51
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Moore RM, Harrison AO, McAllister SM, Polson SW, Wommack KE. Iroki: automatic customization and visualization of phylogenetic trees. PeerJ 2020; 8:e8584. [PMID: 32149022 PMCID: PMC7049256 DOI: 10.7717/peerj.8584] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/17/2020] [Indexed: 12/26/2022] Open
Abstract
Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki’s utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal http://virome.dbi.udel.edu. Iroki’s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.
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Affiliation(s)
- Ryan M Moore
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of America
| | - Amelia O Harrison
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States of America
| | - Sean M McAllister
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States of America
| | - Shawn W Polson
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of America
| | - K Eric Wommack
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of America
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52
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Kraemer S, Ramachandran A, Colatriano D, Lovejoy C, Walsh DA. Diversity and biogeography of SAR11 bacteria from the Arctic Ocean. THE ISME JOURNAL 2020; 14:79-90. [PMID: 31501503 PMCID: PMC6908578 DOI: 10.1038/s41396-019-0499-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 07/30/2019] [Accepted: 08/17/2019] [Indexed: 11/09/2022]
Abstract
The Arctic Ocean is relatively isolated from other oceans and consists of strongly stratified water masses with distinct histories, nutrient, temperature, and salinity characteristics, therefore providing an optimal environment to investigate local adaptation. The globally distributed SAR11 bacterial group consists of multiple ecotypes that are associated with particular marine environments, yet relatively little is known about Arctic SAR11 diversity. Here, we examined SAR11 diversity using ITS analysis and metagenome-assembled genomes (MAGs). Arctic SAR11 assemblages were comprised of the S1a, S1b, S2, and S3 clades, and structured by water mass and depth. The fresher surface layer was dominated by an ecotype (S3-derived P3.2) previously associated with Arctic and brackish water. In contrast, deeper waters of Pacific origin were dominated by the P2.3 ecotype of the S2 clade, within which we identified a novel subdivision (P2.3s1) that was rare outside the Arctic Ocean. Arctic S2-derived SAR11 MAGs were restricted to high latitudes and included MAGs related to the recently defined S2b subclade, a finding consistent with bi-polar ecotypes and Arctic endemism. These results place the stratified Arctic Ocean into the SAR11 global biogeography and have identified SAR11 lineages for future investigation of adaptive evolution in the Arctic Ocean.
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Affiliation(s)
- Susanne Kraemer
- Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, QC, H4B 1R6, Canada
| | - Arthi Ramachandran
- Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, QC, H4B 1R6, Canada
| | - David Colatriano
- Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, QC, H4B 1R6, Canada
| | - Connie Lovejoy
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Québec-Océan, Université Laval, Quebec City, QC, G1K 7P4, Canada
| | - David A Walsh
- Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montreal, QC, H4B 1R6, Canada.
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53
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Hoarfrost A, Nayfach S, Ladau J, Yooseph S, Arnosti C, Dupont CL, Pollard KS. Global ecotypes in the ubiquitous marine clade SAR86. THE ISME JOURNAL 2020; 14:178-188. [PMID: 31611653 PMCID: PMC6908720 DOI: 10.1038/s41396-019-0516-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/23/2019] [Accepted: 09/07/2019] [Indexed: 12/28/2022]
Abstract
SAR86 is an abundant and ubiquitous heterotroph in the surface ocean that plays a central role in the function of marine ecosystems. We hypothesized that despite its ubiquity, different SAR86 subgroups may be endemic to specific ocean regions and functionally specialized for unique marine environments. However, the global biogeographical distributions of SAR86 genes, and the manner in which these distributions correlate with marine environments, have not been investigated. We quantified SAR86 gene content across globally distributed metagenomic samples and modeled these gene distributions as a function of 51 environmental variables. We identified five distinct clusters of genes within the SAR86 pangenome, each with a unique geographic distribution associated with specific environmental characteristics. Gene clusters are characterized by the strong taxonomic enrichment of distinct SAR86 genomes and partial assemblies, as well as differential enrichment of certain functional groups, suggesting differing functional and ecological roles of SAR86 ecotypes. We then leveraged our models and high-resolution, remote sensing-derived environmental data to predict the distributions of SAR86 gene clusters across the world's oceans, creating global maps of SAR86 ecotype distributions. Our results reveal that SAR86 exhibits previously unknown, complex biogeography, and provide a framework for exploring geographic distributions of genetic diversity from other microbial clades.
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Affiliation(s)
- Adrienne Hoarfrost
- Department of Marine Sciences, University of North Carolina, Chapel Hill, NC, USA.
- Department of Biochemistry & Microbiology, Rutgers University, New Brunswick, NJ, USA.
| | - Stephen Nayfach
- Joint Genome Institute, Walnut Creek, CA, USA
- Gladstone Institutes, San Francisco, CA, USA
| | | | - Shibu Yooseph
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Carol Arnosti
- Department of Marine Sciences, University of North Carolina, Chapel Hill, NC, USA
| | | | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, Institute for Human Genetics, Computational Health Sciences Institute, and Quantitative Biology Institute, University of California, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
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54
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Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S, Gregory AC, Labadie K, Marec C, Pelletier E, Royo-Llonch M, Roux S, Sánchez P, Uehara H, Zayed AA, Zeller G, Carmichael M, Dimier C, Ferland J, Kandels S, Picheral M, Pisarev S, Poulain J, Acinas SG, Babin M, Bork P, Bowler C, de Vargas C, Guidi L, Hingamp P, Iudicone D, Karp-Boss L, Karsenti E, Ogata H, Pesant S, Speich S, Sullivan MB, Wincker P, Sunagawa S. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome. Cell 2019; 179:1068-1083.e21. [PMID: 31730850 PMCID: PMC6912165 DOI: 10.1016/j.cell.2019.10.014] [Citation(s) in RCA: 181] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 07/26/2019] [Accepted: 10/11/2019] [Indexed: 12/02/2022]
Abstract
Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. VIDEO ABSTRACT.
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Affiliation(s)
- Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid 28223, Spain; Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Miguelangel Cuenca
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Christopher M Field
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China; Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Corinne Cruaud
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Stefan Engelen
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Ann C Gregory
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Karine Labadie
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Claudie Marec
- Département de biologie, Université Laval, QC G1V 0A6, Canada; Laboratoire d'Oceanographie Physique et Spatiale, UMR 6523, CNRS-IFREMER-IRD-UBO, Plouzané, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Simon Roux
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Hideya Uehara
- Institute for Chemical Research, Kyoto Univerisity, Gokasho, Uji 611-0011, Japan; Hewlett-Packard Japan, 2-2-1, Ojima, Koto-ku, Tokyo 136-8711, Japan
| | - Ahmed A Zayed
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Georg Zeller
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Margaux Carmichael
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Céline Dimier
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, Villefranche-sur-mer 06230, France; Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | - Joannie Ferland
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Takuvik Joint International Laboratory, CNRS-Université Laval, QC G1V 0A6, Canada
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Marc Picheral
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, Villefranche-sur-mer 06230, France
| | - Sergey Pisarev
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow 117997, Russia
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Marcel Babin
- Takuvik Joint International Laboratory, CNRS-Université Laval, QC G1V 0A6, Canada
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany; Max Delbrück Centre for Molecular Medicine, Berlin 13125, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Lionel Guidi
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France; Department of Oceanography, University of Hawaii, Honolulu, HI 96822, USA
| | - Pascal Hingamp
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | | | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME 04469, USA
| | - Eric Karsenti
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France; Directors' Research European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto Univerisity, Gokasho, Uji 611-0011, Japan
| | - Stephane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany; PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | | | - Matthew B Sullivan
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, the Ohio State University, Columbus, OH 43214, USA; Center for RNA Biology, the Ohio State University, Columbus, OH 43214, USA
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland.
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55
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Sakowski E, Uritskiy G, Cooper R, Gomes M, McLaren MR, Meisel JS, Mickol RL, Mintz CD, Mongodin EF, Pop M, Rahman MA, Sanchez A, Timp W, Vela JD, Wolz CM, Zackular JP, Chopyk J, Commichaux S, Davis M, Dluzen D, Ganesan SM, Haruna M, Nasko D, Regan MJ, Sarria S, Shah N, Stacy B, Taylor D, DiRuggiero J, Preheim SP. Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019. mSystems 2019; 4:e00392-19. [PMID: 31594828 PMCID: PMC6787564 DOI: 10.1128/msystems.00392-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Accurate predictions across multiple fields of microbiome research have far-reaching benefits to society, but there are few widely accepted quantitative tools to make accurate predictions about microbial communities and their functions. More discussion is needed about the current state of microbiome analysis and the tools required to overcome the hurdles preventing development and implementation of predictive analyses. We summarize the ideas generated by participants of the Mid-Atlantic Microbiome Meet-up in January 2019. While it was clear from the presentations that most fields have advanced beyond simple associative and descriptive analyses, most fields lack essential elements needed for the development and application of accurate microbiome predictions. Participants stressed the need for standardization, reproducibility, and accessibility of quantitative tools as key to advancing predictions in microbiome analysis. We highlight hurdles that participants identified and propose directions for future efforts that will advance the use of prediction in microbiome research.
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Affiliation(s)
- Eric Sakowski
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Gherman Uritskiy
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Rachel Cooper
- Molecular and Comparative Pathobiology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Maya Gomes
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - Michael R McLaren
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, North Carolina, USA
| | - Jacquelyn S Meisel
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | | | - C David Mintz
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Emmanuel F Mongodin
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, Maryland, USA
| | - Mihai Pop
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | | | - Alvaro Sanchez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven Connecticut, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jeseth Delgado Vela
- Department of Civil and Environmental Engineering, Howard University, Washington, DC, USA
| | - Carly Muletz Wolz
- Center for Conservation Genomics, Smithsonian National Zoological Park & Conservation Biology Institute, Washington, DC, USA
| | - Joseph P Zackular
- Department of Pathology and Laboratory Medicine, University of Pennsylvania and Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jessica Chopyk
- School of Public Health, University of Maryland, College Park, Maryland, USA
| | - Seth Commichaux
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Meghan Davis
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Douglas Dluzen
- Department of Biology, Morgan State University, Baltimore, Maryland, USA
| | - Sukirth M Ganesan
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Muyideen Haruna
- Department of Biology, Morgan State University, Baltimore, Maryland, USA
| | - Dan Nasko
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Mary J Regan
- University of Maryland School of Nursing, Baltimore, Maryland, USA
| | - Saul Sarria
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Nidhi Shah
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Brook Stacy
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Dylan Taylor
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | | | - Sarah P Preheim
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
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56
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de Sousa AGG, Tomasino MP, Duarte P, Fernández-Méndez M, Assmy P, Ribeiro H, Surkont J, Leite RB, Pereira-Leal JB, Torgo L, Magalhães C. Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime. MICROBIAL ECOLOGY 2019; 78:388-408. [PMID: 30623212 DOI: 10.1007/s00248-018-01314-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 12/25/2018] [Indexed: 06/09/2023]
Abstract
One of the most prominent manifestations of climate change is the changing Arctic sea-ice regime with a reduction in the summer sea-ice extent and a shift from thicker, perennial multiyear ice towards thinner, first-year ice. These changes in the physical environment are likely to impact microbial communities, a key component of Arctic marine food webs and biogeochemical cycles. During the Norwegian young sea ICE expedition (N-ICE2015) north of Svalbard, seawater samples were collected at the surface (5 m), subsurface (20 or 50 m), and mesopelagic (250 m) depths on 9 March, 27 April, and 16 June 2015. In addition, several physical and biogeochemical data were recorded to contextualize the collected microbial communities. Through the massively parallel sequencing of the small subunit ribosomal RNA amplicon and metagenomic data, this work allows studying the Arctic's microbial community structure during the late winter to early summer transition. Results showed that, at compositional level, Alpha- (30.7%) and Gammaproteobacteria (28.6%) are the most frequent taxa across the prokaryotic N-ICE2015 collection, and also the most phylogenetically diverse. Winter to early summer trends were quite evident since there was a high relative abundance of thaumarchaeotes in the under-ice water column in late winter while this group was nearly absent during early summer. Moreover, the emergence of Flavobacteria and the SAR92 clade in early summer might be associated with the degradation of a spring bloom of Phaeocystis. High relative abundance of hydrocarbonoclastic bacteria, particularly Alcanivorax (54.3%) and Marinobacter (6.3%), was also found. Richness showed different patterns along the depth gradient for prokaryotic (highest at mesopelagic depth) and protistan communities (higher at subsurface depths). The microbial N-ICE2015 collection analyzed in the present study provides comprehensive new knowledge about the pelagic microbiota below drifting Arctic sea-ice. The higher microbial diversity found in late winter/early spring communities reinforces the need to continue with further studies to properly characterize the winter microbial communities under the pack-ice.
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Affiliation(s)
- António Gaspar G de Sousa
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Rua Campo Alegre s/n, 4169-007, Porto, Portugal.
| | - Maria Paola Tomasino
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
| | - Pedro Duarte
- Norwegian Polar Institute, Fram Centre, N-9296, Tromsø, Norway
| | | | - Philipp Assmy
- Norwegian Polar Institute, Fram Centre, N-9296, Tromsø, Norway
| | - Hugo Ribeiro
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
| | - Jaroslaw Surkont
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Ricardo B Leite
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - José B Pereira-Leal
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Luís Torgo
- LIAAD - Laboratory of Artificial Intelligence and Decision Support, INESC Tec, Porto, Portugal
- Faculty of Computer Science, Dalhousie University, Halifax, Canada, USA
| | - Catarina Magalhães
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua Campo Alegre s/n, 4169-007, Porto, Portugal
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57
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Greenlon A, Chang PL, Damtew ZM, Muleta A, Carrasquilla-Garcia N, Kim D, Nguyen HP, Suryawanshi V, Krieg CP, Yadav SK, Patel JS, Mukherjee A, Udupa S, Benjelloun I, Thami-Alami I, Yasin M, Patil B, Singh S, Sarma BK, von Wettberg EJB, Kahraman A, Bukun B, Assefa F, Tesfaye K, Fikre A, Cook DR. Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria. Proc Natl Acad Sci U S A 2019; 116:15200-15209. [PMID: 31285337 PMCID: PMC6660780 DOI: 10.1073/pnas.1900056116] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Although microorganisms are known to dominate Earth's biospheres and drive biogeochemical cycling, little is known about the geographic distributions of microbial populations or the environmental factors that pattern those distributions. We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of the nitrogen-fixing bacterial symbionts of the crop chickpea, generating 1,027 draft whole-genome sequences at the level of bacterial populations, including 14 high-quality PacBio genomes from a phylogenetically representative subset. We find that diverse Mesorhizobium taxa perform symbiosis with chickpea and have largely overlapping global distributions. However, sampled locations cluster based on the phylogenetic diversity of Mesorhizobium populations, and diversity clusters correspond to edaphic and environmental factors, primarily soil type and latitude. Despite long-standing evolutionary divergence and geographic isolation, the diverse taxa observed to nodulate chickpea share a set of integrative conjugative elements (ICEs) that encode the major functions of the symbiosis. This symbiosis ICE takes 2 forms in the bacterial chromosome-tripartite and monopartite-with tripartite ICEs confined to a broadly distributed superspecies clade. The pairwise evolutionary relatedness of these elements is controlled as much by geographic distance as by the evolutionary relatedness of the background genome. In contrast, diversity in the broader gene content of Mesorhizobium genomes follows a tight linear relationship with core genome phylogenetic distance, with little detectable effect of geography. These results illustrate how geography and demography can operate differentially on the evolution of bacterial genomes and offer useful insights for the development of improved technologies for sustainable agriculture.
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Affiliation(s)
- Alex Greenlon
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Peter L Chang
- Department of Plant Pathology, University of California, Davis, CA 95616
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Zehara Mohammed Damtew
- College of Natural Sciences, Addis Ababa University, Addis Ababa, 32853 Ethiopia
- Debre Zeit Agricultural Research Center, Ethiopian Institute for Agricultural Research, Bishoftu, Ethiopia
| | - Atsede Muleta
- College of Natural Sciences, Addis Ababa University, Addis Ababa, 32853 Ethiopia
| | | | - Donghyun Kim
- International Crop Research Institute for the Semi-Arid Tropics, Hyderabad 502324, India
| | - Hien P Nguyen
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 183-8509 Tokyo, Japan
| | - Vasantika Suryawanshi
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Christopher P Krieg
- Department of Biological Sciences, Florida International University, Miami, FL 33199
| | - Sudheer Kumar Yadav
- Department of Mycology and Plant Pathology, Banaras Hindu University, Varanasi 221005, India
| | - Jai Singh Patel
- Department of Mycology and Plant Pathology, Banaras Hindu University, Varanasi 221005, India
| | - Arpan Mukherjee
- Department of Mycology and Plant Pathology, Banaras Hindu University, Varanasi 221005, India
| | - Sripada Udupa
- Biodiversity and Integrated Gene Management Program, International Center for Agricultural Research in the Dry Areas, 10112 Rabat, Morocco
| | - Imane Benjelloun
- Institute National de la Recherche Agronomique, 10100 Rabat, Morocco
| | - Imane Thami-Alami
- Institute National de la Recherche Agronomique, 10100 Rabat, Morocco
| | | | - Bhuvaneshwara Patil
- Department of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad 580001, India
| | - Sarvjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana 141027, India
| | - Birinchi Kumar Sarma
- Department of Mycology and Plant Pathology, Banaras Hindu University, Varanasi 221005, India
| | - Eric J B von Wettberg
- Department of Biological Sciences, Florida International University, Miami, FL 33199
- Department of Plant and Soil Science, University of Vermont, Burlington, VT 05405
| | - Abdullah Kahraman
- Department of Field Crops, Faculty of Agriculture, Harran University, 63100 Sanliurfa, Turkey
| | - Bekir Bukun
- Department of Plant Protection, Dicle University, 21280 Diyarbakir, Turkey
| | - Fassil Assefa
- College of Natural Sciences, Addis Ababa University, Addis Ababa, 32853 Ethiopia
| | - Kassahun Tesfaye
- College of Natural Sciences, Addis Ababa University, Addis Ababa, 32853 Ethiopia
| | - Asnake Fikre
- Debre Zeit Agricultural Research Center, Ethiopian Institute for Agricultural Research, Bishoftu, Ethiopia
| | - Douglas R Cook
- Department of Plant Pathology, University of California, Davis, CA 95616;
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58
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Righetti D, Vogt M, Gruber N, Psomas A, Zimmermann NE. Global pattern of phytoplankton diversity driven by temperature and environmental variability. SCIENCE ADVANCES 2019; 5:eaau6253. [PMID: 31106265 PMCID: PMC6520023 DOI: 10.1126/sciadv.aau6253] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 04/02/2019] [Indexed: 05/21/2023]
Abstract
Despite their importance to ocean productivity, global patterns of marine phytoplankton diversity remain poorly characterized. Although temperature is considered a key driver of general marine biodiversity, its specific role in phytoplankton diversity has remained unclear. We determined monthly phytoplankton species richness by using niche modeling and >540,000 global phytoplankton observations to predict biogeographic patterns of 536 phytoplankton species. Consistent with metabolic theory, phytoplankton richness in the tropics is about three times that in higher latitudes, with temperature being the most important driver. However, below 19°C, richness is lower than expected, with ~8°- 14°C waters (~35° to 60° latitude) showing the greatest divergence from theoretical predictions. Regions of reduced richness are characterized by maximal species turnover and environmental variability, suggesting that the latter reduces species richness directly, or through enhancing competitive exclusion. The nonmonotonic relationship between phytoplankton richness and temperature suggests unanticipated complexity in responses of marine biodiversity to ocean warming.
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Affiliation(s)
- Damiano Righetti
- Environmental Physics, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
- Corresponding author.
| | - Meike Vogt
- Environmental Physics, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
| | - Nicolas Gruber
- Environmental Physics, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
| | - Achilleas Psomas
- Dynamic Macroecology, Landscape Dynamics, Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Niklaus E. Zimmermann
- Dynamic Macroecology, Landscape Dynamics, Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
- Department of Environmental Systems Science, ETH Zurich, 8092 Zurich, Switzerland
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59
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Ruiz-González C, Logares R, Sebastián M, Mestre M, Rodríguez-Martínez R, Galí M, Sala MM, Acinas SG, Duarte CM, Gasol JM. Higher contribution of globally rare bacterial taxa reflects environmental transitions across the surface ocean. Mol Ecol 2019; 28:1930-1945. [PMID: 30663830 DOI: 10.1111/mec.15026] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/21/2018] [Accepted: 01/14/2019] [Indexed: 01/21/2023]
Abstract
Microbial taxa range from being ubiquitous and abundant across space to extremely rare and endemic, depending on their ecophysiology and on different processes acting locally or regionally. However, little is known about how cosmopolitan or rare taxa combine to constitute communities and whether environmental variations promote changes in their relative abundances. Here we identified the Spatial Abundance Distribution (SpAD) of individual prokaryotic taxa (16S rDNA-defined Operational Taxonomic Units, OTUs) across 108 globally-distributed surface ocean stations. We grouped taxa based on their SpAD shape ("normal-like"- abundant and ubiquitous; "logistic"- globally rare, present in few sites; and "bimodal"- abundant only in certain oceanic regions), and investigated how the abundance of these three categories relates to environmental gradients. Most surface assemblages were numerically dominated by a few cosmopolitan "normal-like" OTUs, yet there was a gradual shift towards assemblages dominated by "logistic" taxa in specific areas with productivity and temperature differing the most from the average conditions in the sampled stations. When we performed the SpAD categorization including additional habitats (deeper layers and particles of varying sizes), the SpAD of many OTUs changed towards fewer "normal-like" shapes, and OTUs categorized as globally rare in the surface ocean became abundant. This suggests that understanding the mechanisms behind microbial rarity and dominance requires expanding the context of study beyond local communities and single habitats. We show that marine bacterial communities comprise taxa displaying a continuum of SpADs, and that variations in their abundances can be linked to habitat transitions or barriers that delimit the distribution of community members.
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Affiliation(s)
| | - Ramiro Logares
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Marta Sebastián
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain.,Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Telde, Spain
| | - Mireia Mestre
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain.,Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile
| | - Raquel Rodríguez-Martínez
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain.,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Martí Galí
- Unité Mixte Internationale Takuvik (Université Laval-CNRS) and Québec-Océan, Département de Biologie, Université Laval, Québec City, Québec, Canada.,Barcelona Supercomputing Centre (BSC), Barcelona, Catalonia, Spain
| | | | - Silvia G Acinas
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Carlos M Duarte
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Josep M Gasol
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain.,Centre for Marine Ecosystem Research, Edith Cowan University, Joondalup, Western Australia, Australia
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60
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Ladau J, Eloe-Fadrosh EA. Spatial, Temporal, and Phylogenetic Scales of Microbial Ecology. Trends Microbiol 2019; 27:662-669. [PMID: 31000488 DOI: 10.1016/j.tim.2019.03.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/04/2019] [Accepted: 03/13/2019] [Indexed: 01/07/2023]
Abstract
Microbial communities play a major role in disease, biogeochemical cycling, agriculture, and bioremediation. However, identifying the ecological processes that govern microbial community assembly and disentangling the relative impacts of those processes has proven challenging. Here, we propose that this discord is due to microbial systems being studied at different spatial, temporal, and phylogenetic scales. We argue that different processes dominate at different scales, and that through a more explicit consideration of spatial, temporal, and phylogenetic grains and extents (the two components of scale) a more accurate, clear, and useful understanding of microbial community assembly can be developed. We demonstrate the value of applying ecological concepts of scale to microbiology, specifically examining their application to nestedness, legacy effects, and taxa-area relationships of microbial systems. These proposed considerations of scale will help resolve long-standing debates in microbial ecology regarding the processes determining the assembly of microbial communities, and provide organizing principles around which hypotheses and theories can be developed.
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61
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Zorz J, Willis C, Comeau AM, Langille MGI, Johnson CL, Li WKW, LaRoche J. Drivers of Regional Bacterial Community Structure and Diversity in the Northwest Atlantic Ocean. Front Microbiol 2019; 10:281. [PMID: 30846975 PMCID: PMC6393369 DOI: 10.3389/fmicb.2019.00281] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 02/04/2019] [Indexed: 11/29/2022] Open
Abstract
The fundamental role of bacteria in global biogeochemical cycles warrants a thorough understanding of the factors controlling bacterial community structure. In this study, the integrated effect of seasonal differences and spatial distribution on bacterial community structure and diversity were investigated at the regional scale. We conducted a comprehensive bacterial survey, with 451 samples of the Scotian Shelf sector of the Northwest Atlantic Ocean during spring and fall of 2014 and 2016, to analyze the effects of physicochemical gradients on bacterial community structure. Throughout the region, Pelagibacteraceae and Rhodobacteraceae were the most common in the free-living fraction, while Flavobacteriia and Deltaproteobacteria were more abundant in the particle-associated fraction. Overall, there was strong covariation of the microbial community diversity from the two size fractions. This relationship existed despite the statistically significant difference in community structure between the free-living and particle-associated size fractions. In both size fractions, distribution patterns of bacterial taxa, and species within taxa, displayed temporal and spatial preferences. Distinct bacterial assemblages specific to season and depth in the water column were identified. These distinct assemblages, consistent for both 2014 and 2016, suggested replicable patterns in microbial communities for spring and fall in this region. Over all sites, temperature and oxygen values were highly correlated with community similarity, and salinity and oxygen values were the most strongly positively- and negatively correlated with alpha diversity, respectively. However, the strengths of these correlations depended on the depth and season sampled. The bathymetry of the Scotian Shelf, the abrupt shelf break to the Scotian Slope and the major ocean currents dominating in the region led to the formation of distinct on-shelf and off-shelf bacterial communities both in spring and fall. The highest species richness was observed at the shelf break, where water masses from the two major currents meet. Our study establishes the baseline for assessing future changes in the bacterial community of the Scotian Shelf waters, a rapidly changing sector of the Atlantic Ocean.
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Affiliation(s)
- Jackie Zorz
- Department of Biology, Dalhousie University, Halifax, NS, Canada.,Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Ciara Willis
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - André M Comeau
- CGEB-Integrated Microbiome Resource, Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Morgan G I Langille
- CGEB-Integrated Microbiome Resource, Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Catherine L Johnson
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, NS, Canada
| | - William K W Li
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, NS, Canada
| | - Julie LaRoche
- Department of Biology, Dalhousie University, Halifax, NS, Canada
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62
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Tipton L, Darcy JL, Hynson NA. A Developing Symbiosis: Enabling Cross-Talk Between Ecologists and Microbiome Scientists. Front Microbiol 2019; 10:292. [PMID: 30842763 PMCID: PMC6391321 DOI: 10.3389/fmicb.2019.00292] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/04/2019] [Indexed: 12/29/2022] Open
Abstract
Like all interactions, the success of cross-discipline collaborations relies on effective communication. Ecology offers theoretical frameworks and lexicons to study microbiomes. Yet some of the terms and concepts borrowed from ecology are being used discordantly by microbiome studies from their traditional definitions. Here we define some of the ecological terms and concepts as they are used in ecology and the study of microbiomes. Where applicable, we have provided the historical context of the terms, highlighted examples from microbiome studies, and considered the research methods involved. We divided these concepts into four sections: Biomes, Diversity, Symbiosis, and Succession. Biomes encompass the interactions within the biotic and abiotic features of an environment. This extends to the term "microbiome," derived from "biome," and includes an environment and all the microbes within it. Diversity encompasses patterns of species richness, abundance, and biogeography, all of which are important to understanding the distribution of microbiomes. Symbiosis emphasizes the relationships between organisms within a community. Symbioses are often misunderstood to be synonymous with mutualism. We discard that implication, in favor of a broader, more historically accurate definition which spans the continuum from parasitism to mutualism. Succession includes classical succession, alternative stable states, community assembly frameworks, and r/K-selection. Our hope is that as microbiome researchers continue to apply ecological terms, and as ecologists continue to gain interest in microbiomes, each will do so in a way that enables cross-talk between them. We recommend initiating these collaborations by using a common lexicon, from which new concepts can emerge.
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Affiliation(s)
- Laura Tipton
- Department of Botany, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - John L. Darcy
- Department of Botany, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Nicole A. Hynson
- Pacific Biosciences Research Center, University of Hawai’i at Mānoa, Honolulu, HI, United States
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63
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Kueneman JG, Bletz MC, McKenzie VJ, Becker CG, Joseph MB, Abarca JG, Archer H, Arellano AL, Bataille A, Becker M, Belden LK, Crottini A, Geffers R, Haddad CFB, Harris RN, Holden WM, Hughey M, Jarek M, Kearns PJ, Kerby JL, Kielgast J, Kurabayashi A, Longo AV, Loudon A, Medina D, Nuñez JJ, Perl RGB, Pinto-Tomás A, Rabemananjara FCE, Rebollar EA, Rodríguez A, Rollins-Smith L, Stevenson R, Tebbe CC, Vargas Asensio G, Waldman B, Walke JB, Whitfield SM, Zamudio KR, Zúñiga Chaves I, Woodhams DC, Vences M. Community richness of amphibian skin bacteria correlates with bioclimate at the global scale. Nat Ecol Evol 2019; 3:381-389. [DOI: 10.1038/s41559-019-0798-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 01/06/2019] [Indexed: 12/15/2022]
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64
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Xia X, Cheung S, Endo H, Suzuki K, Liu H. Latitudinal and Vertical Variation of Synechococcus Assemblage Composition Along 170° W Transect From the South Pacific to the Arctic Ocean. MICROBIAL ECOLOGY 2019; 77:333-342. [PMID: 30610255 DOI: 10.1007/s00248-018-1308-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 12/16/2018] [Indexed: 06/09/2023]
Abstract
Synechococcus is one of the most widely distributed and abundant picocyanobacteria in the global oceans. Although latitudinal variation of Synechococcus assemblage in marine surface waters has been observed, few studies compared Synechococcus assemblage composition in surface and subsurface waters at the basin scale. Here, we report marine Synechococcus diversity in the surface and deep chlorophyll maximum (DCM) layers along 170° W from the South Pacific to the Arctic Ocean in summer. Along the transect, spatial niche partitioning of Synechococcus lineages in the surface waters was clearly observed. Species richness of surface Synechococcus assemblage was positively correlated with water temperature. Clade CRD1 was dominant in the areas (15° S-10° N and 35-40° N) associated with upwelling, and there were 3 different subclades with distinct distribution. CRD1-A was restricted in the North Equatorial Current (5-10° N), CRD1-B dominated in the equatorial upwelling region (15° S-0.17° N), and CRD1-C was only distributed in the North Pacific Current (35-40° N). Similarities between the Synechococcus assemblages in the surface and DCM layers were high at the upwelling regions and areas where the mixed layer was deep, while low in the Subtropical Gyres with strong stratification. Clade I, CRD1-B, and CRD1-C were major Synechococcus lineages in the DCM layer. In particular, clade I, which is composed of 7 subclades with distinct thermal niches, was widely distributed in the DCM layer. Overall, our results provide new insights into not only the latitudinal distribution of Synechococcus assemblages, but also their vertical variation in the central Pacific.
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Affiliation(s)
- Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, People's Republic of China
| | - Shunyuan Cheung
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Hisashi Endo
- Faculty of Environmental Earth Science, Hokkaido University/JST-CREST, North 10 West 5, Kita-ku, Sapporo, 060-0810, Hokkaido, Japan
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Koji Suzuki
- Faculty of Environmental Earth Science, Hokkaido University/JST-CREST, North 10 West 5, Kita-ku, Sapporo, 060-0810, Hokkaido, Japan.
| | - Hongbin Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong.
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65
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Fernández-Gómez B, Díez B, Polz MF, Arroyo JI, Alfaro FD, Marchandon G, Sanhueza C, Farías L, Trefault N, Marquet PA, Molina-Montenegro MA, Sylvander P, Snoeijs-Leijonmalm P. Bacterial community structure in a sympagic habitat expanding with global warming: brackish ice brine at 85-90 °N. THE ISME JOURNAL 2019; 13:316-333. [PMID: 30228379 PMCID: PMC6331608 DOI: 10.1038/s41396-018-0268-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 06/11/2018] [Accepted: 07/24/2018] [Indexed: 01/13/2023]
Abstract
Larger volumes of sea ice have been thawing in the Central Arctic Ocean (CAO) during the last decades than during the past 800,000 years. Brackish brine (fed by meltwater inside the ice) is an expanding sympagic habitat in summer all over the CAO. We report for the first time the structure of bacterial communities in this brine. They are composed of psychrophilic extremophiles, many of them related to phylotypes known from Arctic and Antarctic regions. Community structure displayed strong habitat segregation between brackish ice brine (IB; salinity 2.4-9.6) and immediate sub-ice seawater (SW; salinity 33.3-34.9), expressed at all taxonomic levels (class to genus), by dominant phylotypes as well as by the rare biosphere, and with specialists dominating IB and generalists SW. The dominant phylotypes in IB were related to Candidatus Aquiluna and Flavobacterium, those in SW to Balneatrix and ZD0405, and those shared between the habitats to Halomonas, Polaribacter and Shewanella. A meta-analysis for the oligotrophic CAO showed a pattern with Flavobacteriia dominating in melt ponds, Flavobacteriia and Gammaproteobacteria in solid ice cores, Flavobacteriia, Gamma- and Betaproteobacteria, and Actinobacteria in brine, and Alphaproteobacteria in SW. Based on our results, we expect that the roles of Actinobacteria and Betaproteobacteria in the CAO will increase with global warming owing to the increased production of meltwater in summer. IB contained three times more phylotypes than SW and may act as an insurance reservoir for bacterial diversity that can act as a recruitment base when environmental conditions change.
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Affiliation(s)
- Beatriz Fernández-Gómez
- Department of Molecular Genetics and Microbiology, Pontifical University Catholic of Chile, Santiago, Chile
- INTA-Universidad de Chile, Santiago, Chile
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Pontifical University Catholic of Chile, Santiago, Chile.
- Center for Climate and Resilience Research, Concepción, Chile.
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, USA
| | - José Ignacio Arroyo
- Department of Ecology, Pontifical University Catholic of Chile, Santiago, Chile
| | - Fernando D Alfaro
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago, Chile
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Germán Marchandon
- Department of Molecular Genetics and Microbiology, Pontifical University Catholic of Chile, Santiago, Chile
| | - Cynthia Sanhueza
- Department of Molecular Genetics and Microbiology, Pontifical University Catholic of Chile, Santiago, Chile
| | - Laura Farías
- Center for Climate and Resilience Research, Concepción, Chile
- Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago, Chile
| | - Pablo A Marquet
- Department of Ecology, Pontifical University Catholic of Chile, Santiago, Chile
- Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - Marco A Molina-Montenegro
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centro de Estudios Avanzados en Zonas Áridas, Universidad Católica del Norte, Coquimbo, Chile
| | - Peter Sylvander
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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66
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Lambert S, Tragin M, Lozano JC, Ghiglione JF, Vaulot D, Bouget FY, Galand PE. Rhythmicity of coastal marine picoeukaryotes, bacteria and archaea despite irregular environmental perturbations. THE ISME JOURNAL 2019; 13:388-401. [PMID: 30254323 PMCID: PMC6331585 DOI: 10.1038/s41396-018-0281-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/20/2018] [Accepted: 08/26/2018] [Indexed: 01/15/2023]
Abstract
Seasonality in marine microorganisms has been classically observed in phytoplankton blooms, and more recently studied at the community level in prokaryotes, but rarely investigated at the scale of individual microbial taxa. Here we test if specific marine eukaryotic phytoplankton, bacterial and archaeal taxa display yearly rhythms at a coastal site impacted by irregular environmental perturbations. Our seven-year study in the Bay of Banyuls (North Western Mediterranean Sea) shows that despite some fluctuating environmental conditions, many microbial taxa displayed significant yearly rhythms. The robust rhythmicity was found in both autotrophs (picoeukaryotes and cyanobacteria) and heterotrophic prokaryotes. Sporadic meteorological events and irregular nutrient supplies did, however, trigger the appearance of less common non-rhythmic taxa. Among the environmental parameters that were measured, the main drivers of rhythmicity were temperature and day length. Seasonal autotrophs may thus be setting the pace for rhythmic heterotrophs. Similar environmental niches may be driving seasonality as well. The observed strong association between Micromonas and SAR11, which both need thiamine precursors for growth, could be a first indication that shared nutritional niches may explain some rhythmic patterns of co-occurrence.
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Affiliation(s)
- Stefan Lambert
- CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, Sorbonne Université, Banyuls sur Mer, Paris, France
| | - Margot Tragin
- CNRS, UMR7144, Station Biologique de Roscoff, Sorbonne Université, Roscoff, Paris, France
| | - Jean-Claude Lozano
- CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, Sorbonne Université, Banyuls sur Mer, Paris, France
| | - Jean-François Ghiglione
- CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, Sorbonne Université, Banyuls sur Mer, Paris, France
| | - Daniel Vaulot
- CNRS, UMR7144, Station Biologique de Roscoff, Sorbonne Université, Roscoff, Paris, France
| | - François-Yves Bouget
- CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, Sorbonne Université, Banyuls sur Mer, Paris, France.
| | - Pierre E Galand
- CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Sorbonne Université, Banyuls sur Mer, Paris, France.
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67
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Lu HP, Yeh YC, Shiah FK, Gong GC, Hsieh CH. Evolutionary constraints on species diversity in marine bacterioplankton communities. ISME JOURNAL 2019; 13:1032-1041. [PMID: 30607025 DOI: 10.1038/s41396-018-0336-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 07/23/2018] [Accepted: 12/11/2018] [Indexed: 01/14/2023]
Abstract
Variation in microbial species diversity has typically been explained as the outcome of local ecological factors driving species coexistence, overlooking the roles of evolutionary constraints. Here, we argue that macro-evolutionary niche conservatism and unequal diversification rates among phylum-level lineages are strong determinants of diversity-environment relationships in bacterial systems. That is, apart from stochasticity, environmental effects operate most strongly on phylum composition, which in turn dictates the species diversity of bacterial communities. This concept is demonstrated using bacterioplankton in the surface seawaters of the East China Sea. Furthermore, we show that the species richness of a local bacterioplankton community can generally be estimated based on the relative abundances of phyla and their contributions of species numbers in the global seawater pool-highlighting the important influence of evolutionary constraints on local community diversity.
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Affiliation(s)
- Hsiao-Pei Lu
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Yi-Chun Yeh
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Fuh-Kwo Shiah
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan.,Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan.,Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Gwo-Ching Gong
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan.,Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Chih-Hao Hsieh
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan. .,Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan. .,Department of Life Science, Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan. .,National Center for Theoretical Sciences, Taipei, Taiwan.
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68
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Li H, Mishra M, Ding S, Miyamoto MM. Diversity and Dynamics of "Candidatus Endobugula" and Other Symbiotic Bacteria in Chinese Populations of the Bryozoan, Bugula neritina. MICROBIAL ECOLOGY 2019; 77:243-256. [PMID: 30141128 DOI: 10.1007/s00248-018-1233-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/13/2018] [Indexed: 06/08/2023]
Abstract
Bugula neritina is a common invasive cosmopolitan bryozoan that harbors (like many sessile marine invertebrates) a symbiotic bacterial (SB) community. Among the SB of B. neritina, "Candidatus Endobugula sertula" continues to receive the greatest attention, because it is the source of bryostatins. The bryostatins are potent bioactive polyketides, which have been investigated for their therapeutic potential to treat various cancers, Alzheimer's disease, and AIDS. In this study, we compare the metagenomics sequences for the 16S ribosomal RNA gene of the SB communities from different geographic and life cycle samples of Chinese B. neritina. Using a variety of approaches for estimating alpha/beta diversity and taxonomic abundance, we find that the SB communities vary geographically with invertebrate and fish mariculture and with latitude and environmental temperature. During the B. neritina life cycle, we find that the diversity and taxonomic abundances of the SB communities change with the onset of host metamorphosis, filter feeding, colony formation, reproduction, and increased bryostatin production. "Ca. Endobugula sertula" is confirmed as the symbiont of the Chinese "Ca. Endobugula"/B. neritina symbiosis. Our study extends our knowledge about B. neritina symbiosis from the New to the Old World and offers new insights into the environmental and life cycle factors that can influence its SB communities, "Ca. Endobugula," and bryostatins more globally.
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Affiliation(s)
- Hai Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
- Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005, China
| | - Mrinal Mishra
- Department of Biology, University of Florida, Box 118525, Gainesville, FL, 32611-8525, USA
| | - Shaoxiong Ding
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China.
| | - Michael M Miyamoto
- Department of Biology, University of Florida, Box 118525, Gainesville, FL, 32611-8525, USA
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69
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Hernando-Morales V, Varela MM, Needham DM, Cram J, Fuhrman JA, Teira E. Vertical and Seasonal Patterns Control Bacterioplankton Communities at Two Horizontally Coherent Coastal Upwelling Sites off Galicia (NW Spain). MICROBIAL ECOLOGY 2018; 76:866-884. [PMID: 29675703 DOI: 10.1007/s00248-018-1179-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 03/14/2018] [Indexed: 06/08/2023]
Abstract
Analysis of seasonal patterns of marine bacterial community structure along horizontal and vertical spatial scales can help to predict long-term responses to climate change. Several recent studies have shown predictable seasonal reoccurrence of bacterial assemblages. However, only a few have assessed temporal variability over both horizontal and vertical spatial scales. Here, we simultaneously studied the bacterial community structure at two different locations and depths in shelf waters of a coastal upwelling system during an annual cycle. The most noticeable biogeographic patterns observed were seasonality, horizontal homogeneity, and spatial synchrony in bacterial diversity and community structure related with regional upwelling-downwelling dynamics. Water column mixing eventually disrupted bacterial community structure vertical heterogeneity. Our results are consistent with previous temporal studies of marine bacterioplankton in other temperate regions and also suggest a marked influence of regional factors on the bacterial communities inhabiting this coastal upwelling system. Bacterial-mediated carbon fluxes in this productive region appear to be mainly controlled by community structure dynamics in surface waters, and local environmental factors at the base of the euphotic zone.
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Affiliation(s)
- Víctor Hernando-Morales
- Grupo de Oceanografía Biolóxica, Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, 36310, Vigo, Spain.
- Estación de Ciencias Mariñas de Toralla (ECIMAT), Universidade de Vigo, Illa de Toralla, 36331, Vigo, Spain.
| | - Marta M Varela
- IEO, Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, Apdo 130, 15080, A Coruña, Spain
| | - David M Needham
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA
| | - Jacob Cram
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA
| | - Eva Teira
- Grupo de Oceanografía Biolóxica, Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, 36310, Vigo, Spain
- Estación de Ciencias Mariñas de Toralla (ECIMAT), Universidade de Vigo, Illa de Toralla, 36331, Vigo, Spain
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70
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Oceanographic boundaries constrain microbial diversity gradients in the South Pacific Ocean. Proc Natl Acad Sci U S A 2018; 115:E8266-E8275. [PMID: 30108147 DOI: 10.1073/pnas.1719335115] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Marine microbes along with microeukaryotes are key regulators of oceanic biogeochemical pathways. Here we present a high-resolution (every 0.5° of latitude) dataset describing microbial pro- and eukaryotic richness in the surface and just below the thermocline along a 7,000-km transect from 66°S at the Antarctic ice edge to the equator in the South Pacific Ocean. The transect, conducted in austral winter, covered key oceanographic features including crossing of the polar front (PF), the subtropical front (STF), and the equatorial upwelling region. Our data indicate that temperature does not determine patterns of marine microbial richness, complementing the global model data from Ladau et al. [Ladau J, et al. (2013) ISME J 7:1669-1677]. Rather, NH4+, nanophytoplankton, and primary productivity were the main drivers for archaeal and bacterial richness. Eukaryote richness was highest in the least-productive ocean region, the tropical oligotrophic province. We also observed a unique diversity pattern in the South Pacific Ocean: a regional increase in archaeal and bacterial diversity between 10°S and the equator. Rapoport's rule describes the tendency for the latitudinal ranges of species to increase with latitude. Our data showed that the mean latitudinal ranges of archaea and bacteria decreased with latitude. We show that permanent oceanographic features, such as the STF and the equatorial upwelling, can have a significant influence on both alpha-diversity and beta-diversity of pro- and eukaryotes.
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71
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A strong link between marine microbial community composition and function challenges the idea of functional redundancy. ISME JOURNAL 2018; 12:2470-2478. [PMID: 29925880 DOI: 10.1038/s41396-018-0158-1] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 05/07/2018] [Accepted: 05/09/2018] [Indexed: 12/31/2022]
Abstract
Marine microbes have tremendous diversity, but a fundamental question remains unanswered: why are there so many microbial species in the sea? The idea of functional redundancy for microbial communities has long been assumed, so that the high level of richness is often explained by the presence of different taxa that are able to conduct the exact same set of metabolic processes and that can readily replace each other. Here, we refute the hypothesis of functional redundancy for marine microbial communities by showing that a shift in the community composition altered the overall functional attributes of communities across different temporal and spatial scales. Our metagenomic monitoring of a coastal northwestern Mediterranean site also revealed that diverse microbial communities harbor a high diversity of potential proteins. Working with all information given by the metagenomes (all reads) rather than relying only on known genes (annotated orthologous genes) was essential for revealing the similarity between taxonomic and functional community compositions. Our finding does not exclude the possibility for a partial redundancy where organisms that share some specific function can coexist when they differ in other ecological requirements. It demonstrates, however, that marine microbial diversity reflects a tremendous diversity of microbial metabolism and highlights the genetic potential yet to be discovered in an ocean of microbes.
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72
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American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems 2018; 3:mSystems00031-18. [PMID: 29795809 PMCID: PMC5954204 DOI: 10.1128/msystems.00031-18] [Citation(s) in RCA: 480] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 04/16/2018] [Indexed: 12/15/2022] Open
Abstract
We show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n = 1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet, which we confirm with untargeted metabolomics on hundreds of samples. Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the United States, United Kingdom, and Australia to one another and to environmental samples. Our results show an unexpected range of beta-diversity in human stool microbiomes compared to environmental samples; demonstrate the utility of procedures for removing the effects of overgrowth during room-temperature shipping for revealing phenotype correlations; uncover new molecules and kinds of molecular communities in the human stool metabolome; and examine emergent associations among the microbiome, metabolome, and the diversity of plants that are consumed (rather than relying on reductive categorical variables such as veganism, which have little or no explanatory power). We also demonstrate the utility of the living data resource and cross-cohort comparison to confirm existing associations between the microbiome and psychiatric illness and to reveal the extent of microbiome change within one individual during surgery, providing a paradigm for open microbiome research and education. IMPORTANCE We show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n = 1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet, which we confirm with untargeted metabolomics on hundreds of samples.
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73
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Delgado-Baquerizo M, Reith F, Dennis PG, Hamonts K, Powell JR, Young A, Singh BK, Bissett A. Ecological drivers of soil microbial diversity and soil biological networks in the Southern Hemisphere. Ecology 2018; 99:583-596. [PMID: 29315530 DOI: 10.1002/ecy.2137] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/08/2017] [Accepted: 12/18/2017] [Indexed: 01/07/2023]
Abstract
The ecological drivers of soil biodiversity in the Southern Hemisphere remain underexplored. Here, in a continental survey comprising 647 sites, across 58 degrees of latitude between tropical Australia and Antarctica, we evaluated the major ecological patterns in soil biodiversity and relative abundance of ecological clusters within a co-occurrence network of soil bacteria, archaea and eukaryotes. Six major ecological clusters (modules) of co-occurring soil taxa were identified. These clusters exhibited strong shifts in their relative abundances with increasing distance from the equator. Temperature was the major environmental driver of the relative abundance of ecological clusters when Australia and Antarctica are analyzed together. Temperature, aridity, soil properties and vegetation types were the major drivers of the relative abundance of different ecological clusters within Australia. Our data supports significant reductions in the diversity of bacteria, archaea and eukaryotes in Antarctica vs. Australia linked to strong reductions in temperature. However, we only detected small latitudinal variations in soil biodiversity within Australia. Different environmental drivers regulate the diversity of soil archaea (temperature and soil carbon), bacteria (aridity, vegetation attributes and pH) and eukaryotes (vegetation type and soil carbon) across Australia. Together, our findings provide new insights into the mechanisms driving soil biodiversity in the Southern Hemisphere.
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Affiliation(s)
- Manuel Delgado-Baquerizo
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia.,Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, 80309, USA.,Departamento de Biología, Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, c/ Tulipán s/n, Móstoles, 28933, Spain
| | - Frank Reith
- Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia.,Land and Water, Environmental Contaminant Mitigation and Technologies, PMB2, Glen Osmond, South Australia, 5064, Australia
| | - Paul G Dennis
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Kelly Hamonts
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Andrew Young
- National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, 2601, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia.,Global Centre for Land-Based Innovation, Western Sydney University, Penrith South DC, New South Wales, 2751, Australia
| | - Andrew Bissett
- CSIRO, Oceans and Atmosphere, Hobart, Tasmania, 7000, Australia
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74
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Abundance and community composition of bacterioplankton in the Northern South China Sea during winter: geographic position and water layer influences. Biologia (Bratisl) 2018. [DOI: 10.2478/s11756-018-0023-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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75
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Milan M, Carraro L, Fariselli P, Martino ME, Cavalieri D, Vitali F, Boffo L, Patarnello T, Bargelloni L, Cardazzo B. Microbiota and environmental stress: how pollution affects microbial communities in Manila clams. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 194:195-207. [PMID: 29202271 DOI: 10.1016/j.aquatox.2017.11.019] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/13/2017] [Accepted: 11/26/2017] [Indexed: 06/07/2023]
Abstract
Given the crucial role of microbiota in host development, health, and environmental interactions, genomic analyses focusing on host-microbiota interactions should certainly be considered in the investigation of the adaptive mechanisms to environmental stress. Recently, several studies suggested that microbiota associated to digestive tract is a key, although still not fully understood, player that must be considered to assess the toxicity of environmental contaminants. Bacteria-dependent metabolism of xenobiotics may indeed modulate the host toxicity. Conversely, environmental variables (including pollution) may alter the microbial community and/or its metabolic activity leading to host physiological alterations that may contribute to their toxicity. Here, 16s rRNA gene amplicon sequencing has been applied to characterize the hepatopancreas microbiota composition of the Manila clam, Ruditapes philippinarum. The animals were collected in the Venice lagoon area, which is subject to different anthropogenic pressures, mainly represented by the industrial activities of Porto Marghera (PM). Seasonal and geographic differences in clam microbiotas were explored and linked to host response to chemical stress identified in a previous study at the transcriptome level, establishing potential interactions among hosts, microbes, and environmental parameters. The obtained results showed the recurrent presence of putatively detoxifying bacterial taxa in PM clams during winter and over-representation of several metabolic pathways involved in xenobiotic degradation, which suggested the potential for host-microbial synergistic detoxifying actions. Strong interaction between seasonal and chemically-induced responses was also observed, which partially obscured such potentially synergistic actions. Seasonal variables and exposure to toxicants were therefore shown to interact and substantially affect clam microbiota, which appeared to mirror host response to environmental variation. It is clear that understanding how animals respond to chemical stress cannot ignore a key component of such response, the microbiota.
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Affiliation(s)
- M Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, Italy; CONISMA - Consorzio Nazionale Interuniversitario per le Scienze del Mare, Roma, Italy
| | - L Carraro
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, Italy
| | - P Fariselli
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, Italy
| | - M E Martino
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon, Lyon, France
| | - D Cavalieri
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Firenze, Italy
| | - F Vitali
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Firenze, Italy
| | - L Boffo
- Associazione "Vongola Verace di Chioggia", Italy
| | - T Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, Italy
| | - L Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, Italy; CONISMA - Consorzio Nazionale Interuniversitario per le Scienze del Mare, Roma, Italy
| | - B Cardazzo
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro, Italy
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76
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Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R. A communal catalogue reveals Earth's multiscale microbial diversity. Nature 2017; 551:457-463. [PMID: 29088705 PMCID: PMC6192678 DOI: 10.1038/nature24621] [Citation(s) in RCA: 1293] [Impact Index Per Article: 184.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 10/10/2017] [Indexed: 02/07/2023]
Abstract
Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.
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Affiliation(s)
- Luke R Thompson
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, Mississippi, USA.,Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, California, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Amnon Amir
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Joshua Ladau
- The Gladstone Institutes and University of California San Francisco, San Francisco, California, USA
| | - Kenneth J Locey
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Robert J Prill
- Industrial and Applied Genomics, IBM Almaden Research Center, San Jose, California, USA
| | - Anupriya Tripathi
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Division of Biological Sciences, University of California San Diego, La Jolla, California, USA.,Skaggs School of Pharmacy, University of California San Diego, La Jolla, California, USA
| | - Sean M Gibbons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Jose A Navas-Molina
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Evguenia Kopylova
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Yoshiki Vázquez-Baeza
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Antonio González
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - James T Morton
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, California, USA
| | - Zhenjiang Zech Xu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Lingjing Jiang
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Family Medicine and Public Health, University of California San Diego, La Jolla, California, USA
| | - Mohamed F Haroon
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Jad Kanbar
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Nicholas A Bokulich
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Joshua Lefler
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Gregory Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Sarah M Owens
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Jarrad Hampton-Marcell
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Donna Berg-Lyons
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, USA
| | - Valerie McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA.,Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Aaron Clauset
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, USA.,Department of Computer Science, University of Colorado, Boulder, Colorado, USA
| | - Rick L Stevens
- Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Computer Science, University of Chicago, Chicago, Illinois, USA
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA.,Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA.,Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan, USA
| | - Katherine S Pollard
- The Gladstone Institutes and University of California San Francisco, San Francisco, California, USA
| | - Kelly D Goodwin
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, California, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jack A Gilbert
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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77
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Peay KG, von Sperber C, Cardarelli E, Toju H, Francis CA, Chadwick OA, Vitousek PM. Convergence and contrast in the community structure of Bacteria, Fungi and Archaea along a tropical elevation-climate gradient. FEMS Microbiol Ecol 2017; 93:3586621. [PMID: 28402397 DOI: 10.1093/femsec/fix045] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 04/05/2017] [Indexed: 11/13/2022] Open
Abstract
Changes in species richness along climatological gradients have been instrumental in developing theories about the general drivers of biodiversity. Previous studies on microbial communities along climate gradients on mountainsides have revealed positive, negative and neutral richness trends. We examined changes in richness and composition of Fungi, Bacteria and Archaea in soil along a 50-1000 m elevation, 280-3280 mm/yr precipitation gradient in Hawai'i. Soil properties and their drivers are exceptionally well understood along this gradient. All three microbial groups responded strongly to the gradient, with community ordinations being similar along axes of environmental conditions (pH, rainfall) and resource availability (nitrogen, phosphorus). However, the form of the richness-climate relationship varied between Fungi (positive linear), Bacteria (unimodal) and Archaea (negative linear). These differences were related to resource-ecology and limiting conditions for each group, with fungal richness increasing most strongly with soil carbon, ammonia-oxidizing Archaea increasing with nitrogen mineralization rate, and Bacteria increasing with both carbon and pH. Reponses to the gradient became increasingly variable at finer taxonomic scales and within any taxonomic group most individual OTUs occurred in narrow climate-elevation ranges. These results show that microbial responses to climate gradients are heterogeneous due to complexity of underlying environmental changes and the diverse ecologies of microbial taxa.
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Affiliation(s)
- Kabir G Peay
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Emily Cardarelli
- Department of Earth System Science, Stanford University, Stanford, CA 94305, USA
| | - Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | | | - Oliver A Chadwick
- Geography Department, University of California, Santa Barbara CA 93106, USA
| | - Peter M Vitousek
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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78
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Corinaldesi C, Tangherlini M, Dell'Anno A. From virus isolation to metagenome generation for investigating viral diversity in deep-sea sediments. Sci Rep 2017; 7:8355. [PMID: 28827715 PMCID: PMC5566222 DOI: 10.1038/s41598-017-08783-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 07/13/2017] [Indexed: 11/09/2022] Open
Abstract
Viruses are the most abundant and, likely, one of the most diverse biological components in the oceans. By infecting their hosts, they play key roles in biogeochemical cycles and ecosystem functioning at a global scale. The ocean interior hosts most of the microbial life, and, despite deep-sea sediments represent the main repository of this component and the largest biome on Earth, viral diversity in these ecosystems remains almost completely unknown. We compared a physical-chemical procedure and a previously published sediment washing-based procedure for isolating viruses from benthic deep-sea ecosystems to generate viromes through high-throughput sequencing. The procedure based on a physical-chemical dislodgment of viral particles from the sediments, followed by vacuum filtration was much more efficient allowing us to recover >85% of the extractable viruses. By using this procedure, a high fraction of viral DNA was recovered and new viromes from different benthic deep-sea sites were generated. Such viromes were diversified in terms of both viral families and putative functions. Overall, the results presented here provide new insights for evaluating benthic deep-sea viral diversity through metagenomic analyses, and reveal that deep-sea sediments are a hot spot of novel viral genotypes and functions.
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Affiliation(s)
- Cinzia Corinaldesi
- Department of Sciences and Engineering of Materials, Environment and Urbanistics, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| | - Michael Tangherlini
- Department of Environmental and Life Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Antonio Dell'Anno
- Department of Environmental and Life Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
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79
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Lear G, Lau K, Perchec AM, Buckley HL, Case BS, Neale M, Fierer N, Leff JW, Handley KM, Lewis G. Following Rapoport's Rule: the geographic range and genome size of bacterial taxa decline at warmer latitudes. Environ Microbiol 2017; 19:3152-3162. [PMID: 28504344 DOI: 10.1111/1462-2920.13797] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 10/11/2016] [Accepted: 05/09/2017] [Indexed: 11/28/2022]
Abstract
We sought to test whether stream bacterial communities conform to Rapoport's Rule, a pattern commonly observed for plants and animals whereby taxa exhibit decreased latitudinal range sizes closer to the equator. Using a DNA sequencing approach, we explored the biogeography of biofilm bacterial communities in 204 streams across a ∼1000 km latitudinal gradient. The range sizes of bacterial taxa were strongly correlated with latitude, decreasing closer to the equator, which coincided with a greater than fivefold increase in bacterial taxonomic richness. The relative richness and range size of bacteria were associated with spatially correlated variation in temperature and rainfall. These patterns were observed despite enormous variability in catchment environmental characteristics. Similar results were obtained when restricting the same analyses to native forest catchments, thereby controlling for spatial biases in land use. We analysed genomic data from ∼500 taxa detected in this study, for which data were available and found that bacterial communities at cooler latitudes also tended to possess greater potential metabolic potential. Collectively, these data provide the first evidence of latitudinal variation in the range size distributions of freshwater bacteria, a trend which may be determined, in part, by a trade-off between bacterial genome size and local variation in climatic conditions.
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Affiliation(s)
- Gavin Lear
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Kelvin Lau
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Anne-Marie Perchec
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Hannah L Buckley
- School of Science, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Bradley S Case
- School of Science, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | | | - Noah Fierer
- Department of Ecology and Evolutionary Biology and Cooperative Institute for Research in Environmental Biology, University of Colorado at Boulder, Boulder, CO 80309-0216, USA
| | - Jonathan W Leff
- Department of Ecology and Evolutionary Biology and Cooperative Institute for Research in Environmental Biology, University of Colorado at Boulder, Boulder, CO 80309-0216, USA
| | - Kim M Handley
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Gillian Lewis
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
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80
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Marine Bacterioplankton Seasonal Succession Dynamics. Trends Microbiol 2017; 25:494-505. [DOI: 10.1016/j.tim.2016.12.013] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/13/2016] [Accepted: 12/21/2016] [Indexed: 01/08/2023]
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81
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Affiliation(s)
| | - Thomas Wickman
- History Department, Program in American Studies, Trinity College, Hartford, CT 06106;
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82
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Djurhuus A, Boersch-Supan PH, Mikalsen SO, Rogers AD. Microbe biogeography tracks water masses in a dynamic oceanic frontal system. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170033. [PMID: 28405400 PMCID: PMC5383857 DOI: 10.1098/rsos.170033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 02/14/2017] [Indexed: 05/11/2023]
Abstract
Dispersal limitation, not just environmental selection, plays an important role in microbial biogeography. The distance-decay relationship is thought to be weak in habitats where dispersal is high, such as in the pelagic environment, where ocean currents facilitate microbial dispersal. Most studies of microbial community composition to date have observed little geographical heterogeneity on a regional scale (100 km). We present a study of microbial communities across a dynamic frontal zone in the southwest Indian Ocean and investigate the spatial structure of the microbes with respect to the different water masses separated by these fronts. We collected 153 samples of free-living microorganisms from five seamounts located along a gradient from subtropical to subantarctic waters and across three depth layers: (i) the sub-surface chlorophyll maximum (approx. 40 m), (ii) the bottom of the euphotic zone (approx. 200 m), and (iii) the benthic boundary layer (300-2000 m). Diversity and abundance of microbial operational taxonomic units (OTUs) were assessed by amplification and sequencing of the 16S rRNA gene on an Illumina MiSeq platform. Multivariate analyses showed that microbial communities were structured more strongly by depth than by latitude, with similar phyla occurring within each depth stratum across seamounts. The deep layer was homogeneous across the entire survey area, corresponding to the spread of Antarctic intermediate water. However, within both the sub-surface layer and the intermediate depth stratum there was evidence for OTU turnover across fronts. The microbiome of these layers appears to be divided into three distinct biological regimes corresponding to the subantarctic surface water, the convergence zone and subtropical. We show that microbial biogeography across depth and latitudinal gradients is linked to the water masses the microbes persist in, resulting in regional patterns of microbial biogeography that correspond to the regional scale physical oceanography.
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Affiliation(s)
- Anni Djurhuus
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
- College of Marine Science, University of South Florida, 830 1st St SE, St Petersburg, FL 33701, USA
- Author for correspondence: Anni Djurhuus e-mail:
| | - Philipp H. Boersch-Supan
- Department of Integrative Biology, University of South Florida, 4202 E Fowler Avenue, Tampa, FL 33620, USA
- Department of Geography, University of Florida, Gainesville, FL 32611, USA
| | - Svein-Ole Mikalsen
- Department of Science and Technology, University of the Faroe Islands, Noatun 3, Torshavn, Faroe Islands
| | - Alex D. Rogers
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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83
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Annual community patterns are driven by seasonal switching between closely related marine bacteria. ISME JOURNAL 2017; 11:1412-1422. [PMID: 28234350 DOI: 10.1038/ismej.2017.4] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 12/07/2016] [Accepted: 12/23/2016] [Indexed: 01/16/2023]
Abstract
Marine microbes exhibit seasonal cycles in community composition, yet the key drivers of these patterns and microbial population fidelity to specific environmental conditions remain to be determined. To begin addressing these questions, we characterized microbial dynamics weekly for 3 years at a temperate, coastal site with dramatic environmental seasonality. This high-resolution time series reveals that changes in microbial community composition are not continuous; over the duration of the time series, the community instead resolves into distinct summer and winter profiles with rapid spring and fall transitions between these states. Here, we show that these community shifts involve switching between closely related strains that exhibit either summer or winter preferences. Moreover, taxa repeat this process annually in both this and another temperate coastal time series, suggesting that this phenomenon may be widespread in marine ecosystems. To address potential biogeochemical impacts of these community changes, PICRUSt-based metagenomes predict seasonality in transporters, photosynthetic proteins, peptidases and carbohydrate metabolic pathways in spite of closely related summer- and winter-associated taxa. Thus, even small temperature shifts, such as those predicted by climate change models, could affect both the structure and function of marine ecosystems.
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84
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Nayfach S, Pollard KS. Toward Accurate and Quantitative Comparative Metagenomics. Cell 2016; 166:1103-1116. [PMID: 27565341 DOI: 10.1016/j.cell.2016.08.007] [Citation(s) in RCA: 167] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 04/11/2016] [Accepted: 08/03/2016] [Indexed: 01/08/2023]
Abstract
Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized.
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Affiliation(s)
- Stephen Nayfach
- Integrative Program in Quantitative Biology, University of California, San Francisco, CA 94158, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA 94158, USA; Division of Biostatistics, Institute for Human Genetics, and Institute for Computational Health Sciences, University of California, San Francisco, CA 94158, USA.
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85
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Herlemann DPR, Lundin D, Andersson AF, Labrenz M, Jürgens K. Phylogenetic Signals of Salinity and Season in Bacterial Community Composition Across the Salinity Gradient of the Baltic Sea. Front Microbiol 2016; 7:1883. [PMID: 27933046 PMCID: PMC5121245 DOI: 10.3389/fmicb.2016.01883] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/09/2016] [Indexed: 11/22/2022] Open
Abstract
Understanding the key processes that control bacterial community composition has enabled predictions of bacterial distribution and function within ecosystems. In this study, we used the Baltic Sea as a model system to quantify the phylogenetic signal of salinity and season with respect to bacterioplankton community composition. The abundances of 16S rRNA gene amplicon sequencing reads were analyzed from samples obtained from similar geographic locations in July and February along a brackish to marine salinity gradient in the Baltic Sea. While there was no distinct pattern of bacterial richness at different salinities, the number of bacterial phylotypes in winter was significantly higher than in summer. Bacterial community composition in brackish vs. marine conditions, and in July vs. February was significantly different. Non-metric multidimensional scaling showed that bacterial community composition was primarily separated according to salinity and secondly according to seasonal differences at all taxonomic ranks tested. Similarly, quantitative phylogenetic clustering implicated a phylogenetic signal for both salinity and seasonality. Our results suggest that global patterns of bacterial community composition with respect to salinity and season are the result of phylogenetically clustered ecological preferences with stronger imprints from salinity.
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Affiliation(s)
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus UniversityKalmar, Sweden
| | - Anders F. Andersson
- Science for Life Laboratory, Division of Gene Technology, School of Biotechnology, KTH Royal Institute of TechnologyStockholm, Sweden
| | | | - Klaus Jürgens
- Leibniz Institute for Baltic Sea ResearchWarnemünde, Germany
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86
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Luria CM, Amaral-Zettler LA, Ducklow HW, Rich JJ. Seasonal Succession of Free-Living Bacterial Communities in Coastal Waters of the Western Antarctic Peninsula. Front Microbiol 2016; 7:1731. [PMID: 27857708 PMCID: PMC5093341 DOI: 10.3389/fmicb.2016.01731] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/17/2016] [Indexed: 01/05/2023] Open
Abstract
The marine ecosystem along the Western Antarctic Peninsula undergoes a dramatic seasonal transition every spring, from almost total darkness to almost continuous sunlight, resulting in a cascade of environmental changes, including phytoplankton blooms that support a highly productive food web. Despite having important implications for the movement of energy and materials through this ecosystem, little is known about how these changes impact bacterial succession in this region. Using 16S rRNA gene amplicon sequencing, we measured changes in free-living bacterial community composition and richness during a 9-month period that spanned winter to the end of summer. Chlorophyll a concentrations were relatively low until summer when a major phytoplankton bloom occurred, followed 3 weeks later by a high peak in bacterial production. Richness in bacterial communities varied between ~1,200 and 1,800 observed operational taxonomic units (OTUs) before the major phytoplankton bloom (out of ~43,000 sequences per sample). During peak bacterial production, OTU richness decreased to ~700 OTUs. The significant decrease in OTU richness only lasted a few weeks, after which time OTU richness increased again as bacterial production declined toward pre-bloom levels. OTU richness was negatively correlated with bacterial production and chlorophyll a concentrations. Unlike the temporal pattern in OTU richness, community composition changed from winter to spring, prior to onset of the summer phytoplankton bloom. Community composition continued to change during the phytoplankton bloom, with increased relative abundance of several taxa associated with phytoplankton blooms, particularly Polaribacter. Bacterial community composition began to revert toward pre-bloom conditions as bacterial production declined. Overall, our findings clearly demonstrate the temporal relationship between phytoplankton blooms and seasonal succession in bacterial growth and community composition. Our study highlights the importance of high-resolution time series sampling, especially during the relatively under-sampled Antarctic winter and spring, which enabled us to discover seasonal changes in bacterial community composition that preceded the summertime phytoplankton bloom.
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Affiliation(s)
- Catherine M Luria
- Department of Ecology and Evolutionary Biology, Brown University, Providence RI, USA
| | - Linda A Amaral-Zettler
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods HoleMA, USA; Department of Earth, Environmental and Planetary Sciences, Brown University, ProvidenceRI, USA
| | - Hugh W Ducklow
- Department of Earth and Environmental Sciences, Lamont-Doherty Earth Observatory of Columbia University, Palisades NY, USA
| | - Jeremy J Rich
- School of Marine Sciences and Darling Marine Center, University of Maine, Walpole ME, USA
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87
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Nayfach S, Rodriguez-Mueller B, Garud N, Pollard KS. An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. Genome Res 2016; 26:1612-1625. [PMID: 27803195 PMCID: PMC5088602 DOI: 10.1101/gr.201863.115] [Citation(s) in RCA: 285] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 09/08/2016] [Indexed: 01/19/2023]
Abstract
We present the Metagenomic Intra-species Diversity Analysis System (MIDAS), which is an integrated computational pipeline for quantifying bacterial species abundance and strain-level genomic variation, including gene content and single-nucleotide polymorphisms (SNPs), from shotgun metagenomes. Our method leverages a database of more than 30,000 bacterial reference genomes that we clustered into species groups. These cover the majority of abundant species in the human microbiome but only a small proportion of microbes in other environments, including soil and seawater. We applied MIDAS to stool metagenomes from 98 Swedish mothers and their infants over one year and used rare SNPs to track strains between hosts. Using this approach, we found that although species compositions of mothers and infants converged over time, strain-level similarity diverged. Specifically, early colonizing bacteria were often transmitted from an infant’s mother, while late colonizing bacteria were often transmitted from other sources in the environment and were enriched for spore-formation genes. We also applied MIDAS to 198 globally distributed marine metagenomes and used gene content to show that many prevalent bacterial species have population structure that correlates with geographic location. Strain-level genetic variants present in metagenomes clearly reveal extensive structure and dynamics that are obscured when data are analyzed at a coarser taxonomic resolution.
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Affiliation(s)
- Stephen Nayfach
- Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, California 94158, USA.,Gladstone Institutes, San Francisco, California 94158, USA
| | | | - Nandita Garud
- Gladstone Institutes, San Francisco, California 94158, USA
| | - Katherine S Pollard
- Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, California 94158, USA.,Gladstone Institutes, San Francisco, California 94158, USA.,Institute for Human Genetics, Institute for Computational Health Sciences, and Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California 94158, USA
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88
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The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates. Sci Rep 2016; 6:33555. [PMID: 27633177 PMCID: PMC5025661 DOI: 10.1038/srep33555] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/25/2016] [Indexed: 11/09/2022] Open
Abstract
Illumina reads of the SSU-rDNA-V9 region obtained from the circumglobal Tara Oceans expedition allow the investigation of protistan plankton diversity patterns on a global scale. We analyzed 6,137,350 V9-amplicons from ocean surface waters and the deep chlorophyll maximum, which were taxonomically assigned to the phylum Ciliophora. For open ocean samples global planktonic ciliate diversity is relatively low (ca. 1,300 observed and predicted ciliate OTUs). We found that 17% of all detected ciliate OTUs occurred in all oceanic regions under study. On average, local ciliate OTU richness represented 27% of the global ciliate OTU richness, indicating that a large proportion of ciliates is widely distributed. Yet, more than half of these OTUs shared <90% sequence similarity with reference sequences of described ciliates. While alpha-diversity measures (richness and exp(Shannon H)) are hardly affected by contemporary environmental conditions, species (OTU) turnover and community similarity (β-diversity) across taxonomic groups showed strong correlation to environmental parameters. Logistic regression models predicted significant correlations between the occurrence of specific ciliate genera and individual nutrients, the oceanic carbonate system and temperature. Planktonic ciliates displayed distinct vertical distributions relative to chlorophyll a. In contrast, the Tara Oceans dataset did not reveal any evidence that latitude is structuring ciliate communities.
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89
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Louca S, Parfrey LW, Doebeli M. Decoupling function and taxonomy in the global ocean microbiome. Science 2016; 353:1272-7. [DOI: 10.1126/science.aaf4507] [Citation(s) in RCA: 1097] [Impact Index Per Article: 137.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 08/23/2016] [Indexed: 12/30/2022]
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90
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Kuang J, Huang L, He Z, Chen L, Hua Z, Jia P, Li S, Liu J, Li J, Zhou J, Shu W. Predicting taxonomic and functional structure of microbial communities in acid mine drainage. THE ISME JOURNAL 2016; 10:1527-39. [PMID: 26943622 PMCID: PMC5029178 DOI: 10.1038/ismej.2015.201] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 09/27/2015] [Accepted: 10/02/2015] [Indexed: 01/20/2023]
Abstract
Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray-Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural acidophilic microbial communities.
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Affiliation(s)
- Jialiang Kuang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Linan Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Zhili He
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Linxing Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Zhengshuang Hua
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Pu Jia
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Shengjin Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jun Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jintian Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, People's Republic of China
| | - Wensheng Shu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China
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91
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Bryant JA, Aylward FO, Eppley JM, Karl DM, Church MJ, DeLong EF. Wind and sunlight shape microbial diversity in surface waters of the North Pacific Subtropical Gyre. THE ISME JOURNAL 2016; 10:1308-22. [PMID: 26645474 PMCID: PMC5029195 DOI: 10.1038/ismej.2015.221] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 10/07/2015] [Accepted: 10/25/2015] [Indexed: 11/09/2022]
Abstract
Few microbial time-series studies have been conducted in open ocean habitats having low seasonal variability such as the North Pacific Subtropical Gyre (NPSG), where surface waters experience comparatively mild seasonal variation. To better describe microbial seasonal variability in this habitat, we analyzed rRNA amplicon and shotgun metagenomic data over two years at the Hawaii Ocean Time-series Station ALOHA. We postulated that this relatively stable habitat might reveal different environmental factors that influence planktonic microbial community diversity than those previously observed in more seasonally dynamic habitats. Unexpectedly, the data showed that microbial diversity at 25 m was positively correlated with average wind speed 3 to 10 days prior to sampling. In addition, microbial community composition at 25 m exhibited significant correlations with solar irradiance. Many bacterial groups whose relative abundances varied with solar radiation corresponded to taxa known to exhibit strong seasonality in other oceanic regions. Network co-correlation analysis of 25 m communities showed seasonal transitions in composition, and distinct successional cohorts of co-occurring phylogenetic groups. Similar network analyses of metagenomic data also indicated distinct seasonality in genes originating from cyanophage, and several bacterial clades including SAR116 and SAR324. At 500 m, microbial community diversity and composition did not vary significantly with any measured environmental parameters. The minimal seasonal variability in the NPSG facilitated detection of more subtle environmental influences, such as episodic wind variation, on surface water microbial diversity. Community composition in NPSG surface waters varied in response to solar irradiance, but less dramatically than reported in other ocean provinces.
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Affiliation(s)
- Jessica A Bryant
- Department of Civil and Environmental Engineering Massachusetts Institute of Technology, Cambridge, MA, USA
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, University of Hawaii, Manoa, Honolulu, HI, USA
| | - Frank O Aylward
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, University of Hawaii, Manoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawaii, Manoa, University of Hawaii, Honolulu, HI, USA
| | - John M Eppley
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, University of Hawaii, Manoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawaii, Manoa, University of Hawaii, Honolulu, HI, USA
| | - David M Karl
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, University of Hawaii, Manoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawaii, Manoa, University of Hawaii, Honolulu, HI, USA
| | - Matthew J Church
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, University of Hawaii, Manoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawaii, Manoa, University of Hawaii, Honolulu, HI, USA
| | - Edward F DeLong
- Department of Civil and Environmental Engineering Massachusetts Institute of Technology, Cambridge, MA, USA
- Daniel K. Inouye Center for Microbial Oceanography, Research and Education, University of Hawaii, Manoa, Honolulu, HI, USA
- Department of Oceanography, University of Hawaii, Manoa, University of Hawaii, Honolulu, HI, USA
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92
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Tu Q, Deng Y, Yan Q, Shen L, Lin L, He Z, Wu L, Van Nostrand JD, Buzzard V, Michaletz ST, Enquist BJ, Weiser MD, Kaspari M, Waide RB, Brown JH, Zhou J. Biogeographic patterns of soil diazotrophic communities across six forests in North America. Mol Ecol 2016; 25:2937-48. [PMID: 27085668 DOI: 10.1111/mec.13651] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/23/2016] [Accepted: 04/12/2016] [Indexed: 11/29/2022]
Abstract
Soil diazotrophs play important roles in ecosystem functioning by converting atmospheric N2 into biologically available ammonium. However, the diversity and distribution of soil diazotrophic communities in different forests and whether they follow biogeographic patterns similar to macroorganisms still remain unclear. By sequencing nifH gene amplicons, we surveyed the diversity, structure and biogeographic patterns of soil diazotrophic communities across six North American forests (126 nested samples). Our results showed that each forest harboured markedly different soil diazotrophic communities and that these communities followed traditional biogeographic patterns similar to plant and animal communities, including the taxa-area relationship (TAR) and latitudinal diversity gradient. Significantly higher community diversity and lower microbial spatial turnover rates (i.e. z-values) were found for rainforests (~0.06) than temperate forests (~0.1). The gradient pattern of TARs and community diversity was strongly correlated (r(2) > 0.5) with latitude, annual mean temperature, plant species richness and precipitation, and weakly correlated (r(2) < 0.25) with pH and soil moisture. This study suggests that even microbial subcommunities (e.g. soil diazotrophs) follow general biogeographic patterns (e.g. TAR, latitudinal diversity gradient), and indicates that the metabolic theory of ecology and habitat heterogeneity may be the major underlying ecological mechanisms shaping the biogeographic patterns of soil diazotrophic communities.
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Affiliation(s)
- Qichao Tu
- Department of Marine Sciences, Ocean College, Zhejiang University, Zhejiang, 310058, China.,Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Ye Deng
- Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing, 100085, China
| | - Qingyun Yan
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Lina Shen
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Lu Lin
- Department of Marine Sciences, Ocean College, Zhejiang University, Zhejiang, 310058, China
| | - Zhili He
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Liyou Wu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Joy D Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Vanessa Buzzard
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Sean T Michaletz
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA.,Earth and Environmental Sciences Division, Los Alamos National Laboratory, MS J495, Los Alamos, NM 87545, USA
| | - Brian J Enquist
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA.,The Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM, 87501, USA
| | - Michael D Weiser
- Department of Biology, EEB Graduate Program, University of Oklahoma, Norman, OK, 73019, USA
| | - Michael Kaspari
- Department of Biology, EEB Graduate Program, University of Oklahoma, Norman, OK, 73019, USA.,Smithsonian Tropical Research Institute, Balboa, 0843-03092, Republic of Panama
| | - Robert B Waide
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - James H Brown
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.,Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94270, USA
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93
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Huang LN, Kuang JL, Shu WS. Microbial Ecology and Evolution in the Acid Mine Drainage Model System. Trends Microbiol 2016; 24:581-593. [PMID: 27050827 DOI: 10.1016/j.tim.2016.03.004] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/19/2016] [Accepted: 03/08/2016] [Indexed: 10/22/2022]
Abstract
Acid mine drainage (AMD) is a unique ecological niche for acid- and toxic-metals-adapted microorganisms. These low-complexity systems offer a special opportunity for the ecological and evolutionary analyses of natural microbial assemblages. The last decade has witnessed an unprecedented interest in the study of AMD communities using 16S rRNA high-throughput sequencing and community genomic and postgenomic methodologies, significantly advancing our understanding of microbial diversity, community function, and evolution in acidic environments. This review describes new data on AMD microbial ecology and evolution, especially dynamics of microbial diversity, community functions, and population genomes, and further identifies gaps in our current knowledge that future research, with integrated applications of meta-omics technologies, will fill.
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Affiliation(s)
- Li-Nan Huang
- College of Ecology and Evolution, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jia-Liang Kuang
- College of Ecology and Evolution, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Wen-Sheng Shu
- College of Ecology and Evolution, Sun Yat-sen University, Guangzhou 510275, PR China.
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94
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Bienhold C, Zinger L, Boetius A, Ramette A. Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria. PLoS One 2016; 11:e0148016. [PMID: 26814838 PMCID: PMC4731391 DOI: 10.1371/journal.pone.0148016] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 01/12/2016] [Indexed: 11/19/2022] Open
Abstract
The deep ocean floor covers more than 60% of the Earth's surface, and hosts diverse bacterial communities with important functions in carbon and nutrient cycles. The identification of key bacterial members remains a challenge and their patterns of distribution in seafloor sediment yet remain poorly described. Previous studies were either regionally restricted or included few deep-sea sediments, and did not specifically test biogeographic patterns across the vast oligotrophic bathyal and abyssal seafloor. Here we define the composition of this deep seafloor microbiome by describing those bacterial operational taxonomic units (OTU) that are specifically associated with deep-sea surface sediments at water depths ranging from 1000-5300 m. We show that the microbiome of the surface seafloor is distinct from the subsurface seafloor. The cosmopolitan bacterial OTU were affiliated with the clades JTB255 (class Gammaproteobacteria, order Xanthomonadales) and OM1 (Actinobacteria, order Acidimicrobiales), comprising 21% and 7% of their respective clades, and about 1% of all sequences in the study. Overall, few sequence-abundant bacterial types were globally dispersed and displayed positive range-abundance relationships. Most bacterial populations were rare and exhibited a high degree of endemism, explaining the substantial differences in community composition observed over large spatial scales. Despite the relative physicochemical uniformity of deep-sea sediments, we identified indicators of productivity regimes, especially sediment organic matter content, as factors significantly associated with changes in bacterial community structure across the globe.
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Affiliation(s)
- Christina Bienhold
- HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany, and Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Lucie Zinger
- HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany, and Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Antje Boetius
- HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany, and Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Alban Ramette
- HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany, and Max Planck Institute for Marine Microbiology, Bremen, Germany
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95
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Biteen JS, Blainey PC, Cardon ZG, Chun M, Church GM, Dorrestein PC, Fraser SE, Gilbert JA, Jansson JK, Knight R, Miller JF, Ozcan A, Prather KA, Quake SR, Ruby EG, Silver PA, Taha S, van den Engh G, Weiss PS, Wong GCL, Wright AT, Young TD. Tools for the Microbiome: Nano and Beyond. ACS NANO 2016; 10:6-37. [PMID: 26695070 DOI: 10.1021/acsnano.5b07826] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The microbiome presents great opportunities for understanding and improving the world around us and elucidating the interactions that compose it. The microbiome also poses tremendous challenges for mapping and manipulating the entangled networks of interactions among myriad diverse organisms. Here, we describe the opportunities, technical needs, and potential approaches to address these challenges, based on recent and upcoming advances in measurement and control at the nanoscale and beyond. These technical needs will provide the basis for advancing the largely descriptive studies of the microbiome to the theoretical and mechanistic understandings that will underpin the discipline of microbiome engineering. We anticipate that the new tools and methods developed will also be more broadly useful in environmental monitoring, medicine, forensics, and other areas.
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Affiliation(s)
- Julie S Biteen
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Paul C Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology , and Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02138, United States
| | - Zoe G Cardon
- The Ecosystems Center, Marine Biological Laboratory , Woods Hole, Massachusetts 02543-1015, United States
| | - Miyoung Chun
- The Kavli Foundation , Oxnard, California 93030, United States
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering and Biophysics Program, Harvard University , Boston, Massachusetts 02115, United States
| | | | - Scott E Fraser
- Translational Imaging Center, University of Southern California , Molecular and Computational Biology, Los Angeles, California 90089, United States
| | - Jack A Gilbert
- Institute for Genomic and Systems Biology, Argonne National Laboratory , Argonne, Illinois 60439, United States
- Department of Ecology and Evolution and Department of Surgery, University of Chicago , Chicago, Illinois 60637, United States
| | - Janet K Jansson
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | | | | | | | | | | | - Edward G Ruby
- Kewalo Marine Laboratory, University of Hawaii-Manoa , Honolulu, Hawaii 96813, United States
| | - Pamela A Silver
- Wyss Institute for Biologically Inspired Engineering and Biophysics Program, Harvard University , Boston, Massachusetts 02115, United States
| | - Sharif Taha
- The Kavli Foundation , Oxnard, California 93030, United States
| | - Ger van den Engh
- Center for Marine Cytometry , Concrete, Washington 98237, United States
- Instituto Milenio de Oceanografía, Universidad de Concepción , Concepción, Chile
| | | | | | - Aaron T Wright
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
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96
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Larkin AA, Blinebry SK, Howes C, Lin Y, Loftus SE, Schmaus CA, Zinser ER, Johnson ZI. Niche partitioning and biogeography of high light adapted Prochlorococcus across taxonomic ranks in the North Pacific. ISME JOURNAL 2016; 10:1555-67. [PMID: 26800235 DOI: 10.1038/ismej.2015.244] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 10/30/2015] [Accepted: 11/18/2015] [Indexed: 02/08/2023]
Abstract
The distribution of major clades of Prochlorococcus tracks light, temperature and other environmental variables; yet, the drivers of genomic diversity within these ecotypes and the net effect on biodiversity of the larger community are poorly understood. We examined high light (HL) adapted Prochlorococcus communities across spatial and temporal environmental gradients in the Pacific Ocean to determine the ecological drivers of population structure and diversity across taxonomic ranks. We show that the Prochlorococcus community has the highest diversity at low latitudes, but seasonality driven by temperature, day length and nutrients adds complexity. At finer taxonomic resolution, some 'sub-ecotype' clades have unique, cohesive responses to environmental variables and distinct biogeographies, suggesting that presently defined ecotypes can be further partitioned into ecologically meaningful units. Intriguingly, biogeographies of the HL-I sub-ecotypes are driven by unique combinations of environmental traits, rather than through trait hierarchy, while the HL-II sub-ecotypes appear ecologically similar, thus demonstrating differences among these dominant HL ecotypes. Examining biodiversity across taxonomic ranks reveals high-resolution dynamics of Prochlorococcus evolution and ecology that are masked at phylogenetically coarse resolution. Spatial and seasonal trends of Prochlorococcus communities suggest that the future ocean may be comprised of different populations, with implications for ecosystem structure and function.
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Affiliation(s)
- Alyse A Larkin
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Sara K Blinebry
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Caroline Howes
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Yajuan Lin
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Sarah E Loftus
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Carrie A Schmaus
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Erik R Zinser
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Zackary I Johnson
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
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97
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Low diversity of planktonic bacteria in the tropical ocean. Sci Rep 2016; 6:19054. [PMID: 26750451 PMCID: PMC4707477 DOI: 10.1038/srep19054] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 12/01/2015] [Indexed: 01/10/2023] Open
Abstract
The diversity of macro-organisms increases towards the equator, with almost no exceptions. It is the most conserved biogeographical pattern on earth and is thought to be related to the increase of temperature and productivity in the tropics. The extent and orientation of a latitudinal gradient of marine bacterioplankton diversity is controversial. Here we studied the euphotic zone of the Atlantic Ocean based on a transect covering ~12.000 km from 51°S to 47 °N. Water samples were collected at 26 stations at five depths between 20 and 200 m and sequentially filtered through 8 μm, 3 μm and 0,22 μm filters, resulting in a total of 359 samples. Illumina sequencing of the V5–V6 region of the 16S rRNA gene revealed a clear biogeographic pattern with a double inverted latitudinal gradient. Diversity was higher in mid-latitudinal regions of the Atlantic Ocean and decreased towards the equator. This pattern was conserved for bacteria from all three planktonic size fractions. Diversity showed a non-linear relationship with temperature and was negatively correlated with bacterial cell numbers in the upper depth layers (<100 m). The latitudinal gradients of marine bacterial diversity and the mechanisms that govern them are distinct from those found in macro-organisms.
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98
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Mock T, Daines SJ, Geider R, Collins S, Metodiev M, Millar AJ, Moulton V, Lenton TM. Bridging the gap between omics and earth system science to better understand how environmental change impacts marine microbes. GLOBAL CHANGE BIOLOGY 2016; 22:61-75. [PMID: 25988950 PMCID: PMC4949645 DOI: 10.1111/gcb.12983] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/05/2015] [Accepted: 05/12/2015] [Indexed: 05/17/2023]
Abstract
The advent of genomic-, transcriptomic- and proteomic-based approaches has revolutionized our ability to describe marine microbial communities, including biogeography, metabolic potential and diversity, mechanisms of adaptation, and phylogeny and evolutionary history. New interdisciplinary approaches are needed to move from this descriptive level to improved quantitative, process-level understanding of the roles of marine microbes in biogeochemical cycles and of the impact of environmental change on the marine microbial ecosystem. Linking studies at levels from the genome to the organism, to ecological strategies and organism and ecosystem response, requires new modelling approaches. Key to this will be a fundamental shift in modelling scale that represents micro-organisms from the level of their macromolecular components. This will enable contact with omics data sets and allow acclimation and adaptive response at the phenotype level (i.e. traits) to be simulated as a combination of fitness maximization and evolutionary constraints. This way forward will build on ecological approaches that identify key organism traits and systems biology approaches that integrate traditional physiological measurements with new insights from omics. It will rely on developing an improved understanding of ecophysiology to understand quantitatively environmental controls on microbial growth strategies. It will also incorporate results from experimental evolution studies in the representation of adaptation. The resulting ecosystem-level models can then evaluate our level of understanding of controls on ecosystem structure and function, highlight major gaps in understanding and help prioritize areas for future research programs. Ultimately, this grand synthesis should improve predictive capability of the ecosystem response to multiple environmental drivers.
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Affiliation(s)
- Thomas Mock
- School of Environmental SciencesUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
| | - Stuart J. Daines
- College of Life and Environmental SciencesUniversity of ExeterEX4 4QEExeterUK
| | - Richard Geider
- School of Biological SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
| | - Sinead Collins
- Ashworth LaboratoriesEdinburgh UniversityEH9 3JFEdinburghUK
| | - Metodi Metodiev
- School of Biological SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
| | - Andrew J. Millar
- SynthSys and School of Biological SciencesEdinburgh UniversityEH9 3BFEdinburghUK
| | - Vincent Moulton
- School of Computing SciencesUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
| | - Timothy M. Lenton
- College of Life and Environmental SciencesUniversity of ExeterEX4 4QEExeterUK
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99
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Paknia O, Schierwater B. Global Habitat Suitability and Ecological Niche Separation in the Phylum Placozoa. PLoS One 2015; 10:e0140162. [PMID: 26580806 PMCID: PMC4651326 DOI: 10.1371/journal.pone.0140162] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 09/10/2015] [Indexed: 02/02/2023] Open
Abstract
The enigmatic placozoans, which hold a key position in the metazoan Tree of Life, have attracted substantial attention in many areas of biological and biomedical research. While placozoans have become an emerging model system, their ecology and particularly biogeography remain widely unknown. In this study, we use modelling approaches to explore habitat preferences, and distribution pattern of the placozoans phylum. We provide hypotheses for discrete ecological niche separation between genetic placozoan lineages, which may also help to understand biogeography patterns in other small marine invertebrates. We, here, used maximum entropy modelling to predict placozoan distribution using 20 environmental grids of 9.2 km2 resolution. In addition, we used recently developed metrics of niche overlap to compare habitat suitability models of three genetic clades. The predicted distributions range from 55°N to 44°S and are restricted to regions of intermediate to warm sea surface temperatures. High concentrations of salinity and low nutrient concentrations appear as secondary factors. Tests of niche equivalency reveal the largest differences between placozoan clades I and III. Interestingly, the genetically well-separated clades I and V appear to be ecologically very similar. Our habitat suitability models predict a wider latitudinal distribution for placozoans, than currently described, especially in the northern hemisphere. With respect to biogeography modelling, placozoans show patterns somewhere between higher metazoan taxa and marine microorganisms, with the first group usually showing complex biogeographies and the second usually showing “no biogeography.”
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Affiliation(s)
- Omid Paknia
- ITZ, Ecology and Evolution, TiHo Hannover, Hannover, Germany
- * E-mail:
| | - Bernd Schierwater
- ITZ, Ecology and Evolution, TiHo Hannover, Hannover, Germany
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
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100
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Walsh EA, Kirkpatrick JB, Rutherford SD, Smith DC, Sogin M, D'Hondt S. Bacterial diversity and community composition from seasurface to subseafloor. ISME JOURNAL 2015; 10:979-89. [PMID: 26430855 PMCID: PMC4796937 DOI: 10.1038/ismej.2015.175] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 08/10/2015] [Accepted: 08/13/2015] [Indexed: 12/20/2022]
Abstract
We investigated compositional relationships between bacterial communities in the water column and those in deep-sea sediment at three environmentally distinct Pacific sites (two in the Equatorial Pacific and one in the North Pacific Gyre). Through pyrosequencing of the v4-v6 hypervariable regions of the 16S ribosomal RNA gene, we characterized 450,104 pyrotags representing 29,814 operational taxonomic units (OTUs, 97% similarity). Hierarchical clustering and non-metric multidimensional scaling partition the samples into four broad groups, regardless of geographic location: a photic-zone community, a subphotic community, a shallow sedimentary community and a subseafloor sedimentary community (⩾1.5 meters below seafloor). Abundance-weighted community compositions of water-column samples exhibit a similar trend with depth at all sites, with successive epipelagic, mesopelagic, bathypelagic and abyssopelagic communities. Taxonomic richness is generally highest in the water-column O2 minimum zone and lowest in the subseafloor sediment. OTUs represented by abundant tags in the subseafloor sediment are often present but represented by few tags in the water column, and represented by moderately abundant tags in the shallow sediment. In contrast, OTUs represented by abundant tags in the water are generally absent from the subseafloor sediment. These results are consistent with (i) dispersal of marine sedimentary bacteria via the ocean, and (ii) selection of the subseafloor sedimentary community from within the community present in shallow sediment.
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Affiliation(s)
- Emily A Walsh
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Harvard School of Dental Medicine, Boston, MA, USA
| | - John B Kirkpatrick
- Graduate School of Oceanography, University of Rhode Island, Narragansett Bay Campus, Narragansett, RI, USA
| | - Scott D Rutherford
- Department of Environmental Sciences, Roger Williams University, Bristol, RI, USA
| | - David C Smith
- Graduate School of Oceanography, University of Rhode Island, Narragansett Bay Campus, Narragansett, RI, USA
| | - Mitchell Sogin
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Steven D'Hondt
- Graduate School of Oceanography, University of Rhode Island, Narragansett Bay Campus, Narragansett, RI, USA
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