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Stott C, Diop A, Raymann K, Bobay LM. Co-evolution and Gene Transfers Drive Speciation Patterns in Host-Associated Bacteria. Mol Biol Evol 2024; 41:msae256. [PMID: 39686544 DOI: 10.1093/molbev/msae256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 11/12/2024] [Accepted: 12/02/2024] [Indexed: 12/18/2024] Open
Abstract
Microbial communities that maintain symbiotic relationships with animals evolve by adapting to the specific environmental niche provided by their host, yet understanding their patterns of speciation remains challenging. Whether bacterial speciation occurs primarily through allopatric or sympatric processes remains an open question. In addition, patterns of DNA transfers, which are pervasive in bacteria, are more constrained in a closed host-gut system. Eusocial bees have co-evolved with their specialized microbiota for over 85 million years, constituting a simple and valuable system to study the complex dynamics of host-associated microbial interactions. Here, we studied the patterns of speciation and evolution of seven specialized gut bacteria from three clades of eusocial bee species: western honey bees, eastern honey bees, and bumblebees. We conducted genomic analyses to infer species delineation relative to the patterns of homologous recombination (HR), and horizontal gene transfer (HGT). The studied bacteria presented various modes of evolution and speciation relative to their hosts, but some trends were consistent across all of them. We observed a clear interruption of HR between bacteria inhabiting different bee hosts, which is consistent with a mechanism of allopatric speciation, but we also identified interruptions of HR within hosts, suggesting recent or ongoing sympatric speciation. In contrast to HR, we observed that HGT events were not constrained by species borders. Overall, our findings show that in host-associated bacterial populations, patterns of HR and HGT have different impacts on speciation patterns, which are driven by both allopatric and sympatric speciation processes.
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Affiliation(s)
- Caroline Stott
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Awa Diop
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Kasie Raymann
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Department of Biology, University of North Carolina Greensboro, Greensboro, NC 27412, USA
| | - Louis-Marie Bobay
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Department of Biology, University of North Carolina Greensboro, Greensboro, NC 27412, USA
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2
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Zhou Z, Tran PQ, Adams AM, Kieft K, Breier JA, Fortunato CS, Sheik CS, Huber JA, Li M, Dick GJ, Anantharaman K. Sulfur cycling connects microbiomes and biogeochemistry in deep-sea hydrothermal plumes. THE ISME JOURNAL 2023:10.1038/s41396-023-01421-0. [PMID: 37179442 DOI: 10.1038/s41396-023-01421-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 04/17/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023]
Abstract
In globally distributed deep-sea hydrothermal vent plumes, microbiomes are shaped by the redox energy landscapes created by reduced hydrothermal vent fluids mixing with oxidized seawater. Plumes can disperse over thousands of kilometers and their characteristics are determined by geochemical sources from vents, e.g., hydrothermal inputs, nutrients, and trace metals. However, the impacts of plume biogeochemistry on the oceans are poorly constrained due to a lack of integrated understanding of microbiomes, population genetics, and geochemistry. Here, we use microbial genomes to understand links between biogeography, evolution, and metabolic connectivity, and elucidate their impacts on biogeochemical cycling in the deep sea. Using data from 36 diverse plume samples from seven ocean basins, we show that sulfur metabolism defines the core microbiome of plumes and drives metabolic connectivity in the microbial community. Sulfur-dominated geochemistry influences energy landscapes and promotes microbial growth, while other energy sources influence local energy landscapes. We further demonstrated the consistency of links among geochemistry, function, and taxonomy. Amongst all microbial metabolisms, sulfur transformations had the highest MW-score, a measure of metabolic connectivity in microbial communities. Additionally, plume microbial populations have low diversity, short migration history, and gene-specific sweep patterns after migrating from background seawater. Selected functions include nutrient uptake, aerobic oxidation, sulfur oxidation for higher energy yields, and stress responses for adaptation. Our findings provide the ecological and evolutionary bases of change in sulfur-driven microbial communities and their population genetics in adaptation to changing geochemical gradients in the oceans.
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Affiliation(s)
- Zhichao Zhou
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Patricia Q Tran
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Freshwater and Marine Sciences Graduate Program, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Alyssa M Adams
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Kristopher Kieft
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - John A Breier
- School of Earth, Environmental, and Marine Sciences, The University of Texas Rio Grande Valley, Edinburg, TX, 78539, USA
| | | | - Cody S Sheik
- Department of Biology and Large Lakes Observatory, University of Minnesota Duluth, Duluth, MN, 55812, USA
| | - Julie A Huber
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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3
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Gophna U, Altman-Price N. Horizontal Gene Transfer in Archaea-From Mechanisms to Genome Evolution. Annu Rev Microbiol 2022; 76:481-502. [PMID: 35667126 DOI: 10.1146/annurev-micro-040820-124627] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Archaea remains the least-studied and least-characterized domain of life despite its significance not just to the ecology of our planet but also to the evolution of eukaryotes. It is therefore unsurprising that research into horizontal gene transfer (HGT) in archaea has lagged behind that of bacteria. Indeed, several archaeal lineages may owe their very existence to large-scale HGT events, and thus understanding both the molecular mechanisms and the evolutionary impact of HGT in archaea is highly important. Furthermore, some mechanisms of gene exchange, such as plasmids that transmit themselves via membrane vesicles and the formation of cytoplasmic bridges that allows transfer of both chromosomal and plasmid DNA, may be archaea specific. This review summarizes what we know about HGT in archaea, and the barriers that restrict it, highlighting exciting recent discoveries and pointing out opportunities for future research. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Uri Gophna
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; ,
| | - Neta Altman-Price
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; , .,Department of Natural and Life Sciences, The Open University of Israel, Raanana, Israel
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4
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Olm MR, Crits-Christoph A, Bouma-Gregson K, Firek B, Morowitz MJ, Banfield JF. inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains. Nat Biotechnol 2021; 39:727-736. [PMID: 33462508 PMCID: PMC9223867 DOI: 10.1038/s41587-020-00797-0] [Citation(s) in RCA: 258] [Impact Index Per Article: 64.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 12/11/2020] [Indexed: 01/29/2023]
Abstract
Coexisting microbial cells of the same species often exhibit genetic variation that can affect phenotypes ranging from nutrient preference to pathogenicity. Here we present inStrain, a program that uses metagenomic paired reads to profile intra-population genetic diversity (microdiversity) across whole genomes and compares microbial populations in a microdiversity-aware manner, greatly increasing the accuracy of genomic comparisons when benchmarked against existing methods. We use inStrain to profile >1,000 fecal metagenomes from newborn premature infants and find that siblings share significantly more strains than unrelated infants, although identical twins share no more strains than fraternal siblings. Infants born by cesarean section harbor Klebsiella with significantly higher nucleotide diversity than infants delivered vaginally, potentially reflecting acquisition from hospital rather than maternal microbiomes. Genomic loci that show diversity in individual infants include variants found between other infants, possibly reflecting inoculation from diverse hospital-associated sources. inStrain can be applied to any metagenomic dataset for microdiversity analysis and rigorous strain comparison.
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Affiliation(s)
- Matthew R. Olm
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | | | - Keith Bouma-Gregson
- Office of Information Management and Analysis, California State Water Resources Control Board, Sacramento, CA, USA
| | - Brian Firek
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michael J. Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA,Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA,Chan Zuckerberg Biohub, San Francisco, CA, USA,Corresponding author:
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5
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Van Rossum T, Ferretti P, Maistrenko OM, Bork P. Diversity within species: interpreting strains in microbiomes. Nat Rev Microbiol 2020; 18:491-506. [PMID: 32499497 PMCID: PMC7610499 DOI: 10.1038/s41579-020-0368-1] [Citation(s) in RCA: 234] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2020] [Indexed: 02/06/2023]
Abstract
Studying within-species variation has traditionally been limited to culturable bacterial isolates and low-resolution microbial community fingerprinting. Metagenomic sequencing and technical advances have enabled culture-free, high-resolution strain and subspecies analyses at high throughput and in complex environments. This holds great scientific promise but has also led to an overwhelming number of methods and terms to describe infraspecific variation. This Review aims to clarify these advances by focusing on the diversity within bacterial and archaeal species in the context of microbiomics. We cover foundational microevolutionary concepts relevant to population genetics and summarize how within-species variation can be studied and stratified directly within microbial communities with a focus on metagenomics. Finally, we describe how common applications of within-species variation can be achieved using metagenomic data. We aim to guide the selection of appropriate terms and analytical approaches to facilitate researchers in benefiting from the increasing availability of large, high-resolution microbiome genetic sequencing data.
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Affiliation(s)
- Thea Van Rossum
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Pamela Ferretti
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Oleksandr M Maistrenko
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany.
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany.
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
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6
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Abstract
There is controversy about whether bacterial diversity is clustered into distinct species groups or exists as a continuum. To address this issue, we analyzed bacterial genome databases and reports from several previous large-scale environment studies and identified clear discrete groups of species-level bacterial diversity in all cases. Genetic analysis further revealed that quasi-sexual reproduction via horizontal gene transfer is likely a key evolutionary force that maintains bacterial species integrity. We next benchmarked over 100 metrics to distinguish these bacterial species from each other and identified several genes encoding ribosomal proteins with high species discrimination power. Overall, the results from this study provide best practices for bacterial species delineation based on genome content and insight into the nature of bacterial species population genetics. Longstanding questions relate to the existence of naturally distinct bacterial species and genetic approaches to distinguish them. Bacterial genomes in public databases form distinct groups, but these databases are subject to isolation and deposition biases. To avoid these biases, we compared 5,203 bacterial genomes from 1,457 environmental metagenomic samples to test for distinct clouds of diversity and evaluated metrics that could be used to define the species boundary. Bacterial genomes from the human gut, soil, and the ocean all exhibited gaps in whole-genome average nucleotide identities (ANI) near the previously suggested species threshold of 95% ANI. While genome-wide ratios of nonsynonymous and synonymous nucleotide differences (dN/dS) decrease until ANI values approach ∼98%, two methods for estimating homologous recombination approached zero at ∼95% ANI, supporting breakdown of recombination due to sequence divergence as a species-forming force. We evaluated 107 genome-based metrics for their ability to distinguish species when full genomes are not recovered. Full-length 16S rRNA genes were least useful, in part because they were underrecovered from metagenomes. However, many ribosomal proteins displayed both high metagenomic recoverability and species discrimination power. Taken together, our results verify the existence of sequence-discrete microbial species in metagenome-derived genomes and highlight the usefulness of ribosomal genes for gene-level species discrimination. IMPORTANCE There is controversy about whether bacterial diversity is clustered into distinct species groups or exists as a continuum. To address this issue, we analyzed bacterial genome databases and reports from several previous large-scale environment studies and identified clear discrete groups of species-level bacterial diversity in all cases. Genetic analysis further revealed that quasi-sexual reproduction via horizontal gene transfer is likely a key evolutionary force that maintains bacterial species integrity. We next benchmarked over 100 metrics to distinguish these bacterial species from each other and identified several genes encoding ribosomal proteins with high species discrimination power. Overall, the results from this study provide best practices for bacterial species delineation based on genome content and insight into the nature of bacterial species population genetics.
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7
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Peering into the Genetic Makeup of Natural Microbial Populations Using Metagenomics. POPULATION GENOMICS: MICROORGANISMS 2018. [DOI: 10.1007/13836_2018_14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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8
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Ambur OH, Engelstädter J, Johnsen PJ, Miller EL, Rozen DE. Steady at the wheel: conservative sex and the benefits of bacterial transformation. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0528. [PMID: 27619692 PMCID: PMC5031613 DOI: 10.1098/rstb.2015.0528] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2016] [Indexed: 12/25/2022] Open
Abstract
Many bacteria are highly sexual, but the reasons for their promiscuity remain obscure. Did bacterial sex evolve to maximize diversity and facilitate adaptation in a changing world, or does it instead help to retain the bacterial functions that work right now? In other words, is bacterial sex innovative or conservative? Our aim in this review is to integrate experimental, bioinformatic and theoretical studies to critically evaluate these alternatives, with a main focus on natural genetic transformation, the bacterial equivalent of eukaryotic sexual reproduction. First, we provide a general overview of several hypotheses that have been put forward to explain the evolution of transformation. Next, we synthesize a large body of evidence highlighting the numerous passive and active barriers to transformation that have evolved to protect bacteria from foreign DNA, thereby increasing the likelihood that transformation takes place among clonemates. Our critical review of the existing literature provides support for the view that bacterial transformation is maintained as a means of genomic conservation that provides direct benefits to both individual bacterial cells and to transformable bacterial populations. We examine the generality of this view across bacteria and contrast this explanation with the different evolutionary roles proposed to maintain sex in eukaryotes. This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.
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Affiliation(s)
- Ole Herman Ambur
- Department of Life Sciences and Health, Oslo and Akershus University College of Applied Sciences, 1478 Oslo, Norway
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Pål J Johnsen
- Faculty of Health Sciences, Department of Pharmacy, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
| | - Eric L Miller
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PL, UK
| | - Daniel E Rozen
- Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
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9
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Wagner A, Whitaker RJ, Krause DJ, Heilers JH, van Wolferen M, van der Does C, Albers SV. Mechanisms of gene flow in archaea. Nat Rev Microbiol 2017; 15:492-501. [DOI: 10.1038/nrmicro.2017.41] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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10
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Tan CH, Lee KWK, Burmølle M, Kjelleberg S, Rice SA. All together now: experimental multispecies biofilm model systems. Environ Microbiol 2017; 19:42-53. [DOI: 10.1111/1462-2920.13594] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Chuan Hao Tan
- The Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological University Singapore
| | - Kai Wei Kelvin Lee
- The Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological University Singapore
| | - Mette Burmølle
- Section of Microbiology, Department of BiologyUniversity of CopenhagenCopenhagen Denmark
| | - Staffan Kjelleberg
- The Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological University Singapore
- The School of Biological SciencesNanyang Technological University Singapore
| | - Scott A. Rice
- The Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological University Singapore
- The School of Biological SciencesNanyang Technological University Singapore
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11
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Abstract
Many groups of closely related species have reticulate phylogenies. Recent genomic analyses are showing this in many insects and vertebrates, as well as in microbes and plants. In microbes, lateral gene transfer is the dominant process that spoils strictly tree-like phylogenies, but in multicellular eukaryotes hybridization and introgression among related species is probably more important. Because many species, including the ancestors of ancient major lineages, seem to evolve rapidly in adaptive radiations, some sexual compatibility may exist among them. Introgression and reticulation can thereby affect all parts of the tree of life, not just the recent species at the tips. Our understanding of adaptive evolution, speciation, phylogenetics, and comparative biology must adapt to these mostly recent findings. Introgression has important practical implications as well, not least for the management of genetically modified organisms in pest and disease control.
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Affiliation(s)
- James Mallet
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMAUSA
- Department of Genetics, Evolution and EnvironmentUniversity College LondonLondonUK
| | - Nora Besansky
- Department of Biological Sciences and Eck Institute for Global HealthUniversity of Notre DameNotre DameINUSA
| | - Matthew W. Hahn
- Department of Biology and School of Informatics and ComputingIndiana UniversityBloomingtonINUSA
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12
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Krause DJ, Whitaker RJ. Inferring Speciation Processes from Patterns of Natural Variation in Microbial Genomes. Syst Biol 2015; 64:926-35. [PMID: 26316424 PMCID: PMC4604833 DOI: 10.1093/sysbio/syv050] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 06/09/2015] [Indexed: 01/22/2023] Open
Abstract
Microbial species concepts have long been the focus of contentious debate, fueled by technological limitations to the genetic resolution of species, by the daunting task of investigating phenotypic variation among individual microscopic organisms, and by a lack of understanding of gene flow in reproductively asexual organisms that are prone to promiscuous horizontal gene transfer. Population genomics, the emerging approach of analyzing the complete genomes of a multitude of closely related organisms, is poised to overcome these limitations by providing a window into patterns of genome variation revealing the evolutionary processes through which species diverge. This new approach is more than just an extension of previous multilocus sequencing technologies, in that it provides a comprehensive view of interacting evolutionary processes. Here we argue that the application of population genomic tools in a rigorous population genetic framework will help to identify the processes of microbial speciation and ultimately lead to a general species concept based on the unique biology and ecology of microorganisms.
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Affiliation(s)
- David J Krause
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rachel J Whitaker
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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13
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Functionally relevant diversity of closely related Nitrospira in activated sludge. ISME JOURNAL 2014; 9:643-55. [PMID: 25148481 DOI: 10.1038/ismej.2014.156] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 06/28/2014] [Accepted: 07/18/2014] [Indexed: 11/08/2022]
Abstract
Nitrospira are chemolithoautotrophic nitrite-oxidizing bacteria that catalyze the second step of nitrification in most oxic habitats and are important for excess nitrogen removal from sewage in wastewater treatment plants (WWTPs). To date, little is known about their diversity and ecological niche partitioning within complex communities. In this study, the fine-scale community structure and function of Nitrospira was analyzed in two full-scale WWTPs as model ecosystems. In Nitrospira-specific 16S rRNA clone libraries retrieved from each plant, closely related phylogenetic clusters (16S rRNA identities between clusters ranged from 95.8% to 99.6%) within Nitrospira lineages I and II were found. Newly designed probes for fluorescence in situ hybridization (FISH) allowed the specific detection of several of these clusters, whose coexistence in the WWTPs was shown for prolonged periods of several years. In situ ecophysiological analyses based on FISH, relative abundance and spatial arrangement quantification, as well as microautoradiography revealed functional differences of these Nitrospira clusters regarding the preferred nitrite concentration, the utilization of formate as substrate and the spatial coaggregation with ammonia-oxidizing bacteria as symbiotic partners. Amplicon pyrosequencing of the nxrB gene, which encodes subunit beta of nitrite oxidoreductase of Nitrospira, revealed in one of the WWTPs as many as 121 species-level nxrB operational taxonomic units with highly uneven relative abundances in the amplicon library. These results show a previously unrecognized high diversity of Nitrospira in engineered systems, which is at least partially linked to niche differentiation and may have important implications for process stability.
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14
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Gonzalez G, Koyanagi KO, Aoki K, Kitaichi N, Ohno S, Kaneko H, Ishida S, Watanabe H. Intertypic modular exchanges of genomic segments by homologous recombination at universally conserved segments in human adenovirus species D. Gene 2014; 547:10-7. [PMID: 24726548 DOI: 10.1016/j.gene.2014.04.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 03/28/2014] [Accepted: 04/08/2014] [Indexed: 11/20/2022]
Abstract
Human adenovirus species D (HAdV-D), which is composed of clinically and epidemiologically important pathogens worldwide, contains more taxonomic "types" than any other species of the genus Mastadenovirus, although the mechanisms accounting for the high level of diversity remain to be disclosed. Recent studies of known and new types of HAdV-D have indicated that intertypic recombination between distant types contributes to the increasing diversity of the species. However, such findings raise the question as to how homologous recombination events occur between diversified types since homologous recombination is suppressed as nucleotide sequences diverge. In order to address this question, we investigated the distribution of the recombination boundaries in comparison with the landscape of intergenomic sequence conservation assessed according to the synonymous substitution rate (dS). The results revealed that specific genomic segments are conserved between even the most distantly related genomes; we call these segments "universally conserved segments" (UCSs). These findings suggest that UCSs facilitate homologous recombination, resulting in intergenomic segmental exchanges of UCS-flanking genomic regions as recombination modules. With the aid of such a mechanism, the haploid genomes of HAdV-Ds may have been reshuffled, resulting in chimeric genomes out of diversified repertoires in the HAdV-D population analogous to the MHC region reshuffled via crossing over in vertebrates. In addition, some HAdVs with chimeric genomes may have had the opportunity to avoid host immune responses thereby causing epidemics.
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Affiliation(s)
- Gabriel Gonzalez
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan
| | - Kanako O Koyanagi
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan
| | - Koki Aoki
- Department of Ophthalmology, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
| | - Nobuyoshi Kitaichi
- Department of Ophthalmology, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan; Department of Ophthalmology, Health Sciences University of Hokkaido, Sapporo 002-8072, Japan
| | - Shigeaki Ohno
- Department of Ophthalmology, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
| | - Hisatoshi Kaneko
- Department of Ophthalmology, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan; Hobara Eye clinic, Date 960-0612, Japan
| | - Susumu Ishida
- Department of Ophthalmology, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
| | - Hidemi Watanabe
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan.
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15
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Horizontal gene transfer can rescue prokaryotes from Muller's ratchet: benefit of DNA from dead cells and population subdivision. G3-GENES GENOMES GENETICS 2014; 4:325-39. [PMID: 24347631 PMCID: PMC3931566 DOI: 10.1534/g3.113.009845] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Horizontal gene transfer (HGT) is a major factor in the evolution of prokaryotes. An intriguing question is whether HGT is maintained during evolution of prokaryotes owing to its adaptive value or is a byproduct of selection driven by other factors such as consumption of extracellular DNA (eDNA) as a nutrient. One hypothesis posits that HGT can restore genes inactivated by mutations and thereby prevent stochastic, irreversible deterioration of genomes in finite populations known as Muller’s ratchet. To examine this hypothesis, we developed a population genetic model of prokaryotes undergoing HGT via homologous recombination. Analysis of this model indicates that HGT can prevent the operation of Muller’s ratchet even when the source of transferred genes is eDNA that comes from dead cells and on average carries more deleterious mutations than the DNA of recipient live cells. Moreover, if HGT is sufficiently frequent and eDNA diffusion sufficiently rapid, a subdivided population is shown to be more resistant to Muller’s ratchet than an undivided population of an equal overall size. Thus, to maintain genomic information in the face of Muller’s ratchet, it is more advantageous to partition individuals into multiple subpopulations and let them “cross-reference” each other’s genetic information through HGT than to collect all individuals in one population and thereby maximize the efficacy of natural selection. Taken together, the results suggest that HGT could be an important condition for the long-term maintenance of genomic information in prokaryotes through the prevention of Muller’s ratchet.
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16
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Boon E, Meehan CJ, Whidden C, Wong DHJ, Langille MGI, Beiko RG. Interactions in the microbiome: communities of organisms and communities of genes. FEMS Microbiol Rev 2014; 38:90-118. [PMID: 23909933 PMCID: PMC4298764 DOI: 10.1111/1574-6976.12035] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 07/02/2013] [Accepted: 07/10/2013] [Indexed: 12/17/2022] Open
Abstract
A central challenge in microbial community ecology is the delineation of appropriate units of biodiversity, which can be taxonomic, phylogenetic, or functional in nature. The term 'community' is applied ambiguously; in some cases, the term refers simply to a set of observed entities, while in other cases, it requires that these entities interact with one another. Microorganisms can rapidly gain and lose genes, potentially decoupling community roles from taxonomic and phylogenetic groupings. Trait-based approaches offer a useful alternative, but many traits can be defined based on gene functions, metabolic modules, and genomic properties, and the optimal set of traits to choose is often not obvious. An analysis that considers taxon assignment and traits in concert may be ideal, with the strengths of each approach offsetting the weaknesses of the other. Individual genes also merit consideration as entities in an ecological analysis, with characteristics such as diversity, turnover, and interactions modeled using genes rather than organisms as entities. We identify some promising avenues of research that are likely to yield a deeper understanding of microbial communities that shift from observation-based questions of 'Who is there?' and 'What are they doing?' to the mechanistically driven question of 'How will they respond?'
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Affiliation(s)
- Eva Boon
- Department of Biology, Dalhousie University, Halifax, NS, Canada
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17
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Abstract
Sulfolobus islandicus has been developed as a model system for combining approaches of evolutionary and molecular biology in Archaea. We describe how the application of this interdisciplinary approach can lead to novel hypotheses derived from patterns of natural variation that can be tested in the laboratory when combined with a diversity of natural variants and versatile genetic markers. We review how this approach has highlighted the importance of recombination as an evolutionary parameter and provided insight into a molecular mechanism of recombination that may be unique in the archaeal domain. We review the development and improvement of the model system S. islandicus that will enable us to study the mechanism and genomic architecture of recombination guided by evolutionary genomic analysis of Nature's ongoing experiments in wild populations.
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18
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Yelton AP, Comolli LR, Justice NB, Castelle C, Denef VJ, Thomas BC, Banfield JF. Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea. BMC Genomics 2013; 14:485. [PMID: 23865623 PMCID: PMC3750248 DOI: 10.1186/1471-2164-14-485] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 07/15/2013] [Indexed: 11/10/2022] Open
Abstract
Background Metal sulfide mineral dissolution during bioleaching and acid mine drainage (AMD) formation creates an environment that is inhospitable to most life. Despite dominance by a small number of bacteria, AMD microbial biofilm communities contain a notable variety of coexisting and closely related Euryarchaea, most of which have defied cultivation efforts. For this reason, we used metagenomics to analyze variation in gene content that may contribute to niche differentiation among co-occurring AMD archaea. Our analyses targeted members of the Thermoplasmatales and related archaea. These results greatly expand genomic information available for this archaeal order. Results We reconstructed near-complete genomes for uncultivated, relatively low abundance organisms A-, E-, and Gplasma, members of Thermoplasmatales order, and for a novel organism, Iplasma. Genomic analyses of these organisms, as well as Ferroplasma type I and II, reveal that all are facultative aerobic heterotrophs with the ability to use many of the same carbon substrates, including methanol. Most of the genomes share genes for toxic metal resistance and surface-layer production. Only Aplasma and Eplasma have a full suite of flagellar genes whereas all but the Ferroplasma spp. have genes for pili production. Cryogenic-electron microscopy (cryo-EM) and tomography (cryo-ET) strengthen these metagenomics-based ultrastructural predictions. Notably, only Aplasma, Gplasma and the Ferroplasma spp. have predicted iron oxidation genes and Eplasma and Iplasma lack most genes for cobalamin, valine, (iso)leucine and histidine synthesis. Conclusion The Thermoplasmatales AMD archaea share a large number of metabolic capabilities. All of the uncultivated organisms studied here (A-, E-, G-, and Iplasma) are metabolically very similar to characterized Ferroplasma spp., differentiating themselves mainly in their genetic capabilities for biosynthesis, motility, and possibly iron oxidation. These results indicate that subtle, but important genomic differences, coupled with unknown differences in gene expression, distinguish these organisms enough to allow for co-existence. Overall this study reveals shared features of organisms from the Thermoplasmatales lineage and provides new insights into the functioning of AMD communities.
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Affiliation(s)
- Alexis P Yelton
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
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19
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Williams D, Gogarten JP, Papke RT. Quantifying homologous replacement of loci between haloarchaeal species. Genome Biol Evol 2013; 4:1223-44. [PMID: 23160063 PMCID: PMC3542582 DOI: 10.1093/gbe/evs098] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
In vitro studies of the haloarchaeal genus Haloferax have demonstrated
their ability to frequently exchange DNA between species, whereas rates of homologous
recombination estimated from natural populations in the genus Halorubrum
are high enough to maintain random association of alleles between five loci. To quantify
the effects of gene transfer and recombination of commonly held (relaxed core) genes
during the evolution of the class Halobacteria (haloarchaea), we reconstructed the history
of 21 genomes representing all major groups. Using a novel algorithm and a concatenated
ribosomal protein phylogeny as a reference, we created a directed horizontal genetic
transfer (HGT) network of contemporary and ancestral genomes. Gene order analysis revealed
that 90% of testable HGTs were by direct homologous replacement, rather than
nonhomologous integration followed by a loss. Network analysis revealed an inverse
log-linear relationship between HGT frequency and ribosomal protein evolutionary distance
that is maintained across the deepest divergences in Halobacteria. We use this
mathematical relationship to estimate the total transfers and amino acid substitutions
delivered by HGTs in each genome, providing a measure of chimerism. For the relaxed core
genes of each genome, we conservatively estimate that 11–20% of their
evolution occurred in other haloarchaea. Our findings are unexpected, because the transfer
and homologous recombination of relaxed core genes between members of the class
Halobacteria disrupts the coevolution of genes; however, the generation of new
combinations of divergent but functionally related genes may lead to adaptive phenotypes
not available through cumulative mutations and recombination within a single
population.
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Affiliation(s)
- David Williams
- Department of Molecular and Cell Biology, University of Connecticut, CT, USA
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20
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Fitzsimons MS, Novotny M, Lo CC, Dichosa AEK, Yee-Greenbaum JL, Snook JP, Gu W, Chertkov O, Davenport KW, McMurry K, Reitenga KG, Daughton AR, He J, Johnson SL, Gleasner CD, Wills PL, Parson-Quintana B, Chain PS, Detter JC, Lasken RS, Han CS. Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. Genome Res 2013; 23:878-88. [PMID: 23493677 PMCID: PMC3638143 DOI: 10.1101/gr.142208.112] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The majority of microbial genomic diversity remains unexplored. This is largely due to our inability to culture most microorganisms in isolation, which is a prerequisite for traditional genome sequencing. Single-cell sequencing has allowed researchers to circumvent this limitation. DNA is amplified directly from a single cell using the whole-genome amplification technique of multiple displacement amplification (MDA). However, MDA from a single chromosome copy suffers from amplification bias and a large loss of specificity from even very small amounts of DNA contamination, which makes assembling a genome difficult and completely finishing a genome impossible except in extraordinary circumstances. Gel microdrop cultivation allows culturing of a diverse microbial community and provides hundreds to thousands of genetically identical cells as input for an MDA reaction. We demonstrate the utility of this approach by comparing sequencing results of gel microdroplets and single cells following MDA. Bias is reduced in the MDA reaction and genome sequencing, and assembly is greatly improved when using gel microdroplets. We acquired multiple near-complete genomes for two bacterial species from human oral and stool microbiome samples. A significant amount of genome diversity, including single nucleotide polymorphisms and genome recombination, is discovered. Gel microdroplets offer a powerful and high-throughput technology for assembling whole genomes from complex samples and for probing the pan-genome of naturally occurring populations.
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Affiliation(s)
- Michael S Fitzsimons
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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21
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Polz MF, Alm EJ, Hanage WP. Horizontal gene transfer and the evolution of bacterial and archaeal population structure. Trends Genet 2013; 29:170-5. [PMID: 23332119 PMCID: PMC3760709 DOI: 10.1016/j.tig.2012.12.006] [Citation(s) in RCA: 271] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 11/29/2012] [Accepted: 12/18/2012] [Indexed: 12/28/2022]
Abstract
Many bacterial and archaeal lineages have a history of extensive and ongoing horizontal gene transfer and loss, as evidenced by the large differences in genome content even among otherwise closely related isolates. How ecologically cohesive populations might evolve and be maintained under such conditions of rapid gene turnover has remained controversial. Here we synthesize recent literature demonstrating the importance of habitat and niche in structuring horizontal gene transfer. This leads to a model of ecological speciation via gradual genetic isolation triggered by differential habitat-association of nascent populations. Further, we hypothesize that subpopulations can evolve through local gene-exchange networks by tapping into a gene pool that is adaptive towards local, continuously changing organismic interactions and is, to a large degree, responsible for the observed rapid gene turnover. Overall, these insights help to explain how bacteria and archaea form populations that display both ecological cohesion and high genomic diversity.
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Affiliation(s)
- Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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22
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Abstract
According to theory, sympatric speciation in sexual eukaryotes is favored when relatively few loci in the genome are sufficient for reproductive isolation and adaptation to different niches. Here we show a similar result for clonally reproducing bacteria, but which comes about for different reasons. In simulated microbial populations, there is an evolutionary tradeoff between early and late stages of niche adaptation, which is resolved when relatively few loci are required for adaptation. At early stages, recombination accelerates adaptation to new niches (ecological speciation) by combining multiple adaptive alleles into a single genome. Later on, without assortative mating or other barriers to gene flow, recombination generates unfit intermediate genotypes and homogenizes incipient species. The solution to this tradeoff may be simply to reduce the number of loci required for speciation, or to reduce recombination between species over time. Both solutions appear to be relevant in natural microbial populations, allowing them to diverge into ecological species under similar constraints as sexual eukaryotes, despite differences in their life histories.
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23
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Naor A, Lapierre P, Mevarech M, Papke R, Gophna U. Low Species Barriers in Halophilic Archaea and the Formation of Recombinant Hybrids. Curr Biol 2012; 22:1444-8. [DOI: 10.1016/j.cub.2012.05.056] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2011] [Revised: 04/15/2012] [Accepted: 05/30/2012] [Indexed: 10/28/2022]
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24
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Denef VJ, Banfield JF. In Situ Evolutionary Rate Measurements Show Ecological Success of Recently Emerged Bacterial Hybrids. Science 2012; 336:462-6. [DOI: 10.1126/science.1218389] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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25
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Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szabó G, Polz MF, Alm EJ. Population genomics of early events in the ecological differentiation of bacteria. Science 2012; 336:48-51. [PMID: 22491847 PMCID: PMC3337212 DOI: 10.1126/science.1218198] [Citation(s) in RCA: 355] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Genetic exchange is common among bacteria, but its effect on population diversity during ecological differentiation remains controversial. A fundamental question is whether advantageous mutations lead to selection of clonal genomes or, as in sexual eukaryotes, sweep through populations on their own. Here, we show that in two recently diverged populations of ocean bacteria, ecological differentiation has occurred akin to a sexual mechanism: A few genome regions have swept through subpopulations in a habitat-specific manner, accompanied by gradual separation of gene pools as evidenced by increased habitat specificity of the most recent recombinations. These findings reconcile previous, seemingly contradictory empirical observations of the genetic structure of bacterial populations and point to a more unified process of differentiation in bacteria and sexual eukaryotes than previously thought.
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Affiliation(s)
- B. Jesse Shapiro
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute, Cambridge, MA 02142, USA
| | - Jonathan Friedman
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Otto X. Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sarah P. Preheim
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sonia C. Timberlake
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gitta Szabó
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Martin F. Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eric J. Alm
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute, Cambridge, MA 02142, USA
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26
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Cadillo-Quiroz H, Didelot X, Held NL, Herrera A, Darling A, Reno ML, Krause DJ, Whitaker RJ. Patterns of gene flow define species of thermophilic Archaea. PLoS Biol 2012; 10:e1001265. [PMID: 22363207 PMCID: PMC3283564 DOI: 10.1371/journal.pbio.1001265] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Accepted: 01/06/2012] [Indexed: 12/26/2022] Open
Abstract
Despite a growing appreciation of their vast diversity in nature, mechanisms of speciation are poorly understood in Bacteria and Archaea. Here we use high-throughput genome sequencing to identify ongoing speciation in the thermoacidophilic Archaeon Sulfolobus islandicus. Patterns of homologous gene flow among genomes of 12 strains from a single hot spring in Kamchatka, Russia, demonstrate higher levels of gene flow within than between two persistent, coexisting groups, demonstrating that these microorganisms fit the biological species concept. Furthermore, rates of gene flow between two species are decreasing over time in a manner consistent with incipient speciation. Unlike other microorganisms investigated, we do not observe a relationship between genetic divergence and frequency of recombination along a chromosome, or other physical mechanisms that would reduce gene flow between lineages. Each species has its own genetic island encoding unique physiological functions and a unique growth phenotype that may be indicative of ecological specialization. Genetic differentiation between these coexisting groups occurs in large genomic "continents," indicating the topology of genomic divergence during speciation is not uniform and is not associated with a single locus under strong diversifying selection. These data support a model where species do not require physical barriers to gene flow but are maintained by ecological differentiation.
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Affiliation(s)
- Hinsby Cadillo-Quiroz
- Department of Microbiology and Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois, United States of America
| | - Xavier Didelot
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Nicole L. Held
- Department of Microbiology and Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois, United States of America
| | - Alfa Herrera
- Department of Microbiology and Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois, United States of America
| | - Aaron Darling
- Genome Center, University of California, Davis, Davis, California, United States of America
| | - Michael L. Reno
- Department of Microbiology and Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois, United States of America
| | - David J. Krause
- Department of Microbiology and Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois, United States of America
| | - Rachel J. Whitaker
- Department of Microbiology and Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
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27
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Abstract
Whether or not bacterial species exist remains an unresolved issue of paramount theoretical as well as practical consequences. Here we review and synthesize the findings emerging from metagenomic surveys of natural microbial populations and argue that microbial communities are predominantly organized in genetically and ecologically discernible populations, which possess the attributes expected for species. These sequence-discrete populations represent a major foundation for beginning high-resolution investigations on how populations are organized, interact, and evolve within communities. We also attempt to reconcile these findings with those of previous studies that reported indiscrete species and a genetic continuum within bacterial taxa and discuss the implications for the current bacterial species definition.
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28
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Doroghazi JR, Buckley DH. A model for the effect of homologous recombination on microbial diversification. Genome Biol Evol 2011; 3:1349-56. [PMID: 22071790 PMCID: PMC3240962 DOI: 10.1093/gbe/evr110] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The effect of homologous recombination (HR) on the evolution of microbial genomes remains contentious as competing hypotheses seek to explain the evolutionary dynamics of microbial species. Evidence for HR between microbial genomes is widespread, and this process has been proposed to act as a cohesive force that can constrain the diversification of microbial lineages. We seek to characterize the evolutionary dynamics of sympatric populations to explore the impact of HR on microbial speciation. We describe a simple equation for quantifying the cohesive effect of HR on microbial populations as a function of their nucleotide divergence, μ/ρ = πg10 − 20 πg. The model was verified using a forward-time microbial population simulator that can explore the evolutionary dynamics of sympatric populations in nonoverlapping niche space. The model was also evaluated using multilocus sequence data from a range of microbial species, providing criteria for dividing them into either cohesively recombining or clonally diverging lineages. We conclude that models of microbial diversification that appear contradictory can be explained in a unified manner as the natural and predictable consequence of variation in a small number of population parameters.
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Affiliation(s)
- James R Doroghazi
- Department of Microbiology, Cornell University, Ithaca, New York, USA
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29
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Kämpfer P, Glaeser SP. Prokaryotic taxonomy in the sequencing era - the polyphasic approach revisited. Environ Microbiol 2011; 14:291-317. [DOI: 10.1111/j.1462-2920.2011.02615.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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Ajon M, Fröls S, van Wolferen M, Stoecker K, Teichmann D, Driessen AJM, Grogan DW, Albers SV, Schleper C. UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili. Mol Microbiol 2011; 82:807-17. [DOI: 10.1111/j.1365-2958.2011.07861.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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31
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Abstract
Type IV pili are filamentous structures that are found on the surface of many bacterial and archaeal cells, they are involved in cell motility and surface adhesion. In the crenarchaeon Sulfolobus solfataricus, type IV pili formation is strongly induced by UV irradiation and leads to cellular aggregation. The study by Ajon et al. (2011) published in this issue of Molecular Microbiology shows that UV-induced cellular aggregation greatly stimulates the exchange of chromosomal markers among irradiated cells, and that this strategy helps with cell survival. Sulfolobus knockout strains that are incapable of forming pili proved to be deficient in aggregation, and also showed decreased cellular survival after UV irradiation. The UV-induced pili of three different Sulfolobus species had distinct morphologies, and correspondingly these three species were able to aggregate only with their own kind. This work has defined a new role for type IV pili in both the transfer of genes within species and the recovery from UV-induced DNA damage.
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Affiliation(s)
- Thorsten Allers
- School of Biology, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK.
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32
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Abstract
MOTIVATION Sequencing projects increasingly target samples from non-clonal sources. In particular, metagenomics has enabled scientists to begin to characterize the structure of microbial communities. The software tools developed for assembling and analyzing sequencing data for clonal organisms are, however, unable to adequately process data derived from non-clonal sources. RESULTS We present a new scaffolder, Bambus 2, to address some of the challenges encountered when analyzing metagenomes. Our approach relies on a combination of a novel method for detecting genomic repeats and algorithms that analyze assembly graphs to identify biologically meaningful genomic variants. We compare our software to current assemblers using simulated and real data. We demonstrate that the repeat detection algorithms have higher sensitivity than current approaches without sacrificing specificity. In metagenomic datasets, the scaffolder avoids false joins between distantly related organisms while obtaining long-range contiguity. Bambus 2 represents a first step toward automated metagenomic assembly. AVAILABILITY Bambus 2 is open source and available from http://amos.sf.net. CONTACT mpop@umiacs.umd.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sergey Koren
- Department of Computer Science, University of Maryland, College Park, MD 20742, USA
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33
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Belnap CP, Pan C, Denef VJ, Samatova NF, Hettich RL, Banfield JF. Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions. THE ISME JOURNAL 2011; 5:1152-61. [PMID: 21228889 PMCID: PMC3146278 DOI: 10.1038/ismej.2010.200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 11/05/2010] [Accepted: 11/10/2010] [Indexed: 11/08/2022]
Abstract
Extensive genomic characterization of multi-species acid mine drainage microbial consortia combined with laboratory cultivation has enabled the application of quantitative proteomic analyses at the community level. In this study, quantitative proteomic comparisons were used to functionally characterize laboratory-cultivated acidophilic communities sustained in pH 1.45 or 0.85 conditions. The distributions of all proteins identified for individual organisms indicated biases for either high or low pH, and suggests pH-specific niche partitioning for low abundance bacteria and archaea. Although the proteome of the dominant bacterium, Leptospirillum group II, was largely unaffected by pH treatments, analysis of functional categories indicated proteins involved in amino acid and nucleotide metabolism, as well as cell membrane/envelope biogenesis were overrepresented at high pH. Comparison of specific protein abundances indicates higher pH conditions favor Leptospirillum group III, whereas low pH conditions promote the growth of certain archaea. Thus, quantitative proteomic comparisons revealed distinct differences in community composition and metabolic function of individual organisms during different pH treatments. Proteomic analysis revealed other aspects of community function. Different numbers of phage proteins were identified across biological replicates, indicating stochastic spatial heterogeneity of phage outbreaks. Additionally, proteomic data were used to identify a previously unknown genotypic variant of Leptospirillum group II, an indication of selection for a specific Leptospirillum group II population in laboratory communities. Our results confirm the importance of pH and related geochemical factors in fine-tuning acidophilic microbial community structure and function at the species and strain level, and demonstrate the broad utility of proteomics in laboratory community studies.
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Affiliation(s)
- Christopher P Belnap
- Microbiology Graduate Group, Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Chongle Pan
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Vincent J Denef
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Nagiza F Samatova
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
- Microbial Graduate Group, Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
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Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates. ISME JOURNAL 2011; 5:1722-34. [PMID: 21562597 DOI: 10.1038/ismej.2011.55] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We investigated the genomic diversity of a local population of the symbiotic bacterium Sinorhizobium medicae, isolated from the roots of wild Medicago lupulina plants, in order to assess genomic diversity, to identify genomic regions influenced by duplication, deletion or strong selection, and to explore the composition of the pan-genome. Partial genome sequences of 12 isolates were obtained by Roche 454 shotgun sequencing (average 5.3 Mb per isolate) and compared with the published sequence of S. medicae WSM 419. Homologous recombination appears to have less impact on the polymorphism patterns of the chromosome than on the chromid pSMED01 and megaplasmid pSMED02. Moreover, pSMED02 is a hot spot of insertions and deletions. The whole chromosome is characterized by low sequence polymorphism, consistent with the high density of housekeeping genes. Similarly, the level of polymorphism of symbiosis genes (low) and of genes involved in polysaccharide synthesis (high) may reflect different selection. Finally, some isolates carry genes that may confer adaptations that S. medicae WSM 419 lacks, including homologues of genes encoding rhizobitoxine synthesis, iron uptake, response to autoinducer-2, and synthesis of distinct polysaccharides. The presence or absence of these genes was confirmed by PCR in each of these 12 isolates and a further 27 isolates from the same population. All isolates had rhizobitoxine genes, while the other genes were co-distributed, suggesting that they may be on the same mobile element. These results are discussed in relation to the ecology of Medicago symbionts and in the perspective of population genomics studies.
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35
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Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species. Proc Natl Acad Sci U S A 2011; 108:7200-5. [PMID: 21482770 DOI: 10.1073/pnas.1015622108] [Citation(s) in RCA: 236] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Defining bacterial species remains a challenging problem even for the model bacterium Escherichia coli and has major practical consequences for reliable diagnosis of infectious disease agents and regulations for transport and possession of organisms of economic importance. E. coli traditionally is thought to live within the gastrointestinal tract of humans and other warm-blooded animals and not to survive for extended periods outside its host; this understanding is the basis for its widespread use as a fecal contamination indicator. Here, we report the genome sequences of nine environmentally adapted strains that are phenotypically and taxonomically indistinguishable from typical E. coli (commensal or pathogenic). We find, however, that the commensal genomes encode for more functions that are important for fitness in the human gut, do not exchange genetic material with their environmental counterparts, and hence do not evolve according to the recently proposed fragmented speciation model. These findings are consistent with a more stringent and ecologic definition for bacterial species than the current definition and provide means to start replacing traditional approaches of defining distinctive phenotypes for new species with omics-based procedures. They also have important implications for reliable diagnosis and regulation of pathogenic E. coli and for the coliform cell-counting test.
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36
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Ladoukakis ED, Theologidis I, Rodakis GC, Zouros E. Homologous recombination between highly diverged mitochondrial sequences: examples from maternally and paternally transmitted genomes. Mol Biol Evol 2011; 28:1847-59. [PMID: 21220759 DOI: 10.1093/molbev/msr007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Homologous recombination is restricted to sequences of low divergence. This is attributed to the mismatch repairing system (MMR), which does not allow recombination between sequences that are highly divergent. This acts as a safeguard against recombination between nonhomologous sequences that could result in genome imbalance. Here, we report recombination between maternal and paternal mitochondrial genomes of the sea mussel, whose sequences differ by >20%. We propose that the strict maternal inheritance of the animal mitochondrial DNA and the ensuing homoplasmy has relieved the MMR system of the animal mitochondrion from the pressure to tolerate recombination only among sequences with a high degree of similarity.
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Caro-Quintero A, Deng J, Auchtung J, Brettar I, Höfle MG, Klappenbach J, Konstantinidis KT. Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea. ISME JOURNAL 2010; 5:131-40. [PMID: 20596068 DOI: 10.1038/ismej.2010.93] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
High-throughput sequencing studies during the last decade have uncovered that bacterial genomes are very diverse and dynamic, resulting primarily from the frequent and promiscuous horizontal gene exchange that characterizes the bacterial domain of life. However, a robust understanding of the rates of genetic exchange for most bacterial species under natural conditions and the influence of the ecological settings on the rates remain elusive, severely limiting our view of the microbial world. Here, we analyzed the complete genomic sequences and expressed transcriptomes of several Shewanella baltica isolates recovered from different depths in the Baltic Sea and found that isolates from more similar depths had exchanged a larger fraction of their core and auxiliary genome, up to 20% of the total, compared with isolates from more different depths. The exchanged genes seem to be ecologically important and contribute to the successful adaptation of the isolates to the unique physicochemical conditions of the depth. Importantly, the latter genes were exchanged in very recent past, presumably as an effect of isolate's seasonal migration across the water column, and reflected sexual speciation within the same depth. Therefore, our findings reveal that genetic exchange in response to environmental settings may be surprisingly rapid, which has important broader impacts for understanding bacterial speciation and evolution and for modeling bacterial responses to human-induced environmental impacts.
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Doroghazi JR, Buckley DH. Widespread homologous recombination within and between Streptomyces species. ISME JOURNAL 2010; 4:1136-43. [DOI: 10.1038/ismej.2010.45] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature. ISME JOURNAL 2010; 4:599-610. [PMID: 20164865 DOI: 10.1038/ismej.2009.158] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Similar to virtually all components of natural environments, microbial systems are inherently complex and dynamic. Advances in cultivation-independent molecular methods have provided a route to study microbial consortia in their natural surroundings and to begin resolving the community structure, dominant metabolic processes and inter-organism interactions. However, the utility of these methods generally scales inversely with community complexity. By applying genomics-enabled methods to the study of natural microbial communities with reduced levels of species richness, a relatively comprehensive understanding of the metabolic networks and evolutionary processes within these communities can be attained. In such well-defined model systems, it is also possible to link emergent ecological patterns to their molecular and evolutionary underpinnings, facilitating construction of predictive ecosystem models. In this study, we review over a decade of research on one such system-acid mine drainage biofilm communities. We discuss the value and limitations of tractable model microbial communities in developing molecular methods for microbial ecology and in uncovering principles that may explain behavior in more complex systems.
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Denef VJ, Kalnejais LH, Mueller RS, Wilmes P, Baker BJ, Thomas BC, VerBerkmoes NC, Hettich RL, Banfield JF. Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc Natl Acad Sci U S A 2010; 107:2383-90. [PMID: 20133593 PMCID: PMC2823883 DOI: 10.1073/pnas.0907041107] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial species concepts are controversial. More widely accepted is the need to understand how differences in gene content and sequence lead to ecological divergence. To address this relationship in ecosystem context, we investigated links between genotype and ecology of two genotypic groups of Leptospirillum group II bacteria in comprehensively characterized, natural acidophilic biofilm communities. These groups share 99.7% 16S rRNA gene sequence identity and 95% average amino acid identity between their orthologs. One genotypic group predominates during early colonization, and the other group typically proliferates in later successional stages, forming distinct patches tens to hundreds of micrometers in diameter. Among early colonizing populations, we observed dominance of five genotypes that differed from each other by the extent of recombination with the late colonizing type. Our analyses suggest that the specific recombinant variant within the early colonizing group is selected for by environmental parameters such as temperature, consistent with recombination as a mechanism for ecological fine tuning. Evolutionary signatures, and strain-resolved expression patterns measured via mass spectrometry-based proteomics, indicate increased cobalamin biosynthesis, (de)methylation, and glycine cleavage in the late colonizer. This may suggest environmental changes within the biofilm during development, accompanied by redirection of compatible solutes from osmoprotectants toward metabolism. Across 27 communities, comparative proteogenomic analyses show that differential regulation of shared genes and expression of a small subset of the approximately 15% of genes unique to each genotype are involved in niche partitioning. In summary, the results show how subtle genetic variations can lead to distinct ecological strategies.
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Affiliation(s)
| | | | | | - Paul Wilmes
- University of California, Berkeley, CA 94720; and
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Dworzanski JP, Dickinson DN, Deshpande SV, Snyder AP, Eckenrode BA. Discrimination and Phylogenomic Classification of Bacillus anthracis-cereus-thuringiensis Strains Based on LC-MS/MS Analysis of Whole Cell Protein Digests. Anal Chem 2009; 82:145-55. [DOI: 10.1021/ac9015648] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jacek P. Dworzanski
- Science Applications International Corporation, Aberdeen Proving Ground, Maryland 21010-0068, Northrop Grumman Electronic Systems, Baltimore, Maryland 21203, Science and Technology Corporation, Edgewood, Maryland 21040, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and FBI Counterterrorism and Forensic Science Research Unit, Quantico, Virginia 22135
| | - Danielle N. Dickinson
- Science Applications International Corporation, Aberdeen Proving Ground, Maryland 21010-0068, Northrop Grumman Electronic Systems, Baltimore, Maryland 21203, Science and Technology Corporation, Edgewood, Maryland 21040, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and FBI Counterterrorism and Forensic Science Research Unit, Quantico, Virginia 22135
| | - Samir V. Deshpande
- Science Applications International Corporation, Aberdeen Proving Ground, Maryland 21010-0068, Northrop Grumman Electronic Systems, Baltimore, Maryland 21203, Science and Technology Corporation, Edgewood, Maryland 21040, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and FBI Counterterrorism and Forensic Science Research Unit, Quantico, Virginia 22135
| | - A. Peter Snyder
- Science Applications International Corporation, Aberdeen Proving Ground, Maryland 21010-0068, Northrop Grumman Electronic Systems, Baltimore, Maryland 21203, Science and Technology Corporation, Edgewood, Maryland 21040, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and FBI Counterterrorism and Forensic Science Research Unit, Quantico, Virginia 22135
| | - Brian A. Eckenrode
- Science Applications International Corporation, Aberdeen Proving Ground, Maryland 21010-0068, Northrop Grumman Electronic Systems, Baltimore, Maryland 21203, Science and Technology Corporation, Edgewood, Maryland 21040, U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010-5424, and FBI Counterterrorism and Forensic Science Research Unit, Quantico, Virginia 22135
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Johnson PLF, Slatkin M. Inference of microbial recombination rates from metagenomic data. PLoS Genet 2009; 5:e1000674. [PMID: 19798447 PMCID: PMC2745702 DOI: 10.1371/journal.pgen.1000674] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 09/02/2009] [Indexed: 11/18/2022] Open
Abstract
Metagenomic sequencing projects from environments dominated by a small number of species produce genome-wide population samples. We present a two-site composite likelihood estimator of the scaled recombination rate, rho = 2N(e)c, that operates on metagenomic assemblies in which each sequenced fragment derives from a different individual. This new estimator properly accounts for sequencing error, as quantified by per-base quality scores, and missing data, as inferred from the placement of reads in a metagenomic assembly. We apply our estimator to data from a sludge metagenome project to demonstrate how this method will elucidate the rates of exchange of genetic material in natural microbial populations. Surprisingly, for a fixed amount of sequencing, this estimator has lower variance than similar methods that operate on more traditional population genetic samples of comparable size. In addition, we can infer variation in recombination rate across the genome because metagenomic projects sample genetic diversity genome-wide, not just at particular loci. The method itself makes no assumption specific to microbial populations, opening the door for application to any mixed population sample where the number of individuals sampled is much greater than the number of fragments sequenced.
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Affiliation(s)
- Philip L F Johnson
- Biophysics Graduate Group, University of California Berkeley, Berkeley, California, United States of America.
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Dick GJ, Andersson AF, Baker BJ, Simmons SL, Thomas BC, Yelton AP, Banfield JF. Community-wide analysis of microbial genome sequence signatures. Genome Biol 2009; 10:R85. [PMID: 19698104 PMCID: PMC2745766 DOI: 10.1186/gb-2009-10-8-r85] [Citation(s) in RCA: 385] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 07/10/2009] [Accepted: 08/21/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Analyses of DNA sequences from cultivated microorganisms have revealed genome-wide, taxa-specific nucleotide compositional characteristics, referred to as genome signatures. These signatures have far-reaching implications for understanding genome evolution and potential application in classification of metagenomic sequence fragments. However, little is known regarding the distribution of genome signatures in natural microbial communities or the extent to which environmental factors shape them. RESULTS We analyzed metagenomic sequence data from two acidophilic biofilm communities, including composite genomes reconstructed for nine archaea, three bacteria, and numerous associated viruses, as well as thousands of unassigned fragments from strain variants and low-abundance organisms. Genome signatures, in the form of tetranucleotide frequencies analyzed by emergent self-organizing maps, segregated sequences from all known populations sharing < 50 to 60% average amino acid identity and revealed previously unknown genomic clusters corresponding to low-abundance organisms and a putative plasmid. Signatures were pervasive genome-wide. Clusters were resolved because intra-genome differences resulting from translational selection or protein adaptation to the intracellular (pH approximately 5) versus extracellular (pH approximately 1) environment were small relative to inter-genome differences. We found that these genome signatures stem from multiple influences but are primarily manifested through codon composition, which we propose is the result of genome-specific mutational biases. CONCLUSIONS An important conclusion is that shared environmental pressures and interactions among coevolving organisms do not obscure genome signatures in acid mine drainage communities. Thus, genome signatures can be used to assign sequence fragments to populations, an essential prerequisite if metagenomics is to provide ecological and biochemical insights into the functioning of microbial communities.
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Affiliation(s)
- Gregory J Dick
- Department of Earth and Planetary Science, University of California, 307 McCone Hall, Berkeley, CA 94720, USA
- Current address: Department of Geological Sciences, University of Michigan, 1100 N. University Ave, Ann Arbor, MI 48109-1005, USA
| | - Anders F Andersson
- Department of Earth and Planetary Science, University of California, 307 McCone Hall, Berkeley, CA 94720, USA
- Current address: Evolutionary Biology Centre, Department of Limnology, Uppsala University, Norbyv. 18 D, SE-75236, Uppsala, Sweden
- Current address: Department of Bacteriology, Swedish Institute for Infectious Disease Control, Nobels väg 18 SE-17182 Solna, Sweden
| | - Brett J Baker
- Department of Earth and Planetary Science, University of California, 307 McCone Hall, Berkeley, CA 94720, USA
| | - Sheri L Simmons
- Department of Earth and Planetary Science, University of California, 307 McCone Hall, Berkeley, CA 94720, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, 307 McCone Hall, Berkeley, CA 94720, USA
| | - A Pepper Yelton
- Department of Earth and Planetary Science, University of California, 307 McCone Hall, Berkeley, CA 94720, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, 307 McCone Hall, Berkeley, CA 94720, USA
- Department of Environmental Science, Policy, and Management, University of California, Hilgard Hall, Berkeley, CA 94720, USA
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Brocks JJ, Banfield J. Unravelling ancient microbial history with community proteogenomics and lipid geochemistry. Nat Rev Microbiol 2009; 7:601-9. [PMID: 19609261 DOI: 10.1038/nrmicro2167] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Our window into the Earth's ancient microbial past is narrow and obscured by missing data. However, we can glean information about ancient microbial ecosystems using fossil lipids (biomarkers) that are extracted from billion-year-old sedimentary rocks. In this Opinion article, we describe how environmental genomics and related methodologies will give molecular fossil research a boost, by increasing our knowledge about how evolutionary innovations in microorganisms have changed the surface of planet Earth.
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Affiliation(s)
- Jochen J Brocks
- Research School of Earth Sciences, and Centre for Macroevolution and Macroecology, The Australian National University, Canberra, ACT 0200, Australia.
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Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms. Appl Environ Microbiol 2009; 75:4599-615. [PMID: 19429552 DOI: 10.1128/aem.02943-08] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We analyzed near-complete population (composite) genomic sequences for coexisting acidophilic iron-oxidizing Leptospirillum group II and III bacteria (phylum Nitrospirae) and an extrachromosomal plasmid from a Richmond Mine, Iron Mountain, CA, acid mine drainage biofilm. Community proteomic analysis of the genomically characterized sample and two other biofilms identified 64.6% and 44.9% of the predicted proteins of Leptospirillum groups II and III, respectively, and 20% of the predicted plasmid proteins. The bacteria share 92% 16S rRNA gene sequence identity and >60% of their genes, including integrated plasmid-like regions. The extrachromosomal plasmid carries conjugation genes with detectable sequence similarity to genes in the integrated conjugative plasmid, but only those on the extrachromosomal element were identified by proteomics. Both bacterial groups have genes for community-essential functions, including carbon fixation and biosynthesis of vitamins, fatty acids, and biopolymers (including cellulose); proteomic analyses reveal these activities. Both Leptospirillum types have multiple pathways for osmotic protection. Although both are motile, signal transduction and methyl-accepting chemotaxis proteins are more abundant in Leptospirillum group III, consistent with its distribution in gradients within biofilms. Interestingly, Leptospirillum group II uses a methyl-dependent and Leptospirillum group III a methyl-independent response pathway. Although only Leptospirillum group III can fix nitrogen, these proteins were not identified by proteomics. The abundances of core proteins are similar in all communities, but the abundance levels of unique and shared proteins of unknown function vary. Some proteins unique to one organism were highly expressed and may be key to the functional and ecological differentiation of Leptospirillum groups II and III.
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Wilmes P, Simmons SL, Denef VJ, Banfield JF. The dynamic genetic repertoire of microbial communities. FEMS Microbiol Rev 2008; 33:109-32. [PMID: 19054116 PMCID: PMC2704941 DOI: 10.1111/j.1574-6976.2008.00144.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Community genomic data have revealed multiple levels of variation between and within microbial consortia. This variation includes large-scale differences in gene content between ecosystems as well as within-population sequence heterogeneity. In the present review, we focus specifically on how fine-scale variation within microbial and viral populations is apparent from community genomic data. A major unresolved question is how much of the observed variation is due to neutral vs. adaptive processes. Limited experimental data hint that some of this fine-scale variation may be in part functionally relevant, whereas sequence-based and modeling analyses suggest that much of it may be neutral. While methods for interpreting population genomic data are still in their infancy, we discuss current interpretations of existing datasets in the light of evolutionary processes and models. Finally, we highlight the importance of virus–host dynamics in generating and shaping within-population diversity.
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Affiliation(s)
- Paul Wilmes
- Department of Earth and Planetary Science, University of California at Berkeley, Berkeley, CA 94720, USA
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Simmons SL, DiBartolo G, Denef VJ, Goltsman DSA, Thelen MP, Banfield JF. Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation. PLoS Biol 2008; 6:e177. [PMID: 18651792 PMCID: PMC2475542 DOI: 10.1371/journal.pbio.0060177] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Accepted: 06/12/2008] [Indexed: 12/20/2022] Open
Abstract
Deeply sampled community genomic (metagenomic) datasets enable comprehensive analysis of heterogeneity in natural microbial populations. In this study, we used sequence data obtained from the dominant member of a low-diversity natural chemoautotrophic microbial community to determine how coexisting closely related individuals differ from each other in terms of gene sequence and gene content, and to uncover evidence of evolutionary processes that occur over short timescales. DNA sequence obtained from an acid mine drainage biofilm was reconstructed, taking into account the effects of strain variation, to generate a nearly complete genome tiling path for a Leptospirillum group II species closely related to L. ferriphilum (sampling depth ∼20×). The population is dominated by one sequence type, yet we detected evidence for relatively abundant variants (>99.5% sequence identity to the dominant type) at multiple loci, and a few rare variants. Blocks of other Leptospirillum group II types (∼94% sequence identity) have recombined into one or more variants. Variant blocks of both types are more numerous near the origin of replication. Heterogeneity in genetic potential within the population arises from localized variation in gene content, typically focused in integrated plasmid/phage-like regions. Some laterally transferred gene blocks encode physiologically important genes, including quorum-sensing genes of the LuxIR system. Overall, results suggest inter- and intrapopulation genetic exchange involving distinct parental genome types and implicate gain and loss of phage and plasmid genes in recent evolution of this Leptospirillum group II population. Population genetic analyses of single nucleotide polymorphisms indicate variation between closely related strains is not maintained by positive selection, suggesting that these regions do not represent adaptive differences between strains. Thus, the most likely explanation for the observed patterns of polymorphism is divergence of ancestral strains due to geographic isolation, followed by mixing and subsequent recombination. Communities of microbes in nature consist of a large number of distinct individuals. The variation in DNA sequence between these individuals contains a record of the evolutionary processes that have shaped each community. In most environments, however, the high number of distinct species makes obtaining information about the nature of this variation difficult or impossible. We obtained large amounts of sequence data for a natural community in an acid mine drainage system consisting of only a few species. This enabled us to reconstruct the genome of the dominant bacterium (Leptospirillum group II) and obtain detailed information about sequence variation between individuals, including differences in both gene content and gene sequence. Our analysis shows extensive recombination between closely related populations, as well as fewer instances of recombination between more distantly related individuals. Additionally, viruses and plasmids account for high variability in gene content between individuals. We conclude that sequence-level variation in this population is maintained through neutral processes (migration, recombination, and genetic drift) rather than natural selection. This suggests that closely related strains of the Leptospirillum group II population may not be ecologically distinct. Deep sequencing of a low-complexity microbial community revealed extensive recombination as well as polymorphic and gene content variation between individuals of the dominant organism. We show that strains defined by linked polymorphisms are not maintained by positive selection; instead, they are predominantly maintained by the forces of migration and drift.
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Affiliation(s)
- Sheri L Simmons
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, United States of America
| | - Genevieve DiBartolo
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, United States of America
| | - Vincent J Denef
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, United States of America
| | - Daniela S. Aliaga Goltsman
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, United States of America
| | - Michael P Thelen
- Chemistry Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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Vos M, Didelot X. A comparison of homologous recombination rates in bacteria and archaea. ISME JOURNAL 2008; 3:199-208. [PMID: 18830278 DOI: 10.1038/ismej.2008.93] [Citation(s) in RCA: 390] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
It is a standard practice to test for the signature of homologous recombination in studies examining the genetic diversity of bacterial populations. Although it has emerged that homologous recombination rates can vary widely between species, comparing the results from different studies is made difficult by the diversity of estimation methods used. Here, Multi Locus Sequence Typing (MLST) datasets from a wide variety of bacteria and archaea are analyzed using the ClonalFrame method. This enables a direct comparison between species and allows for a first exploration of the question whether phylogeny or ecology is the primary determinant of homologous recombination rate.
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Affiliation(s)
- Michiel Vos
- Department of Zoology, University of Oxford, Oxford, UK.
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Denef VJ, VerBerkmoes NC, Shah MB, Abraham P, Lefsrud M, Hettich RL, Banfield JF. Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation. Environ Microbiol 2008; 11:313-25. [PMID: 18826438 DOI: 10.1111/j.1462-2920.2008.01769.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Analyses of ecological and evolutionary processes that shape microbial consortia are facilitated by comprehensive studies of ecosystems with low species richness. In the current study we evaluated the role of recombination in altering the fitness of chemoautotrophic bacteria in their natural environment. Proteomics-inferred genome typing (PIGT) was used to genotype the dominant Leptospirillum group II populations in 27 biofilms sampled from six locations in the Richmond Mine acid mine drainage system (Iron Mountain, CA) over a 4-year period. We observed six distinct genotypes that are recombinants comprised of segments from two 'parental' genotypes. Community genomic analyses revealed additional low abundance recombinant variants. The dominance of some genotypes despite a larger available genome pool, and patterns of spatiotemporal distribution within the ecosystem, indicate selection for distinct recombinants. Genes involved in motility, signal transduction and transport were over-represented in the tens to hundreds of kilobase recombinant blocks, whereas core metabolic functions were significantly under-represented. Our findings demonstrate the power of PIGT and reveal that recombination is a mechanism for fine-scale adaptation in this system.
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Konstantinidis KT, DeLong EF. Genomic patterns of recombination, clonal divergence and environment in marine microbial populations. ISME JOURNAL 2008; 2:1052-65. [PMID: 18580971 DOI: 10.1038/ismej.2008.62] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microorganisms represent the largest reservoir of biodiversity on Earth, both in numbers and total genetic diversity, but it remains unclear whether this biodiversity is organized in discrete units that correspond to ecologically coherent species. To further explore this question, we examined patterns of genomic diversity in sympatric microbial populations. Analyses of a total of approximately 200 Mb of microbial community genomic DNA sequence recovered from 4000 m depth in the Pacific Ocean revealed discrete sequence-defined populations of Bacteria and Archaea, with intrapopulation genomic sequence divergence ranging from approximately 1% to approximately 6%. The populations appeared to be maintained, at least in part, by intrapopulation genetic exchange (homologous recombination), although the frequency of recombination was estimated to be about three times lower than that observed previously in thermoacidophilic archaeal biofilm populations. Furthermore, the genotypes of a given population were clearly distinguishable from their closest co-occurring relatives based on their relative abundance in situ. The genetic distinctiveness and the matching sympatric abundances imply that these genotypes share similar ecophysiological properties, and therefore may represent fundamental units of microbial diversity in the deep sea. Comparisons to surface-dwelling relatives of the Sargasso Sea revealed that distinct sequence-based clusters were not always detectable, presumably due to environmental variations, further underscoring the important relationship between environmental contexts and genetic mechanisms, which together shape and sustain microbial population structure.
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