prevent eDNA from widespread adoption and benefit, and the emerging technologies that may address those challenges.
Collapse
Affiliation(s)
- Luke R Thompson
- Northern Gulf Institute, Mississippi State University, 2 Research Blvd, Starkville, MS 39759, USA; Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, 4301 Rickenbacker Cswy, Miami, FL 33149, USA.
| | - Peter Thielen
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD 20723-6099, USA
| |
Collapse
|
|
13
|
Geller-McGrath D, Mara P, Taylor GT, Suter E, Edgcomb V, Pachiadaki M. Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin. Nat Commun 2023; 14:656. [PMID: 36746960 PMCID: PMC9902471 DOI: 10.1038/s41467-023-36026-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/12/2023] [Indexed: 02/08/2023] Open
Abstract
Secondary metabolites play essential roles in ecological interactions and nutrient acquisition, and are of interest for their potential uses in medicine and biotechnology. Genome mining for biosynthetic gene clusters (BGCs) can be used for the discovery of new compounds. Here, we use metagenomics and metatranscriptomics to analyze BGCs in free-living and particle-associated microbial communities through the stratified water column of the Cariaco Basin, Venezuela. We recovered 565 bacterial and archaeal metagenome-assembled genomes (MAGs) and identified 1154 diverse BGCs. We show that differences in water redox potential and microbial lifestyle (particle-associated vs. free-living) are associated with variations in the predicted composition and production of secondary metabolites. Our results indicate that microbes, including understudied clades such as Planctomycetota, potentially produce a wide range of secondary metabolites in these anoxic/euxinic waters.
Collapse
Affiliation(s)
| | - Paraskevi Mara
- Geology & Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Elizabeth Suter
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
- Biology, Chemistry and Environmental Studies Department, Molloy College, Rockville Centre, NY, USA
| | - Virginia Edgcomb
- Geology & Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - Maria Pachiadaki
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| |
Collapse
|
|
14
|
Patin NV, Goodwin KD. Capturing marine microbiomes and environmental DNA: A field sampling guide. Front Microbiol 2023; 13:1026596. [PMID: 36713215 PMCID: PMC9877356 DOI: 10.3389/fmicb.2022.1026596] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/22/2022] [Indexed: 01/15/2023] Open
Abstract
The expanding interest in marine microbiome and eDNA sequence data has led to a demand for sample collection and preservation standard practices to enable comparative assessments of results across studies and facilitate meta-analyses. We support this effort by providing guidelines based on a review of published methods and field sampling experiences. The major components considered here are environmental and resource considerations, sample processing strategies, sample storage options, and eDNA extraction protocols. It is impossible to provide universal recommendations considering the wide range of eDNA applications; rather, we provide information to design fit-for-purpose protocols. To manage scope, the focus here is on sampling collection and preservation of prokaryotic and microeukaryotic eDNA. Even with a focused view, the practical utility of any approach depends on multiple factors, including habitat type, available resources, and experimental goals. We broadly recommend enacting rigorous decontamination protocols, pilot studies to guide the filtration volume needed to characterize the target(s) of interest and minimize PCR inhibitor collection, and prioritizing sample freezing over (only) the addition of preservation buffer. An annotated list of studies that test these parameters is included for more detailed investigation on specific steps. To illustrate an approach that demonstrates fit-for-purpose methodologies, we provide a protocol for eDNA sampling aboard an oceanographic vessel. These guidelines can aid the decision-making process for scientists interested in sampling and sequencing marine microbiomes and/or eDNA.
Collapse
Affiliation(s)
- Nastassia Virginia Patin
- Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, National Oceanic and Atmospheric Administration, Miami, FL, United States,Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States,Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, United States,*Correspondence: Nastassia Virginia Patin,
| | - Kelly D. Goodwin
- Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, National Oceanic and Atmospheric Administration, Miami, FL, United States,Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, United States
| |
Collapse
|
|
15
|
Pinhassi J, Farnelid H, García SM, Teira E, Galand PE, Obernosterer I, Quince C, Vila-Costa M, Gasol JM, Lundin D, Andersson AF, Labrenz M, Riemann L. Functional responses of key marine bacteria to environmental change - toward genetic counselling for coastal waters. Front Microbiol 2022; 13:869093. [PMID: 36532459 PMCID: PMC9751014 DOI: 10.3389/fmicb.2022.869093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 11/11/2022] [Indexed: 10/31/2024] Open
Abstract
Coastal ecosystems deteriorate globally due to human-induced stress factors, like nutrient loading and pollution. Bacteria are critical to marine ecosystems, e.g., by regulating nutrient cycles, synthesizing vitamins, or degrading pollutants, thereby providing essential ecosystem services ultimately affecting economic activities. Yet, until now bacteria are overlooked both as mediators and indicators of ecosystem health, mainly due to methodological limitations in assessing bacterial ecosystem functions. However, these limitations are largely overcome by the advances in molecular biology and bioinformatics methods for characterizing the genetics that underlie functional traits of key bacterial populations - "key" in providing important ecosystem services, being abundant, or by possessing high metabolic rates. It is therefore timely to analyze and define the functional responses of bacteria to human-induced effects on coastal ecosystem health. We posit that categorizing the responses of key marine bacterial populations to changes in environmental conditions through modern microbial oceanography methods will allow establishing the nascent field of genetic counselling for our coastal waters. This requires systematic field studies of linkages between functional traits of key bacterial populations and their ecosystem functions in coastal seas, complemented with systematic experimental analyses of the responses to different stressors. Research and training in environmental management along with dissemination of results and dialogue with societal actors are equally important to ensure the role of bacteria is understood as fundamentally important for coastal ecosystems. Using the responses of microorganisms as a tool to develop genetic counselling for coastal ecosystems can ultimately allow for integrating bacteria as indicators of environmental change.
Collapse
Affiliation(s)
- Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Hanna Farnelid
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Sandra Martínez García
- Departamento de Ecoloxía e Bioloxía Animal, Centro de Investigación Mariña, Universidade de Vigo, Vigo, Spain
| | - Eva Teira
- Departamento de Ecoloxía e Bioloxía Animal, Centro de Investigación Mariña, Universidade de Vigo, Vigo, Spain
| | - Pierre E. Galand
- CNRS, Laboratoire d’Ecogéochimie des Environnements Benthiques (LECOB), Sorbonne Université, Banyuls-sur-Mer, France
| | - Ingrid Obernosterer
- CNRS, Laboratoire d’Océanographie Microbienne (LOMIC), Sorbonne Université, Banyuls-sur-Mer, France
| | | | | | | | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Anders F. Andersson
- Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Lasse Riemann
- Marine Biology Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| |
Collapse
|
|
16
|
Dinasquet J, Landa M, Obernosterer I. SAR11 clade microdiversity and activity during the early spring blooms off Kerguelen Island, Southern Ocean. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:907-916. [PMID: 36028477 DOI: 10.1111/1758-2229.13117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/10/2022] [Indexed: 05/17/2023]
Abstract
The ecology of the SAR11 clade, the most abundant bacterial group in the ocean, has been intensively studied in temperate and tropical regions, but its distribution remains largely unexplored in the Southern Ocean. Through amplicon sequencing of the 16S rRNA gene, we assessed the contribution of the SAR11 clade to bacterial community composition in the naturally iron fertilized region off Kerguelen Island. We investigated the upper 300 m at seven sites located in early spring phytoplankton blooms and at one high-nutrient low-chlorophyll site. Despite pronounced vertical patterns of the bacterioplankton assemblages, the SAR11 clade had high relative abundances at all depths and sites, averaging 40% (±15%) of the total community relative abundance. Micro-autoradiography combined with CARD-FISH further revealed that the clade had an overall stable contribution (45%-60% in surface waters) to bacterial biomass production (determined by 3 H-leucine incorporation) during different early bloom stages. The spatio-temporal partitioning of some of the SAR11 subclades suggests a niche specificity and periodic selection of different subclades in response to the fluctuating extreme conditions of the Southern Ocean. These observations improve our understanding of the ecology of the SAR11 clade and its implications in biogeochemical cycles in the rapidly changing Southern Ocean.
Collapse
Affiliation(s)
- Julie Dinasquet
- CNRS, Sorbonne Université, Laboratoire d'Océanographie Microbienne, LOMIC, Banyuls-sur-Mer, France
- Marine Biology Research Division and Climate, Atmospheric Science & Physical Oceanography Department, Scripps Institution of Oceanography, San Diego, California, USA
| | - Marine Landa
- CNRS, Sorbonne Université, Laboratoire d'Océanographie Microbienne, LOMIC, Banyuls-sur-Mer, France
- Sorbonne Université/Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Ingrid Obernosterer
- CNRS, Sorbonne Université, Laboratoire d'Océanographie Microbienne, LOMIC, Banyuls-sur-Mer, France
| |
Collapse
|
|
17
|
Rogers AD, Appeltans W, Assis J, Ballance LT, Cury P, Duarte C, Favoretto F, Hynes LA, Kumagai JA, Lovelock CE, Miloslavich P, Niamir A, Obura D, O'Leary BC, Ramirez-Llodra E, Reygondeau G, Roberts C, Sadovy Y, Steeds O, Sutton T, Tittensor DP, Velarde E, Woodall L, Aburto-Oropeza O. Discovering marine biodiversity in the 21st century. ADVANCES IN MARINE BIOLOGY 2022; 93:23-115. [PMID: 36435592 DOI: 10.1016/bs.amb.2022.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
We review the current knowledge of the biodiversity of the ocean as well as the levels of decline and threat for species and habitats. The lack of understanding of the distribution of life in the ocean is identified as a significant barrier to restoring its biodiversity and health. We explore why the science of taxonomy has failed to deliver knowledge of what species are present in the ocean, how they are distributed and how they are responding to global and regional to local anthropogenic pressures. This failure prevents nations from meeting their international commitments to conserve marine biodiversity with the results that investment in taxonomy has declined in many countries. We explore a range of new technologies and approaches for discovery of marine species and their detection and monitoring. These include: imaging methods, molecular approaches, active and passive acoustics, the use of interconnected databases and citizen science. Whilst no one method is suitable for discovering or detecting all groups of organisms many are complementary and have been combined to give a more complete picture of biodiversity in marine ecosystems. We conclude that integrated approaches represent the best way forwards for accelerating species discovery, description and biodiversity assessment. Examples of integrated taxonomic approaches are identified from terrestrial ecosystems. Such integrated taxonomic approaches require the adoption of cybertaxonomy approaches and will be boosted by new autonomous sampling platforms and development of machine-speed exchange of digital information between databases.
Collapse
Affiliation(s)
- Alex D Rogers
- REV Ocean, Lysaker, Norway; Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom.
| | - Ward Appeltans
- Intergovernmental Oceanographic Commission of UNESCO, Oostende, Belgium
| | - Jorge Assis
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Lisa T Ballance
- Marine Mammal Institute, Oregon State University, Newport, OR, United States
| | | | - Carlos Duarte
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia
| | - Fabio Favoretto
- Autonomous University of Baja California Sur, La Paz, Baja California Sur, Mexico
| | - Lisa A Hynes
- Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom
| | - Joy A Kumagai
- Senckenberg Biodiversity and Climate Research Institute, Frankfurt am Main, Germany
| | - Catherine E Lovelock
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Patricia Miloslavich
- Scientific Committee on Oceanic Research (SCOR), College of Earth, Ocean and Environment, University of Delaware, Newark, DE, United States; Departamento de Estudios Ambientales, Universidad Simón Bolívar, Venezuela & Scientific Committee for Oceanic Research (SCOR), Newark, DE, United States
| | - Aidin Niamir
- Senckenberg Biodiversity and Climate Research Institute, Frankfurt am Main, Germany
| | | | - Bethan C O'Leary
- Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom; Department of Environment and Geography, University of York, York, United Kingdom
| | - Eva Ramirez-Llodra
- REV Ocean, Lysaker, Norway; Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom
| | - Gabriel Reygondeau
- Yale Center for Biodiversity Movement and Global Change, Yale University, New Haven, CT, United States; Nippon Foundation-Nereus Program, Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC, Canada
| | - Callum Roberts
- Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | - Yvonne Sadovy
- School of Biological Sciences, Swire Institute of Marine Science, The University of Hong Kong, Hong Kong
| | - Oliver Steeds
- Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom
| | - Tracey Sutton
- Nova Southeastern University, Halmos College of Natural Sciences and Oceanography, Dania Beach, FL, United States
| | | | - Enriqueta Velarde
- Instituto de Ciencias Marinas y Pesquerías, Universidad Veracruzana, Veracruz, Mexico
| | - Lucy Woodall
- Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom; Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | |
Collapse
|
|
18
|
Genomes from Uncultivated Pelagiphages Reveal Multiple Phylogenetic Clades Exhibiting Extensive Auxiliary Metabolic Genes and Cross-Family Multigene Transfers. mSystems 2022; 7:e0152221. [PMID: 35972150 PMCID: PMC9599517 DOI: 10.1128/msystems.01522-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
For the abundant marine Alphaproteobacterium Pelagibacter (SAR11), and other bacteria, phages are powerful forces of mortality. However, little is known about the most abundant Pelagiphages in nature, such as the widespread HTVC023P-type, which is currently represented by two cultured phages. Using viral metagenomic data sets and fluorescence-activated cell sorting, we recovered 80 complete, undescribed Podoviridae genomes that form 10 phylogenomically distinct clades (herein, named Clades I to X) related to the HTVC023P-type. These expanded the HTVC023P-type pan-genome by 15-fold and revealed 41 previously unknown auxiliary metabolic genes (AMGs) in this viral lineage. Numerous instances of partner-AMGs (colocated and involved in related functions) were observed, including partners in nucleotide metabolism, DNA hypermodification, and Curli biogenesis. The Type VIII secretion system (T8SS) responsible for Curli biogenesis was identified in nine genomes and expanded the repertoire of T8SS proteins reported thus far in viruses. Additionally, the identified T8SS gene cluster contained an iron-dependent regulator (FecR), as well as a histidine kinase and adenylate cyclase that can be implicated in T8SS function but are not within T8SS operons in bacteria. While T8SS are lacking in known Pelagibacter, they contribute to aggregation and biofilm formation in other bacteria. Phylogenetic reconstructions of partner-AMGs indicate derivation from cellular lineages with a more recent transfer between viral families. For example, homologs of all T8SS genes are present in syntenic regions of distant Myoviridae Pelagiphages, and they appear to have alphaproteobacterial origins with a later transfer between viral families. The results point to an unprecedented multipartner-AMG transfer between marine Myoviridae and Podoviridae. Together with the expansion of known metabolic functions, our studies provide new prospects for understanding the ecology and evolution of marine phages and their hosts. IMPORTANCE One of the most abundant and diverse marine bacterial groups is Pelagibacter. Phages have roles in shaping Pelagibacter ecology; however, several Pelagiphage lineages are represented by only a few genomes. This paucity of data from even the most widespread lineages has imposed limits on the understanding of the diversity of Pelagiphages and their impacts on hosts. Here, we report 80 complete genomes, assembled directly from environmental data, which are from undescribed Pelagiphages and render new insights into the manipulation of host metabolism during infection. Notably, the viruses have functionally related partner genes that appear to be transferred between distant viruses, including a suite that encode a secretion system which both brings a new functional capability to the host and is abundant in phages across the ocean. Together, these functions have important implications for phage evolution and for how Pelagiphage infection influences host biology in manners extending beyond canonical viral lysis and mortality.
Collapse
|
|
19
|
Rodrigues CJC, de Carvalho CCCR. Marine Bioprospecting, Biocatalysis and Process Development. Microorganisms 2022; 10:1965. [PMID: 36296241 PMCID: PMC9610463 DOI: 10.3390/microorganisms10101965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/22/2022] [Accepted: 09/30/2022] [Indexed: 11/22/2022] Open
Abstract
Oceans possess tremendous diversity in microbial life. The enzymatic machinery that marine bacteria present is the result of extensive evolution to assist cell survival under the harsh and continuously changing conditions found in the marine environment. Several bacterial cells and enzymes are already used at an industrial scale, but novel biocatalysts are still needed for sustainable industrial applications, with benefits for both public health and the environment. Metagenomic techniques have enabled the discovery of novel biocatalysts, biosynthetic pathways, and microbial identification without their cultivation. However, a key stage for application of novel biocatalysts is the need for rapid evaluation of the feasibility of the bioprocess. Cultivation of not-yet-cultured bacteria is challenging and requires new methodologies to enable growth of the bacteria present in collected environmental samples, but, once a bacterium is isolated, its enzyme activities are easily measured. High-throughput screening techniques have also been used successfully, and innovative in vitro screening platforms to rapidly identify relevant enzymatic activities continue to improve. Small-scale approaches and process integration could improve the study and development of new bioprocesses to produce commercially interesting products. In this work, the latest studies related to (i) the growth of marine bacteria under laboratorial conditions, (ii) screening techniques for bioprospecting, and (iii) bioprocess development using microreactors and miniaturized systems are reviewed and discussed.
Collapse
Affiliation(s)
- Carlos J. C. Rodrigues
- Department of Bioengineering, iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Carla C. C. R. de Carvalho
- Department of Bioengineering, iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| |
Collapse
|
|
20
|
Lara E, Singer D, Geisen S. Discrepancies between prokaryotes and eukaryotes need to be considered in soil DNA-based studies. Environ Microbiol 2022; 24:3829-3839. [PMID: 35437903 PMCID: PMC9790305 DOI: 10.1111/1462-2920.16019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 12/30/2022]
Abstract
Metabarcoding approaches are exponentially increasing our understanding of soil biodiversity, with a major focus on the bacterial part of the microbiome. Part of the soil diversity are also eukaryotes that include fungi, algae, protists and Metazoa. Nowadays, soil eukaryotes are targeted with the same approaches developed for bacteria and archaea (prokaryotes). However, fundamental differences exist between domains. After providing a short historical overview of the developments of metabarcoding applied to environmental microbiology, we compile the most important differences between domains that prevent direct method transfers between prokaryotic and eukaryotic soil metabarcoding approaches, currently dominated by short-read sequencing. These include the existence of divergent diversity concepts and the variations in eukaryotic morphology that affect sampling and DNA extraction. Furthermore, eukaryotes experienced much more variable evolutionary rates than prokaryotes, which prevent capturing the entire eukaryotic diversity in a soil with a single amplification protocol fit for short-read sequencing. In the final part we focus on future potentials for optimization of eukaryotic metabarcoding that include superior possibility of functionally characterizing eukaryotes and to extend the current information obtained, such as by adding a real quantitative component. This review should optimize future metabarcoding approaches targeting soil eukaryotes and kickstart this promising research direction.
Collapse
Affiliation(s)
- Enrique Lara
- Real Jardín Botánico‐CSIC, Plaza de Murillo 2Madrid28014Spain
| | - David Singer
- UMR CNRS 6112 LPG‐BIAFAngers University, 2 Boulevard LavoisierAngers49045France
| | - Stefan Geisen
- Laboratory of NematologyWageningen UniversityWageningen6700 AAThe Netherlands
| |
Collapse
|
|
21
|
Comstock J, Nelson CE, James A, Wear E, Baetge N, Remple K, Juknavorian A, Carlson CA. Bacterioplankton communities reveal horizontal and vertical influence of an Island Mass Effect. Environ Microbiol 2022; 24:4193-4208. [PMID: 35691616 PMCID: PMC9796716 DOI: 10.1111/1462-2920.16092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 05/26/2022] [Accepted: 05/31/2022] [Indexed: 01/07/2023]
Abstract
Coral reefs are highly productive ecosystems with distinct biogeochemistry and biology nestled within unproductive oligotrophic gyres. Coral reef islands have often been associated with a nearshore enhancement in phytoplankton, a phenomenon known as the Island Mass Effect (IME). Despite being documented more than 60 years ago, much remains unknown about the extent and drivers of IMEs. Here we utilized 16S rRNA gene metabarcoding as a biological tracer to elucidate horizontal and vertical influence of an IME around the islands of Mo'orea and Tahiti, French Polynesia. We show that those nearshore oceanic stations with elevated chlorophyll a included bacterioplankton found in high abundance in the reef environment, suggesting advection of reef water is the source of altered nearshore biogeochemistry. We also observed communities in the nearshore deep chlorophyll maximum (DCM) with enhanced abundances of upper euphotic bacterioplankton that correlated with intrusions of low-density, O2 rich water, suggesting island influence extends into the DCM.
Collapse
Affiliation(s)
- Jacqueline Comstock
- Department of Ecology, Evolution and Marine Biology and Marine Science InstituteUniversity of California Santa BarbaraSanta BarbaraCAUSA
| | - Craig E. Nelson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College ProgramUniversity of Hawai'i at MānoaHonoluluHIUSA
| | - Anna James
- Department of Ecology, Evolution and Marine Biology and Marine Science InstituteUniversity of California Santa BarbaraSanta BarbaraCAUSA
| | - Emma Wear
- Department of Ecology, Evolution and Marine Biology and Marine Science InstituteUniversity of California Santa BarbaraSanta BarbaraCAUSA
| | - Nicholas Baetge
- Department of Ecology, Evolution and Marine Biology and Marine Science InstituteUniversity of California Santa BarbaraSanta BarbaraCAUSA
| | - Kristina Remple
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College ProgramUniversity of Hawai'i at MānoaHonoluluHIUSA
| | | | - Craig A. Carlson
- Department of Ecology, Evolution and Marine Biology and Marine Science InstituteUniversity of California Santa BarbaraSanta BarbaraCAUSA
| |
Collapse
|
|
22
|
Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity. BIOLOGY 2022; 11:biology11091297. [PMID: 36138776 PMCID: PMC9495823 DOI: 10.3390/biology11091297] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/20/2022]
Abstract
Simple Summary The innovative concept of environmental DNA has found its foot in aquatic ecosystems but remains an unexplored area of research concerning terrestrial ecosystems. When making management choices, it is important to understand the rate of eDNA degradation, the persistence of DNA in terrestrial habitats, and the variables affecting eDNA detectability for a target species. Therefore an attempt has been made to provide comprehensive information regarding the exertion of eDNA in terrestrial ecosystems from 2012 to 2022. The information provided will assist ecologists, researchers and decision-makers in developing a holistic understanding of environmental DNA and its applicability as a biodiversity monitoring contrivance. Abstract The dearth of cardinal data on species presence, dispersion, abundance, and habitat prerequisites, besides the threats impeded by escalating human pressure has enormously affected biodiversity conservation. The innovative concept of eDNA, has been introduced as a way of overcoming many of the difficulties of rigorous conventional investigations, and is hence becoming a prominent and novel method for assessing biodiversity. Recently the demand for eDNA in ecology and conservation has expanded exceedingly, despite the lack of coordinated development in appreciation of its strengths and limitations. Therefore it is pertinent and indispensable to evaluate the extent and significance of eDNA-based investigations in terrestrial habitats and to classify and recognize the critical considerations that need to be accounted before using such an approach. Presented here is a brief review to summarize the prospects and constraints of utilizing eDNA in terrestrial ecosystems, which has not been explored and exploited in greater depth and detail in such ecosystems. Given these obstacles, we focused primarily on compiling the most current research findings from journals accessible in eDNA analysis that discuss terrestrial ecosystems (2012–2022). In the current evaluation, we also review advancements and limitations related to the eDNA technique.
Collapse
|
|
23
|
Zheng J, Yan Y, Li Z, Song N. Genetic structure of the small yellow croaker ( Larimichthys polyactis) across the Yellow Sea and the East China Sea by microsatellite DNA variation: implications for the division of management units. PeerJ 2022; 10:e13789. [PMID: 36061743 PMCID: PMC9435522 DOI: 10.7717/peerj.13789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 07/05/2022] [Indexed: 01/17/2023] Open
Abstract
The small yellow croaker, Larimichthys polyactis, is a commercial fish of the order Perciformes that mainly inhabit estuaries and coastal waters.In recent years, the resources and catch of L. polyactis have undergone huge fluctuations. To detect genetic variations caused by the fluctuation of resources, genetic diversity of L. polyactis in the coastal waters of China were analyzed in this study using microsatellite DNA marker. The results revealed high genetic diversity of this species. The STRUCTURE, DAPC and F ST results all indicated that there was no genetic structure consistent with the distribution pattern. Overall, our main findings are in agreement with previous studies, indicating that L. polyactis showed high genetic diversity and low genetic differentiation. Our results for high genetic connectivity among L. polyactis localities provide insights into the development of management strategies, that is, to manage this species as a single management unit.
Collapse
Affiliation(s)
- Jian Zheng
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, China
| | - Yunrong Yan
- Guangdong Ocean University, Zhanjiang, China
| | - Zhonglu Li
- Guangdong Ocean University, Zhanjiang, China
| | - Na Song
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, China
| |
Collapse
|
|
24
|
Rodrigues CJC, de Carvalho CCCR. Cultivating marine bacteria under laboratory conditions: Overcoming the “unculturable” dogma. Front Bioeng Biotechnol 2022; 10:964589. [PMID: 36061424 PMCID: PMC9428589 DOI: 10.3389/fbioe.2022.964589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/26/2022] [Indexed: 11/22/2022] Open
Abstract
Underexplored seawater environments may contain biological resources with potential for new biotechnological applications. Metagenomic techniques revolutionized the study of bacterial communities but culture dependent methods will still be important to help the biodiscovery of new products and enzymes from marine bacteria. In this context, we promoted the growth of bacteria from a marine rock pond by culture dependent techniques and compared the results with culture independent methods. The total number of bacteria and diversity were studied in different agar plate media during 6 weeks. Agar plate counting was of the same order of magnitude of direct microscopy counts. The highest efficiency of cultivation was 45% attained in marine agar medium. Molecular analysis revealed 10 different phyla of which only four were isolated by the culture dependent method. On the other hand, four taxonomic orders were detected by cultivation but not by the molecular technique. These include bacteria from the phyla Bacillota and Actinomycetota. Our study shows that it is possible to grow more than the traditionally considered 1% of bacteria from a seawater sample using standard agar plate techniques and laboratorial conditions. The results also demonstrate the importance of culture methods to grow bacteria not detected by molecular approaches for future biotechnological applications.
Collapse
Affiliation(s)
- Carlos J. C. Rodrigues
- Department of Bioengineering, iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory I4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Carla C. C. R. de Carvalho
- Department of Bioengineering, iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory I4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- *Correspondence: Carla C. C. R. de Carvalho,
| |
Collapse
|
|
25
|
Adeniyi A, Bello I, Mukaila T, Hammed A. A Review of Microbial Molecular Profiling during Biomass Valorization. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0026-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
|
26
|
A Critical Assessment of the Congruency between Environmental DNA and Palaeoecology for the Biodiversity Monitoring and Palaeoenvironmental Reconstruction. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19159445. [PMID: 35954801 PMCID: PMC9368151 DOI: 10.3390/ijerph19159445] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 02/01/2023]
Abstract
The present study suggests that standardized methodology, careful site selection, and stratigraphy are essential for investigating ancient ecosystems in order to evaluate biodiversity and DNA-based time series. Based on specific keywords, this investigation reviewed 146 publications using the SCOPUS, Web of Science (WoS), PUBMED, and Google Scholar databases. Results indicate that environmental deoxyribose nucleic acid (eDNA) can be pivotal for assessing and conserving ecosystems. Our review revealed that in the last 12 years (January 2008–July 2021), 63% of the studies based on eDNA have been reported from aquatic ecosystems, 25% from marine habitats, and 12% from terrestrial environments. Out of studies conducted in aquatic systems using the environmental DNA (eDNA) technique, 63% of the investigations have been reported from freshwater ecosystems, with an utmost focus on fish diversity (40%). Further analysis of the literature reveals that during the same period, 24% of the investigations using the environmental DNA technique were carried out on invertebrates, 8% on mammals, 7% on plants, 6% on reptiles, and 5% on birds. The results obtained clearly indicate that the environmental DNA technique has a clear-cut edge over other biodiversity monitoring methods. Furthermore, we also found that eDNA, in conjunction with different dating techniques, can provide better insight into deciphering eco-evolutionary feedback. Therefore, an attempt has been made to offer extensive information on the application of dating methods for different taxa present in diverse ecosystems. Last, we provide suggestions and elucidations on how to overcome the caveats and delineate some of the research avenues that will likely shape this field in the near future. This paper aims to identify the gaps in environmental DNA (eDNA) investigations to help researchers, ecologists, and decision-makers to develop a holistic understanding of environmental DNA (eDNA) and its utility as a palaeoenvironmental contrivance.
Collapse
|
|
27
|
Wornell K, Pardesi B, Lee K, Boycheva S, Roberton AM, White WL. High-throughput Method for Novel Medium Development for Culture of Anaerobic Gut Bacteria. Curr Protoc 2022; 2:e463. [PMID: 35822953 DOI: 10.1002/cpz1.463] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Gut microbiota play important roles in the health of their host and detailed investigation of these organisms requires in vitro culture. Culturing strictly anaerobic bacteria can be a challenge as the gut environment they inhabit is nutritionally complex. Use of complex media containing nutritionally rich but undefined gut fluid reduces the accuracy of physiological and metabolomic studies. Here we present a high-throughput protocol for comparing growth rates of fastidiously anaerobic bacteria on different media. These protocols can be used to develop a solid medium made up of commercially sourced ingredients, providing replicable growth conditions for previously uncultured anaerobic bacteria. As many fastidious bacteria grow poorly in a liquid broth, these protocols measure bacterial growth rate on solid media. These protocols speed up and simplify the growth rate measurement process by using a multiwell format and equations in place of physical McFarland standards to calculate approximate cell density. Bacterial strains belonging to the families Erysipelotrichaceae and Lachnospiraceae (phylum Firmicutes) isolated from the hindgut of Kyphosus sydneyanus were used to demonstrate the efficacy of these protocols. Bacterial growth rates were compared between a nutritionally rich medium with gut fluid versus a novel replicable medium with mannitol. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of solid YCFA growth medium Basic Protocol 2: Collection of fish gut samples and plating to single isolates Basic Protocol 3: Genetic identification of single isolates with colony PCR and 16S rRNA gene sequencing Basic Protocol 4: Measurement of bacterial growth rates on solid media.
Collapse
Affiliation(s)
- Kristina Wornell
- Department of Environmental Science, Auckland University of Technology, Auckland, New Zealand
| | - Bikiran Pardesi
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Kevin Lee
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Svetlana Boycheva
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Anthony M Roberton
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - W Lindsey White
- Department of Environmental Science, Auckland University of Technology, Auckland, New Zealand
| |
Collapse
|
|
28
|
Grujcic V, Taylor GT, Foster RA. One Cell at a Time: Advances in Single-Cell Methods and Instrumentation for Discovery in Aquatic Microbiology. Front Microbiol 2022; 13:881018. [PMID: 35677911 PMCID: PMC9169044 DOI: 10.3389/fmicb.2022.881018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
Studying microbes from a single-cell perspective has become a major theme and interest within the field of aquatic microbiology. One emerging trend is the unfailing observation of heterogeneity in activity levels within microbial populations. Wherever researchers have looked, intra-population variability in biochemical composition, growth rates, and responses to varying environmental conditions has been evident and probably reflect coexisting genetically distinct strains of the same species. Such observations of heterogeneity require a shift away from bulk analytical approaches and development of new methods or adaptation of existing techniques, many of which were first pioneered in other, unrelated fields, e.g., material, physical, and biomedical sciences. Many co-opted approaches were initially optimized using model organisms. In a field with so few cultivable models, method development has been challenging but has also contributed tremendous insights, breakthroughs, and stimulated curiosity. In this perspective, we present a subset of methods that have been effectively applied to study aquatic microbes at the single-cell level. Opportunities and challenges for innovation are also discussed. We suggest future directions for aquatic microbiological research that will benefit from open access to sophisticated instruments and highly interdisciplinary collaborations.
Collapse
Affiliation(s)
- Vesna Grujcic
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Rachel A Foster
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| |
Collapse
|
|
29
|
Kaari M, Manikkam R, Baskaran A. Exploring Newer Biosynthetic Gene Clusters in Marine Microbial Prospecting. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:448-467. [PMID: 35394575 DOI: 10.1007/s10126-022-10118-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Marine microbes genetically evolved to survive varying salinity, temperature, pH, and other stress factors by producing different bioactive metabolites. These microbial secondary metabolites (SMs) are novel, have high potential, and could be used as lead molecule. Genome sequencing of microbes revealed that they have the capability to produce numerous novel bioactive metabolites than observed under standard in vitro culture conditions. Microbial genome has specific regions responsible for SM assembly, termed biosynthetic gene clusters (BGCs), possessing all the necessary genes to encode different enzymes required to generate SM. In order to augment the microbial chemo diversity and to activate these gene clusters, various tools and techniques are developed. Metagenomics with functional gene expression studies aids in classifying novel peptides and enzymes and also in understanding the biosynthetic pathways. Genome shuffling is a high-throughput screening approach to improve the development of SMs by incorporating genomic recombination. Transcriptionally silent or lower level BGCs can be triggered by artificially knocking promoter of target BGC. Additionally, bioinformatic tools like antiSMASH, ClustScan, NAPDOS, and ClusterFinder are effective in identifying BGCs of existing class for annotation in genomes. This review summarizes the significance of BGCs and the different approaches for detecting and elucidating BGCs from marine microbes.
Collapse
Affiliation(s)
- Manigundan Kaari
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India
| | - Radhakrishnan Manikkam
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India.
| | - Abirami Baskaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India
| |
Collapse
|
|
30
|
Li M, Liu R, Li Y, Wang C, Ma W, Zheng L, Zhang K, Fu X, Li X, Su Y, Huang G, Zhong Y, Liao H. Functional Investigation of Plant Growth Promoting Rhizobacterial Communities in Sugarcane. Front Microbiol 2022; 12:783925. [PMID: 35058904 PMCID: PMC8763851 DOI: 10.3389/fmicb.2021.783925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/30/2021] [Indexed: 11/24/2022] Open
Abstract
Plant microbiota are of great importance for host nutrition and health. As a C4 plant species with a high carbon fixation capacity, sugarcane also associates with beneficial microbes, though mechanisms underlying sugarcane root-associated community development remain unclear. Here, we identify microbes that are specifically enriched around sugarcane roots and report results of functional testing of potentially beneficial microbes propagating with sugarcane plants. First, we analyzed recruitment of microbes through analysis of 16S rDNA enrichment in greenhouse cultured sugarcane seedlings growing in field soil. Then, plant-associated microbes were isolated and assayed for beneficial activity, first in greenhouse experiments, followed by field trials for selected microbial strains. The promising beneficial microbe SRB-109, which quickly colonized both roots and shoots of sugarcane plants, significantly promoted sugarcane growth in field trials, nitrogen and potassium acquisition increasing by 35.68 and 28.35%, respectively. Taken together, this report demonstrates successful identification and utilization of beneficial plant-associated microbes in sugarcane production. Further development might facilitate incorporation of such growth-promoting microbial applications in large-scale sugarcane production, which may not only increase yields but also reduce fertilizer costs and runoff.
Collapse
Affiliation(s)
- Mingjia Li
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ran Liu
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanjun Li
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Cunhu Wang
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenjing Ma
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lei Zheng
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kefei Zhang
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xing Fu
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinxin Li
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yachun Su
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guoqiang Huang
- National Engineering Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongjia Zhong
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hong Liao
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
|
31
|
Choudhari J, Choubey J, Verma M, Chatterjee T, Sahariah B. Metagenomics: the boon for microbial world knowledge and current challenges. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00022-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
|
32
|
Rodriguez-Valera F, Pushkarev A, Rosselli R, Béjà O. Searching Metagenomes for New Rhodopsins. Methods Mol Biol 2022; 2501:101-108. [PMID: 35857224 DOI: 10.1007/978-1-0716-2329-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Most microbial groups have not been cultivated yet, and the only way to approach the enormous diversity of rhodopsins that they contain in a sensible timeframe is through the analysis of their genomes. High-throughput sequencing technologies have allowed the release of community genomics (metagenomics) of many habitats in the photic zones of the ocean and lakes. Already the harvest is impressive and included from the first bacterial rhodopsin (proteorhodopsin) to the recent discovery of heliorhodopsin by functional metagenomics. However, the search continues using bioinformatic or biochemical routes.
Collapse
Affiliation(s)
- Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Alina Pushkarev
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Riccardo Rosselli
- Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel.
| |
Collapse
|
|
33
|
Mohamed Qadir R, Assafi MS. The association between body mass index and the oral Firmicutes and Bacteroidetes profiles of healthy individuals. MALAYSIAN FAMILY PHYSICIAN : THE OFFICIAL JOURNAL OF THE ACADEMY OF FAMILY PHYSICIANS OF MALAYSIA 2021; 16:36-43. [PMID: 34938391 PMCID: PMC8680938 DOI: 10.51866/oa1129] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
INTRODUCTION Microbiome status is considered an important factor that contributes to obesity. Investigations have shown that the oral microbiome comprises a vast array of bacterial species that can influence human health. OBJECTIVE To determine the association between the presence of the bacterial phyla Firmicutes and Bacteroidetes and the body mass index (BMI) status of normal, overweight and obese subjects in Duhok, Iraq. Additionally, to investigate the composition of oral Firmicutes and Bacteroidetes profiles for individuals with different BMI statuses. METHODS A total of 155 saliva samples were collected from participants in Duhok, Iraq. Bacterial genomic DNA was then extracted from the collected saliva. The presence of Firmicutes and Bacteroidetes phyla was detected via polymerase chain reaction. RESULTS Firmicutes and Bacteroidetes were detected in 63.2 and 37.4% of the population, respectively. Differences in the carriage rates of oral Firmicutes in overweight (78%) and obese individuals (83%) were statistically significant when compared to normal weight individuals (36%) (P<0.0001). The percentage rates of Bacteroidetes in obese individuals (26.4%) was statistically significant when compared to normal weight individuals (50.8%) (P=0.0078). The Firmicutes/ Bacteroidetes ratios (obese=3.1, overweight= 2.5 and normal weight=0.7) were higher with increasing BMI. CONCLUSION This study provides evidence of the Firmicutes/Bacteroidetes ratio growing with increasing BMI. High rates of Firmicutes could serve a role in the development of obesity. Further studies are required to clarify the exact relationship between oral bacteria and obesity, which could lead to a promising therapeutic method for improving the physical health of humans.
Collapse
Affiliation(s)
- Roshna Mohamed Qadir
- MSc, Department of Biology, College of Science, University of Duhok, Duhok Kurdistan Region, Iraq
| | - Mahde Saleh Assafi
- PhD, Department of Biology, College of Science, University of Duhok, Duhok Kurdistan Region, Iraq,
| |
Collapse
|
|
34
|
Phylogenomics of SAR116 Clade Reveals Two Subclades with Different Evolutionary Trajectories and an Important Role in the Ocean Sulfur Cycle. mSystems 2021; 6:e0094421. [PMID: 34609172 PMCID: PMC8547437 DOI: 10.1128/msystems.00944-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The SAR116 clade within the class Alphaproteobacteria represents one of the most abundant groups of heterotrophic bacteria inhabiting the surface of the ocean. The small number of cultured representatives of SAR116 (only two to date) is a major bottleneck that has prevented an in-depth study at the genomic level to understand the relationship between genome diversity and its role in the marine environment. In this study, we use all publicly available genomes to provide a genomic overview of the phylogeny, metabolism, and biogeography within the SAR116 clade. This increased genomic diversity has led to the discovery of two subclades that, despite coexisting in the same environment, display different properties in their genomic makeup. One represents a novel subclade for which no pure cultures have been isolated and is composed mainly of single-amplified genomes (SAGs). Genomes within this subclade showed convergent evolutionary trajectories with more streamlined features, such as low GC content (ca. 30%), short intergenic spacers (<22 bp), and strong purifying selection (low ratio of nonsynonymous to synonymous polymorphisms [dN/dS]). Besides, they were more abundant in metagenomic databases recruiting at the deep chlorophyll maximum. Less abundant and restricted to the upper photic layers of the global ocean, the other subclade of SAR116, enriched in metagenome-assembled genomes (MAGs), included the only two pure cultures. Genomic analysis suggested that both clades have a significant role in the sulfur cycle with differences in the way both clades can metabolize dimethylsulfoniopropionate (DMSP). IMPORTANCE The SAR116 clade of Alphaproteobacteria is a ubiquitous group of heterotrophic bacteria inhabiting the surface of the ocean, but the information about their ecology and population genomic diversity is scarce due to the difficulty of getting pure culture isolates. The combination of single-cell genomics and metagenomics has become an alternative approach to study these kinds of microbes. Our results expand the understanding of the genomic diversity, distribution, and lifestyles within this clade and provide evidence of different evolutionary trajectories in the genomic makeup of the two subclades that could serve to illustrate how evolutionary pressure can drive different adaptations to the same environment. Therefore, the SAR116 clade represents an ideal model organism for the study of the evolutionary streamlining of genomes in microbes that have relatively close relatedness to each other.
Collapse
|
|
35
|
McDaniel EA, Wahl SA, Ishii S, Pinto A, Ziels R, Nielsen PH, McMahon KD, Williams RBH. Prospects for multi-omics in the microbial ecology of water engineering. WATER RESEARCH 2021; 205:117608. [PMID: 34555741 DOI: 10.1016/j.watres.2021.117608] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions - including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enabled linking powerful functional predictions to specific taxonomical groups with increasing fidelity. Additionally, related developments in both whole community gene expression surveys and metabolite profiling have permitted for direct surveys of community-scale functions in specific environmental settings. These advances have allowed for a shift in microbiome science away from descriptive studies and towards mechanistic and predictive frameworks for designing and harnessing microbial communities for desired beneficial outcomes. Water engineers, microbiologists, and microbial ecologists studying activated sludge, anaerobic digestion, and drinking water distribution systems have applied various (meta)omics techniques for connecting microbial community dynamics and physiologies to overall process parameters and system performance. However, the rapid pace at which new omics-based approaches are developed can appear daunting to those looking to apply these state-of-the-art practices for the first time. Here, we review how modern genome-resolved metagenomic approaches have been applied to a variety of water engineering applications from lab-scale bioreactors to full-scale systems. We describe integrated omics analysis across engineered water systems and the foundations for pairing these insights with modeling approaches. Lastly, we summarize emerging omics-based technologies that we believe will be powerful tools for water engineering applications. Overall, we provide a framework for microbial ecologists specializing in water engineering to apply cutting-edge omics approaches to their research questions to achieve novel functional insights. Successful adoption of predictive frameworks in engineered water systems could enable more economically and environmentally sustainable bioprocesses as demand for water and energy resources increases.
Collapse
Affiliation(s)
- Elizabeth A McDaniel
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA.
| | | | - Shun'ichi Ishii
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Yokosuka 237-0061, Japan
| | - Ameet Pinto
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, USA
| | - Ryan Ziels
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
| | | | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA; Department of Civil and Environmental Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Republic of Singapore.
| |
Collapse
|
|
36
|
Xu CCY, Ramsay C, Cowan M, Dehghani M, Lasko P, Barrett RDH. Transgenes of genetically modified animals detected non-invasively via environmental DNA. PLoS One 2021; 16:e0249439. [PMID: 34437552 PMCID: PMC8389434 DOI: 10.1371/journal.pone.0249439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 08/09/2021] [Indexed: 11/23/2022] Open
Abstract
We demonstrate that simple, non-invasive environmental DNA (eDNA) methods can detect transgenes of genetically modified (GM) animals from terrestrial and aquatic sources in invertebrate and vertebrate systems. We detected transgenic fragments between 82–234 bp through targeted PCR amplification of environmental DNA extracted from food media of GM fruit flies (Drosophila melanogaster), feces, urine, and saliva of GM laboratory mice (Mus musculus), and aquarium water of GM tetra fish (Gymnocorymbus ternetzi). With rapidly growing accessibility of genome-editing technologies such as CRISPR, the prevalence and diversity of GM animals will increase dramatically. GM animals have already been released into the wild with more releases planned in the future. eDNA methods have the potential to address the critical need for sensitive, accurate, and cost-effective detection and monitoring of GM animals and their transgenes in nature.
Collapse
Affiliation(s)
- Charles C. Y. Xu
- Redpath Museum, McGill University, Montreal, Quebec, Canada
- Department of Biology, McGill University, Montreal, Quebec, Canada
- * E-mail:
| | - Claire Ramsay
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Mitra Cowan
- McGill Integrated Core for Animal Modeling (MICAM), McGill University, Montreal, Quebec, Canada
| | | | - Paul Lasko
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Rowan D. H. Barrett
- Redpath Museum, McGill University, Montreal, Quebec, Canada
- Department of Biology, McGill University, Montreal, Quebec, Canada
| |
Collapse
|
|
37
|
Schäffer AA, McVeigh R, Robbertse B, Schoch CL, Johnston A, Underwood BA, Karsch-Mizrachi I, Nawrocki EP. Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation. BMC Bioinformatics 2021; 22:400. [PMID: 34384346 PMCID: PMC8359073 DOI: 10.1186/s12859-021-04316-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/03/2021] [Indexed: 02/01/2023] Open
Abstract
Background The DNA sequences encoding ribosomal RNA genes (rRNAs) are commonly used as markers to identify species, including in metagenomics samples that may combine many organismal communities. The 16S small subunit ribosomal RNA (SSU rRNA) gene is typically used to identify bacterial and archaeal species. The nuclear 18S SSU rRNA gene, and 28S large subunit (LSU) rRNA gene have been used as DNA barcodes and for phylogenetic studies in different eukaryote taxonomic groups. Because of their popularity, the National Center for Biotechnology Information (NCBI) receives a disproportionate number of rRNA sequence submissions and BLAST queries. These sequences vary in quality, length, origin (nuclear, mitochondria, plastid), and organism source and can represent any region of the ribosomal cistron. Results To improve the timely verification of quality, origin and loci boundaries, we developed Ribovore, a software package for sequence analysis of rRNA sequences. The ribotyper and ribosensor programs are used to validate incoming sequences of bacterial and archaeal SSU rRNA. The ribodbmaker program is used to create high-quality datasets of rRNAs from different taxonomic groups. Key algorithmic steps include comparing candidate sequences against rRNA sequence profile hidden Markov models (HMMs) and covariance models of rRNA sequence and secondary-structure conservation, as well as other tests. Nine freely available blastn rRNA databases created and maintained with Ribovore are used for checking incoming GenBank submissions and used by the blastn browser interface at NCBI. Since 2018, Ribovore has been used to analyze more than 50 million prokaryotic SSU rRNA sequences submitted to GenBank, and to select at least 10,435 fungal rRNA RefSeq records from type material of 8350 taxa. Conclusion Ribovore combines single-sequence and profile-based methods to improve GenBank processing and analysis of rRNA sequences. It is a standalone, portable, and extensible software package for the alignment, classification and validation of rRNA sequences. Researchers planning on submitting SSU rRNA sequences to GenBank are encouraged to download and use Ribovore to analyze their sequences prior to submission to determine which sequences are likely to be automatically accepted into GenBank.
Collapse
Affiliation(s)
- Alejandro A Schäffer
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Richard McVeigh
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Conrad L Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Anjanette Johnston
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Beverly A Underwood
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Eric P Nawrocki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
| |
Collapse
|
|
38
|
Screening of Neutrophil Activating Factors from a Metagenome Library of Sponge-Associated Bacteria. Mar Drugs 2021; 19:md19080427. [PMID: 34436266 PMCID: PMC8402132 DOI: 10.3390/md19080427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/15/2021] [Accepted: 07/23/2021] [Indexed: 12/15/2022] Open
Abstract
Marine sponge-associated bacteria are known as bio-active compound produce. We have constructed metagenome libraries of the bacteria and developed a metagenomic screening approach. Activity-based screening successfully identified novel genes and novel enzymes; however, the efficiency was only in 1 out of 104 clones. Therefore, in this study, we thought that bioinformatics could help to reduce screening efforts, and combined activity-based screening with database search. Neutrophils play an important role for the immune system to recognize excreted bacterial by-products as chemotactic factors and are recruited to infection sites to kill pathogens via phagocytosis. These excreted by-products are considered critical triggers that engage the immune system to mount a defense against infection, and identifying these factors may guide developments in medicine and diagnostics. We focused on genes encoding amino acid ligase and peptide synthetase and selected from an in-house sponge metagenome database. Cell-free culture medium of each was used in a neutrophil chemiluminescence assay in luminol reaction. The clone showing maximum activity had a genomic sequence expected to produce a molecule like a phospho-N-acetylmuramyl pentapeptide by the metagenome fragment analysis.
Collapse
|
|
39
|
Hugenholtz P, Chuvochina M, Oren A, Parks DH, Soo RM. Prokaryotic taxonomy and nomenclature in the age of big sequence data. THE ISME JOURNAL 2021; 15:1879-1892. [PMID: 33824426 PMCID: PMC8245423 DOI: 10.1038/s41396-021-00941-x] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 02/01/2023]
Abstract
The classification of life forms into a hierarchical system (taxonomy) and the application of names to this hierarchy (nomenclature) is at a turning point in microbiology. The unprecedented availability of genome sequences means that a taxonomy can be built upon a comprehensive evolutionary framework, a longstanding goal of taxonomists. However, there is resistance to adopting a single framework to preserve taxonomic freedom, and ever increasing numbers of genomes derived from uncultured prokaryotes threaten to overwhelm current nomenclatural practices, which are based on characterised isolates. The challenge ahead then is to reach a consensus on the taxonomic framework and to adapt and scale the existing nomenclatural code, or create a new code, to systematically incorporate uncultured taxa into the chosen framework.
Collapse
Affiliation(s)
- Philip Hugenholtz
- grid.1003.20000 0000 9320 7537Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD Australia
| | - Maria Chuvochina
- grid.1003.20000 0000 9320 7537Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD Australia
| | - Aharon Oren
- grid.9619.70000 0004 1937 0538Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Edmond J. Safra campus, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Donovan H. Parks
- grid.1003.20000 0000 9320 7537Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD Australia
| | - Rochelle M. Soo
- grid.1003.20000 0000 9320 7537Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD Australia
| |
Collapse
|
|
40
|
Wylezich C, Höper D. Meta-Ribosomalomics: RNA Sequencing Is an Unbiased Method for Parasite Detection of Different Sample Types. Front Microbiol 2021; 12:614553. [PMID: 34234748 PMCID: PMC8256892 DOI: 10.3389/fmicb.2021.614553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 05/26/2021] [Indexed: 01/23/2023] Open
Abstract
In this perspective article, we review the past use of ribosomal sequences to address scientific and diagnostic questions. We highlight a variety of sequencing approaches including metagenomics and DNA barcoding and their different demands and requirements. Meta-ribosomalomics is introduced as an unbiased approach to exploit high-throughput sequencing datasets for eukaryotic and prokaryotic ribosomal sequences. Prerequisites, benefits, drawbacks, and future perspectives are elaborated and compared to other sequencing approaches.
Collapse
Affiliation(s)
- Claudia Wylezich
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| |
Collapse
|
|
41
|
Sander D, Yu Y, Sukul P, Schäkermann S, Bandow JE, Mukherjee T, Mukhopadhyay SK, Leichert LI. Metaproteomic Discovery and Characterization of a Novel Lipolytic Enzyme From an Indian Hot Spring. Front Microbiol 2021; 12:672727. [PMID: 34149658 PMCID: PMC8212958 DOI: 10.3389/fmicb.2021.672727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/19/2021] [Indexed: 11/18/2022] Open
Abstract
Lipolytic enzymes are produced by animals, plants and microorganisms. With their chemo-, regio-, and enantio-specific characteristics, lipolytic enzymes are important biocatalysts useful in several industrial applications. They are widely used in the processing of fats and oils, detergents, food processing, paper and cosmetics production. In this work, we used a new functional metaproteomics approach to screen sediment samples of the Indian Bakreshwar hot spring for novel thermo- and solvent-stable lipolytic enzymes. We were able to identify an enzyme showing favorable characteristics. DS-007 showed high hydrolytic activity with substrates with shorter chain length (C10, significantly less hydrolytic activity was observed. A preference for short chain acyl groups is characteristic for esterases, suggesting that DS-007 is an esterase. Consistent with the high temperature at its site of isolation, DS-007 showed a temperature optimum at 55°C and retained 80% activity even after prolonged exposure to temperatures as high as 60°C. The enzyme showed optimum activity at pH 9.5, with more than 50% of its optimum activity between pH 8.0 and pH 9.5. DS-007 also exhibited tolerance toward organic solvents at a concentration of 1% (v/v). One percent of methanol increased the activity of DS-007 by 40% in comparison to the optimum conditions without solvent. In the presence of 10% methanol, DMSO or isopropanol DS-007 still showed around 50% activity. This data indicates that DS-007 is a temperature- and solvent-stable thermophilic enzyme with reasonable activity even at lower temperatures as well as a catalyst that can be used at a broad range of pH values with an optimum in the alkaline range, showing the adaptation to the habitat's temperature and alkaline pH.
Collapse
Affiliation(s)
- Dennis Sander
- Department of Microbial Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Yanfei Yu
- Department of Microbial Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Premankur Sukul
- Department of Microbial Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Sina Schäkermann
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Julia E. Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Trinetra Mukherjee
- Department of Microbial Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- Department of Microbiology, The University of Burdwan, Burdwan, India
| | | | - Lars I. Leichert
- Department of Microbial Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| |
Collapse
|
|
42
|
Hashemi S, Hashemi SE, Lien KM, Lamb JJ. Molecular Microbial Community Analysis as an Analysis Tool for Optimal Biogas Production. Microorganisms 2021; 9:microorganisms9061162. [PMID: 34071282 PMCID: PMC8226781 DOI: 10.3390/microorganisms9061162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/17/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
The microbial diversity in anaerobic digestion (AD) is important because it affects process robustness. High-throughput sequencing offers high-resolution data regarding the microbial diversity and robustness of biological systems including AD; however, to understand the dynamics of microbial processes, knowing the microbial diversity is not adequate alone. Advanced meta-omic techniques have been established to determine the activity and interactions among organisms in biological processes like AD. Results of these methods can be used to identify biomarkers for AD states. This can aid a better understanding of system dynamics and be applied to producing comprehensive models for AD. The paper provides valuable knowledge regarding the possibility of integration of molecular methods in AD. Although meta-genomic methods are not suitable for on-line use due to long operating time and high costs, they provide extensive insight into the microbial phylogeny in AD. Meta-proteomics can also be explored in the demonstration projects for failure prediction. However, for these methods to be fully realised in AD, a biomarker database needs to be developed.
Collapse
Affiliation(s)
- Seyedbehnam Hashemi
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
| | - Sayed Ebrahim Hashemi
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
| | - Kristian M. Lien
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
| | - Jacob J. Lamb
- Department of Energy and Process Engineering & Enersense, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway; (S.H.); (S.E.H.); (K.M.L.)
- Department of Electronic Systems, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway
- Correspondence:
| |
Collapse
|
|
43
|
Mu DS, Ouyang Y, Chen GJ, Du ZJ. Strategies for culturing active/dormant marine microbes. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:121-131. [PMID: 37073338 PMCID: PMC10077298 DOI: 10.1007/s42995-020-00053-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/18/2020] [Indexed: 05/03/2023]
Abstract
Microorganisms are ubiquitous in the ocean environment and they play key roles in marine ecosystem function and service. However, many of their functions and phenotypes remain unknown because indigenous marine bacteria are mostly difficult to culture. Although many novel techniques have brought previously uncultured microbes into laboratory culture, there are still many most-wanted or key players that need to be cultured from marine environments. This review discusses possible reasons for 'unculturable microbes' and categorizes uncultured bacteria into three groups: dominant active bacteria, rare active bacteria, and dormant bacteria. This review also summarizes advances in cultivation techniques for culturing each group of unculturable bacteria. Simulating the natural environment is an effective strategy for isolating dominant active bacteria, whereas culturomics and enrichment culture methods are proposed for isolating rare active bacteria. For dormant bacteria, resuscitation culture is an appropriate strategy. Furthermore, the review provides a list of the most-wanted bacteria and proposes potential strategies for culturing these bacteria in marine environments. The review provides new insight into the development of strategies for the cultivation of specific groups of uncultured bacteria and therefore paves the way for the detection of novel microbes and their functions in marine ecosystems.
Collapse
Affiliation(s)
- Da-Shuai Mu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
- Marine College, Shandong University, Weihai, 264209 China
| | - Yang Ouyang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK USA
| | - Guan-Jun Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
- Marine College, Shandong University, Weihai, 264209 China
| | - Zong-Jun Du
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 China
- Marine College, Shandong University, Weihai, 264209 China
| |
Collapse
|
|
44
|
Pascoal F, Costa R, Magalhães C. The microbial rare biosphere: current concepts, methods and ecological principles. FEMS Microbiol Ecol 2021; 97:5974270. [PMID: 33175111 DOI: 10.1093/femsec/fiaa227] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/06/2020] [Indexed: 01/04/2023] Open
Abstract
Our ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions and metabolic activity which make-up this communal pool, usually referred to as the 'rare biosphere', across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition and function.
Collapse
Affiliation(s)
- Francisco Pascoal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixoes, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Rodrigo Costa
- Department of Bioengineering, Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais 1049-001, Lisbon, Portugal.,Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.,U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, CA 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, CA 94720 Berkeley, USA
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixoes, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.,School of Science, University of Waikato, Gate 1, Knighton Road 3240, Hamilton, New Zealand.,Ocean Frontier Institute, Dalhousie University, Steele Ocean Sciences Building, Dalhousie University 1355 Oxford St., B3H4R2 Halifax, NS, Canada
| |
Collapse
|
|
45
|
Mujakić I, Andrei AŞ, Shabarova T, Fecskeová LK, Salcher MM, Piwosz K, Ghai R, Koblížek M. Common Presence of Phototrophic Gemmatimonadota in Temperate Freshwater Lakes. mSystems 2021; 6:e01241-20. [PMID: 33727400 PMCID: PMC8547001 DOI: 10.1128/msystems.01241-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/21/2021] [Indexed: 12/11/2022] Open
Abstract
Members of the bacterial phylum Gemmatimonadota are ubiquitous in most natural environments and represent one of the top 10 most abundant bacterial phyla in soil. Sequences affiliated with Gemmatimonadota were also reported from diverse aquatic habitats; however, it remains unknown whether they are native organisms or represent bacteria passively transported from sediment or soil. To address this question, we analyzed metagenomes constructed from five freshwater lakes in central Europe. Based on the 16S rRNA gene frequency, Gemmatimonadota represented from 0.02 to 0.6% of all bacteria in the epilimnion and between 0.1 and 1% in the hypolimnion. These proportions were independently confirmed using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Some cells in the epilimnion were attached to diatoms (Fragilaria sp.) or cyanobacteria (Microcystis sp.), which suggests a close association with phytoplankton. In addition, we reconstructed 45 metagenome-assembled genomes (MAGs) related to Gemmatimonadota They represent several novel lineages, which persist in the studied lakes during the seasons. Three lineages contained photosynthesis gene clusters. One of these lineages was related to Gemmatimonas phototrophica and represented the majority of Gemmatimonadota retrieved from the lakes' epilimnion. The other two lineages came from hypolimnion and probably represented novel photoheterotrophic genera. None of these phototrophic MAGs contained genes for carbon fixation. Since most of the identified MAGs were present during the whole year and cells associated with phytoplankton were observed, we conclude that they represent truly limnic Gemmatimonadota distinct from the previously described species isolated from soils or sediments.IMPORTANCE Photoheterotrophic bacterial phyla such as Gemmatimonadota are key components of many natural environments. Its first photoheterotrophic cultured member, Gemmatimonas phototrophica, was isolated in 2014 from a shallow lake in the Gobi Desert. It contains a unique type of photosynthetic complex encoded by a set of genes which were likely received via horizontal transfer from Proteobacteria We were intrigued to discover how widespread this group is in the natural environment. In the presented study, we analyzed 45 metagenome-assembled genomes (MAGs) that were obtained from five freshwater lakes in Switzerland and Czechia. Interestingly, it was found that phototrophic Gemmatimonadota are relatively common in euphotic zones of the studied lakes, whereas heterotrophic Gemmatimonadota prevail in deeper waters. Moreover, our analysis of the MAGs documented that these freshwater species contain almost the same set of photosynthesis genes identified before in Gemmatimonas phototrophica originating from the Gobi Desert.
Collapse
Affiliation(s)
- Izabela Mujakić
- Laboratory of Anoxygenic Phototrophs, Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Adrian-Ştefan Andrei
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Tanja Shabarova
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Lívia Kolesár Fecskeová
- Laboratory of Anoxygenic Phototrophs, Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Michaela M Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Kasia Piwosz
- Laboratory of Anoxygenic Phototrophs, Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| |
Collapse
|
|
46
|
Abstract
Microbial ecology is the study of microorganisms present in nature. It particularly focuses on microbial interactions with any biota and with surrounding environments. Microbial ecology is entering its golden age with innovative multi-omics methods triggered by next-generation sequencing technologies. However, the extraction of ecologically relevant information from ever-increasing omics data remains one of the most challenging tasks in microbial ecology. This special issue includes 11 review articles that provide an overview of the state of the art of omics-based approaches in the field of microbial ecology, with particular emphasis on the interpretation of omics data, environmental pollution tracking, interactions in microbiomes, and viral ecology.
Collapse
|
|
47
|
de Jonge DSW, Merten V, Bayer T, Puebla O, Reusch TBH, Hoving HJT. A novel metabarcoding primer pair for environmental DNA analysis of Cephalopoda (Mollusca) targeting the nuclear 18S rRNA region. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201388. [PMID: 33972853 PMCID: PMC8074623 DOI: 10.1098/rsos.201388] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/04/2021] [Indexed: 05/19/2023]
Abstract
Cephalopods are pivotal components of marine food webs, but biodiversity studies are hampered by challenges to sample these agile marine molluscs. Metabarcoding of environmental DNA (eDNA) is a potentially powerful technique to study oceanic cephalopod biodiversity and distribution but has not been applied thus far. We present a novel universal primer pair for metabarcoding cephalopods from eDNA, Ceph18S (Forward: 5'-CGC GGC GCT ACA TAT TAG AC-3', Reverse: 5'-GCA CTT AAC CGA CCG TCG AC-3'). The primer pair targets the hypervariable region V2 of the nuclear 18S rRNA gene and amplifies a relatively short target sequence of approximately 200 bp in order to allow the amplification of degraded DNA. In silico tests on a reference database and empirical tests on DNA extracts from cephalopod tissue estimate that 44-66% of cephalopod species, corresponding to about 310-460 species, can be amplified and identified with this primer pair. A multi-marker approach with the novel Ceph18S and two previously published cephalopod mitochondrial 16S rRNA primer sets targeting the same region (Jarman et al. 2006 Mol. Ecol. Notes. 6, 268-271; Peters et al. 2015 Mar. Ecol. 36, 1428-1439) is estimated to amplify and identify 89% of all cephalopod species, of which an estimated 19% can only be identified by Ceph18S. All sequences obtained with Ceph18S were submitted to GenBank, resulting in new 18S rRNA sequences for 13 cephalopod taxa.
Collapse
Affiliation(s)
- Daniëlle S. W. de Jonge
- Faculty of Mathematics and Natural Sciences, University of Groningen, Groningen, The Netherlands
| | - Véronique Merten
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Till Bayer
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Oscar Puebla
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Ecology Department, Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
| | - Thorsten B. H. Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Henk-Jan T. Hoving
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| |
Collapse
|
|
48
|
DeLong EF. Genome-enabled exploration of microbial ecology and evolution in the sea: a rising tide lifts all boats. Environ Microbiol 2021; 23:1301-1321. [PMID: 33459471 PMCID: PMC8049014 DOI: 10.1111/1462-2920.15403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/26/2022]
Abstract
As a young bacteriologist just launching my career during the early days of the 'microbial revolution' in the 1980s, I was fortunate to participate in some early discoveries, and collaborate in the development of cross-disciplinary methods now commonly referred to as "metagenomics". My early scientific career focused on applying phylogenetic and genomic approaches to characterize 'wild' bacteria, archaea and viruses in their natural habitats, with an emphasis on marine systems. These central interests have not changed very much for me over the past three decades, but knowledge, methodological advances and new theoretical perspectives about the microbial world certainly have. In this invited 'How we did it' perspective, I trace some of the trajectories of my lab's collective efforts over the years, including phylogenetic surveys of microbial assemblages in marine plankton and sediments, development of microbial community gene- and genome-enabled surveys, and application of genome-guided, cultivation-independent functional characterization of novel enzymes, pathways and their relationships to in situ biogeochemistry. Throughout this short review, I attempt to acknowledge, all the mentors, students, postdocs and collaborators who enabled this research. Inevitably, a brief autobiographical review like this cannot be fully comprehensive, so sincere apologies to any of my great colleagues who are not explicitly mentioned herein. I salute you all as well!
Collapse
Affiliation(s)
- Edward F DeLong
- Daniel K. Inouye Centre for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI, 96822, USA
| |
Collapse
|
|
49
|
Sangannavar PA, Kumar JS, Subrahmanyam G, Kutala S. Genomics and omics tools to assess complex microbial communities in silkworms: A paradigm shift towards translational research. J Microbiol Methods 2021. [DOI: 10.1016/bs.mim.2021.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
|
50
|
Abstract
Ultra-small microorganisms are ubiquitous in Earth’s environments. Ultramicrobacteria, which are defined as having a cell volume of <0.1 μm3, are often numerically dominant in aqueous environments. Cultivated representatives among these bacteria, such as members of the marine SAR11 clade (e.g., “Candidatus Pelagibacter ubique”) and freshwater Actinobacteria and Betaproteobacteria, possess highly streamlined, small genomes and unique ecophysiological traits. Many ultramicrobacteria may pass through a 0.2-μm-pore-sized filter, which is commonly used for filter sterilization in various fields and processes. Cultivation efforts focusing on filterable small microorganisms revealed that filtered fractions contained not only ultramicrocells (i.e., miniaturized cells because of external factors) and ultramicrobacteria, but also slender filamentous bacteria sometimes with pleomorphic cells, including a special reference to members of Oligoflexia, the eighth class of the phylum Proteobacteria. Furthermore, the advent of culture-independent “omics” approaches to filterable microorganisms yielded the existence of candidate phyla radiation (CPR) bacteria (also referred to as “Ca. Patescibacteria”) and ultra-small members of DPANN (an acronym of the names of the first phyla included in this superphyla) archaea. Notably, certain groups in CPR and DPANN are predicted to have minimal or few biosynthetic capacities, as reflected by their extremely small genome sizes, or possess no known function. Therefore, filtered fractions contain a greater variety and complexity of microorganisms than previously expected. This review summarizes the broad diversity of overlooked filterable agents remaining in “sterile” (<0.2-μm filtered) environmental samples.
Collapse
Affiliation(s)
- Ryosuke Nakai
- Applied Molecular Microbiology Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| |
Collapse
|