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Zhong J, Osborn T, Del Rosario Hernández T, Kyrysyuk O, Tully BJ, Anderson RE. Increasing transposase abundance with ocean depth correlates with a particle-associated lifestyle. mSystems 2024; 9:e0006724. [PMID: 38380923 PMCID: PMC10949469 DOI: 10.1128/msystems.00067-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 01/25/2024] [Indexed: 02/22/2024] Open
Abstract
Transposases are mobile genetic elements that move within and between genomes, promoting genomic plasticity in microorganisms. In marine microbial communities, the abundance of transposases increases with depth, but the reasons behind this trend remain unclear. Our analysis of metagenomes from the Tara Oceans and Malaspina Expeditions suggests that a particle-associated lifestyle is the main covariate for the high occurrence of transposases in the deep ocean, and this trend holds true for individual genomes as well as in a community-wide sense. We observed a strong and depth-independent correlation between transposase abundance and the presence of biofilm-associated genes, as well as the prevalence of secretory enzymes. This suggests that mobile genetic elements readily propagate among microbial communities within crowded biofilms. Furthermore, we show that particle association positively correlates with larger genome size, which is in turn associated with higher transposase abundance. Cassette sequences associated with transposons are enriched with genes related to defense mechanisms, which are more highly expressed in the deep sea. Thus, while transposons spread at the expense of their microbial hosts, they also introduce novel genes and potentially benefit the hosts in helping to compete for limited resources. Overall, our results suggest a new understanding of deep ocean particles as highways for gene sharing among defensively oriented microbial genomes.IMPORTANCEGenes can move within and between microbial genomes via mobile genetic elements, which include transposases and transposons. In the oceans, there is a puzzling increase in transposase abundance in microbial genomes as depth increases. To gain insight into this trend, we conducted an extensive analysis of marine microbial metagenomes and metatranscriptomes. We found a significant correlation between transposase abundance and a particle-associated lifestyle among marine microbes at both the metagenome and genome-resolved levels. We also observed a link between transposase abundance and genes related to defense mechanisms. These results suggest that as microbes become densely packed into crowded particles, mobile genes are more likely to spread and carry genetic material that provides a competitive advantage in crowded habitats. This may enable deep sea microbes to effectively compete in such environments.
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Affiliation(s)
- Juntao Zhong
- Carleton College, Northfield, Minnesota, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Troy Osborn
- Carleton College, Northfield, Minnesota, USA
| | - Thais Del Rosario Hernández
- Carleton College, Northfield, Minnesota, USA
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Oleksandr Kyrysyuk
- Carleton College, Northfield, Minnesota, USA
- Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Benjamin J. Tully
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
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Alexander H, Hu SK, Krinos AI, Pachiadaki M, Tully BJ, Neely CJ, Reiter T. Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton. mBio 2023; 14:e0167623. [PMID: 37947402 PMCID: PMC10746220 DOI: 10.1128/mbio.01676-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/27/2023] [Indexed: 11/12/2023] Open
Abstract
Metagenomics is a powerful method for interpreting the ecological roles and physiological capabilities of mixed microbial communities. Yet, many tools for processing metagenomic data are neither designed to consider eukaryotes nor are they built for an increasing amount of sequence data. EukHeist is an automated pipeline to retrieve eukaryotic and prokaryotic metagenome-assembled genomes (MAGs) from large-scale metagenomic sequence data sets. We developed the EukHeist workflow to specifically process large amounts of both metagenomic and/or metatranscriptomic sequence data in an automated and reproducible fashion. Here, we applied EukHeist to the large-size fraction data (0.8-2,000 µm) from Tara Oceans to recover both eukaryotic and prokaryotic MAGs, which we refer to as TOPAZ (Tara Oceans Particle-Associated MAGs). The TOPAZ MAGs consisted of >900 environmentally relevant eukaryotic MAGs and >4,000 bacterial and archaeal MAGs. The bacterial and archaeal TOPAZ MAGs expand upon the phylogenetic diversity of likely particle- and host-associated taxa. We use these MAGs to demonstrate an approach to infer the putative trophic mode of the recovered eukaryotic MAGs. We also identify ecological cohorts of co-occurring MAGs, which are driven by specific environmental factors and putative host-microbe associations. These data together add to a number of growing resources of environmentally relevant eukaryotic genomic information. Complementary and expanded databases of MAGs, such as those provided through scalable pipelines like EukHeist, stand to advance our understanding of eukaryotic diversity through increased coverage of genomic representatives across the tree of life.IMPORTANCESingle-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers' efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.
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Affiliation(s)
- Harriet Alexander
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Sarah K. Hu
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Arianna I. Krinos
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
- MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Cambridge and Woods Hole, Massachusetts, USA
| | - Maria Pachiadaki
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Benjamin J. Tully
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Christopher J. Neely
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Taylor Reiter
- Population Health and Reproduction, University of California, Davis, Davis, California, USA
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3
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Manck LE, Park J, Tully BJ, Poire AM, Bundy RM, Dupont CL, Barbeau KA. Petrobactin, a siderophore produced by Alteromonas, mediates community iron acquisition in the global ocean. ISME J 2022; 16:358-369. [PMID: 34341506 PMCID: PMC8776838 DOI: 10.1038/s41396-021-01065-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 02/07/2023]
Abstract
It is now widely accepted that siderophores play a role in marine iron biogeochemical cycling. However, the mechanisms by which siderophores affect the availability of iron from specific sources and the resulting significance of these processes on iron biogeochemical cycling as a whole have remained largely untested. In this study, we develop a model system for testing the effects of siderophore production on iron bioavailability using the marine copiotroph Alteromonas macleodii ATCC 27126. Through the generation of the knockout cell line ΔasbB::kmr, which lacks siderophore biosynthetic capabilities, we demonstrate that the production of the siderophore petrobactin enables the acquisition of iron from mineral sources and weaker iron-ligand complexes. Notably, the utilization of lithogenic iron, such as that from atmospheric dust, indicates a significant role for siderophores in the incorporation of new iron into marine systems. We have also detected petrobactin, a photoreactive siderophore, directly from seawater in the mid-latitudes of the North Pacific and have identified the biosynthetic pathway for petrobactin in bacterial metagenome-assembled genomes widely distributed across the global ocean. Together, these results improve our mechanistic understanding of the role of siderophore production in iron biogeochemical cycling in the marine environment wherein iron speciation, bioavailability, and residence time can be directly influenced by microbial activities.
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Affiliation(s)
- Lauren E Manck
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
| | - Jiwoon Park
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Benjamin J Tully
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA
| | - Alfonso M Poire
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA, USA
| | - Randelle M Bundy
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Christopher L Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Human Health, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Synthetic Biology, J. Craig Venter Institute, La Jolla, CA, USA
| | - Katherine A Barbeau
- Geosciences Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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4
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Graham ED, Tully BJ. Marine Dadabacteria exhibit genome streamlining and phototrophy-driven niche partitioning. ISME J 2021; 15:1248-1256. [PMID: 33230264 PMCID: PMC8115339 DOI: 10.1038/s41396-020-00834-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/27/2020] [Accepted: 11/05/2020] [Indexed: 01/29/2023]
Abstract
The remineralization of organic material via heterotrophy in the marine environment is performed by a diverse and varied group of microorganisms that can specialize in the type of organic material degraded and the niche they occupy. The marine Dadabacteria are cosmopolitan in the marine environment and belong to a candidate phylum for which there has not been a comprehensive assessment of the available genomic data to date. Here in, we assess the functional potential of the marine pelagic Dadabacteria in comparison to members of the phylum that originate from terrestrial, hydrothermal, and subsurface environments. Our analysis reveals that the marine pelagic Dadabacteria have streamlined genomes, corresponding to smaller genome sizes and lower nitrogen content of their DNA and predicted proteome, relative to their phylogenetic counterparts. Collectively, the Dadabacteria have the potential to degrade microbial dissolved organic matter, specifically peptidoglycan and phospholipids. The marine Dadabacteria belong to two clades with apparent distinct ecological niches in global metagenomic data: a clade with the potential for photoheterotrophy through the use of proteorhodopsin, present predominantly in surface waters up to 100 m depth; and a clade lacking the potential for photoheterotrophy that is more abundant in the deep photic zone.
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Affiliation(s)
- Elaina D Graham
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Benjamin J Tully
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA.
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5
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Seyler LM, Trembath-Reichert E, Tully BJ, Huber JA. Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community. ISME J 2021; 15:1192-1206. [PMID: 33273721 PMCID: PMC8115675 DOI: 10.1038/s41396-020-00843-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/27/2020] [Accepted: 11/11/2020] [Indexed: 01/29/2023]
Abstract
The oceanic crustal aquifer is one of the largest habitable volumes on Earth, and it harbors a reservoir of microbial life that influences global-scale biogeochemical cycles. Here, we use time series metagenomic and metatranscriptomic data from a low-temperature, ridge flank environment representative of the majority of global hydrothermal fluid circulation in the ocean to reconstruct microbial metabolic potential, transcript abundance, and community dynamics. We also present metagenome-assembled genomes from recently collected fluids that are furthest removed from drilling disturbances. Our results suggest that the microbial community in the North Pond aquifer plays an important role in the oxidation of organic carbon within the crust. This community is motile and metabolically flexible, with the ability to use both autotrophic and organotrophic pathways, as well as function under low oxygen conditions by using alternative electron acceptors such as nitrate and thiosulfate. Anaerobic processes are most abundant in subseafloor horizons deepest in the aquifer, furthest from connectivity with the deep ocean, and there was little overlap in the active microbial populations between sampling horizons. This work highlights the heterogeneity of microbial life in the subseafloor aquifer and provides new insights into biogeochemical cycling in ocean crust.
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Affiliation(s)
- Lauren M Seyler
- School of Natural and Mathematical Sciences, Stockton University, Galloway, NJ, USA.
- Blue Marble Space Institute of Science, Seattle, WA, USA.
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | | | - Benjamin J Tully
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA
| | - Julie A Huber
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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6
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Martí-Carreras J, Gener AR, Miller SD, Brito AF, Camacho CE, Connor R, Deboutte W, Glickman C, Kristensen DM, Meyer WK, Modha S, Norris AL, Saha S, Belford AK, Biederstedt E, Brister JR, Buchmann JP, Cooley NP, Edwards RA, Javkar K, Muchow M, Muralidharan HS, Pepe-Ranney C, Shah N, Shakya M, Tisza MJ, Tully BJ, Vanmechelen B, Virta VC, Weissman JL, Zalunin V, Efremov A, Busby B. NCBI's Virus Discovery Codeathon: Building "FIVE" -The Federated Index of Viral Experiments API Index. Viruses 2020; 12:v12121424. [PMID: 33322070 PMCID: PMC7764237 DOI: 10.3390/v12121424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/02/2020] [Indexed: 02/05/2023] Open
Abstract
Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. However, some consequences of previously decentralized (unfederated) data are lack of consensus or comparisons between feature annotations. Unifying or displaying alternative annotations should be a priority both for communities with robust entry representation and for nascent communities with burgeoning data sources. To this end, during this three-day continuation of the Virus Hunting Toolkit codeathon series (VHT-2), a new integrated and federated viral index was elaborated. This Federated Index of Viral Experiments (FIVE) integrates pre-existing and novel functional and taxonomy annotations and virus–host pairings. Variability in the context of viral genomic diversity is often overlooked in virus databases. As a proof-of-concept, FIVE was the first attempt to include viral genome variation for HIV, the most well-studied human pathogen, through viral genome diversity graphs. As per the publication of this manuscript, FIVE is the first implementation of a virus-specific federated index of such scope. FIVE is coded in BigQuery for optimal access of large quantities of data and is publicly accessible. Many projects of database or index federation fail to provide easier alternatives to access or query information. To this end, a Python API query system was developed to enhance the accessibility of FIVE.
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Affiliation(s)
- Joan Martí-Carreras
- Laboratory of Clinical and Epidemiological Virology, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, BE3000 Leuven, Belgium; (W.D.); (C.G.); (B.V.)
- Correspondence: (J.M.-C); (A.R.G.); (R.C.); (B.B.)
| | - Alejandro Rafael Gener
- Integrative Molecular and Biomedical Sciences Program, Baylor College of Medicine, Houston, TX 77030, USA
- Margaret M. and Albert B. Alkek Department of Medicine, Nephrology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Genetics, MD Anderson Cancer Center, Houston, TX 77030, USA
- School of Medicine, Universidad Central del Caribe, Bayamón, PR 00960, USA
- Correspondence: (J.M.-C); (A.R.G.); (R.C.); (B.B.)
| | - Sierra D. Miller
- Genetics & Molecular Biology, Millersville University, 40 Dilworth Rd, Millersville, PA 17551, USA;
| | - Anderson F. Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health (YSPH), 60 College Street, New Haven, CT 06510, USA;
| | - Christiam E. Camacho
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA; (C.E.C.); (J.R.B.); (V.Z.); (A.E.)
| | - Ryan Connor
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA; (C.E.C.); (J.R.B.); (V.Z.); (A.E.)
- Correspondence: (J.M.-C); (A.R.G.); (R.C.); (B.B.)
| | - Ward Deboutte
- Laboratory of Clinical and Epidemiological Virology, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, BE3000 Leuven, Belgium; (W.D.); (C.G.); (B.V.)
| | - Cody Glickman
- Laboratory of Clinical and Epidemiological Virology, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, BE3000 Leuven, Belgium; (W.D.); (C.G.); (B.V.)
| | - David M. Kristensen
- Computational Bioscience Program, University of Colorado Anschutz, Aurora, CO 80045, USA;
| | - Wynn K. Meyer
- AAAS Science and Technology Policy Fellow, Office of Data Science Strategy, Division of Program Coordination, Planning, and Strategic Initiatives, Office of the Director, National Institutes of Health, 31 Center Dr., Bethesda, MD 20894, USA;
| | - Sejal Modha
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK;
| | - Alexis L. Norris
- Biotechnology Graduate Program, University of Maryland Global Campus, 1616 McCormick Drive, Largo, MD 20774, USA;
| | - Surya Saha
- Boyce Thompson Institute, Ithaca, NY 14850, USA;
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ 85721, USA
| | - Anna K. Belford
- Laboratory of Cellular Oncology, National Cancer Institute, 37 Convent Dr., Bethesda, MD 20894, USA; (A.K.B.); (M.J.T.)
| | - Evan Biederstedt
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - James Rodney Brister
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA; (C.E.C.); (J.R.B.); (V.Z.); (A.E.)
| | - Jan P. Buchmann
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia;
| | - Nicholas P. Cooley
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15260, USA;
| | - Robert A. Edwards
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia;
| | - Kiran Javkar
- Department of Computer Science, University of Maryland, College Park, MD 20740, USA; (K.J.); (H.S.M.); (N.S.)
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, MD 20740, USA
| | - Michael Muchow
- Novel Microdevices, Nucleic Acids, Baltimore, MD 21202, USA;
| | - Harihara Subrahmaniam Muralidharan
- Department of Computer Science, University of Maryland, College Park, MD 20740, USA; (K.J.); (H.S.M.); (N.S.)
- Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20740, USA
| | | | - Nidhi Shah
- Department of Computer Science, University of Maryland, College Park, MD 20740, USA; (K.J.); (H.S.M.); (N.S.)
| | - Migun Shakya
- Bioscience Division, Bikini Atoll Road, Los Alamos National Laboratory, Los Alamos, NM 87545, USA;
| | - Michael J. Tisza
- Laboratory of Cellular Oncology, National Cancer Institute, 37 Convent Dr., Bethesda, MD 20894, USA; (A.K.B.); (M.J.T.)
| | - Benjamin J. Tully
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA 90089, USA;
| | - Bert Vanmechelen
- Laboratory of Clinical and Epidemiological Virology, KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, BE3000 Leuven, Belgium; (W.D.); (C.G.); (B.V.)
| | - Valerie C. Virta
- AAAS Science & Technology Policy Fellow, National Institutes of Health, Center for Information Technology, 6555 Rock Spring Drive, Bethesda, MD 20817, USA;
| | - JL Weissman
- Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA 90089, USA;
| | - Vadim Zalunin
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA; (C.E.C.); (J.R.B.); (V.Z.); (A.E.)
| | - Alexandre Efremov
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA; (C.E.C.); (J.R.B.); (V.Z.); (A.E.)
| | - Ben Busby
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20894, USA; (C.E.C.); (J.R.B.); (V.Z.); (A.E.)
- DNANexus, 1975 W El Camino Real #204, Mountain View, CA 94040, USA
- Correspondence: (J.M.-C); (A.R.G.); (R.C.); (B.B.)
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Abstract
BACKGROUND Advances in sequencing, assembly, and assortment of contigs into species-specific bins has enabled the reconstruction of genomes from metagenomic data (MAGs). Though a powerful technique, it is difficult to determine whether assembly and binning techniques are accurate when applied to environmental metagenomes due to a lack of complete reference genome sequences against which to check the resulting MAGs. METHODS We compared MAGs derived from an enrichment culture containing ~20 organisms to complete genome sequences of 10 organisms isolated from the enrichment culture. Factors commonly considered in binning software-nucleotide composition and sequence repetitiveness-were calculated for both the correctly binned and not-binned regions. This direct comparison revealed biases in sequence characteristics and gene content in the not-binned regions. Additionally, the composition of three public data sets representing MAGs reconstructed from the Tara Oceans metagenomic data was compared to a set of representative genomes available through NCBI RefSeq to verify that the biases identified were observable in more complex data sets and using three contemporary binning software packages. RESULTS Repeat sequences were frequently not binned in the genome reconstruction processes, as were sequence regions with variant nucleotide composition. Genes encoded on the not-binned regions were strongly biased towards ribosomal RNAs, transfer RNAs, mobile element functions and genes of unknown function. Our results support genome reconstruction as a robust process and suggest that reconstructions determined to be >90% complete are likely to effectively represent organismal function; however, population-level genotypic heterogeneity in natural populations, such as uneven distribution of plasmids, can lead to incorrect inferences.
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Affiliation(s)
- William C. Nelson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Benjamin J. Tully
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA
| | - Jennifer M. Mobberley
- Chemical and Biological Signature Science Group, Pacific Northwest National Laboratory, Richland, WA, USA
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8
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Neely CJ, Graham ED, Tully BJ. MetaSanity: an integrated microbial genome evaluation and annotation pipeline. Bioinformatics 2020; 36:4341-4344. [PMID: 32426808 PMCID: PMC7520038 DOI: 10.1093/bioinformatics/btaa512] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 04/25/2020] [Accepted: 05/13/2020] [Indexed: 11/12/2022] Open
Abstract
SUMMARY As the importance of microbiome research continues to become more prevalent and essential to understanding a wide variety of ecosystems (e.g. marine, built, host associated, etc.), there is a need for researchers to be able to perform highly reproducible and quality analysis of microbial genomes. MetaSanity incorporates analyses from 11 existing and widely used genome evaluation and annotation suites into a single, distributable workflow, thereby decreasing the workload of microbiologists by allowing for a flexible, expansive data analysis pipeline. MetaSanity has been designed to provide separate, reproducible workflows that (i) can determine the overall quality of a microbial genome, while providing a putative phylogenetic assignment, and (ii) can assign structural and functional gene annotations with varying degrees of specificity to suit the needs of the researcher. The software suite combines the results from several tools to provide broad insights into overall metabolic function. Importantly, this software provides built-in optimization for 'big data' analysis by storing all relevant outputs in an SQL database, allowing users to query all the results for the elements that will most impact their research. AVAILABILITY AND IMPLEMENTATION MetaSanity is provided under the GNU General Public License v.3.0 and is available for download at https://github.com/cjneely10/MetaSanity. This application is distributed as a Docker image. MetaSanity is implemented in Python3/Cython and C++. Instructions for its installation and use are available within the GitHub wiki page at https://github.com/cjneely10/MetaSanity/wiki, and additional instructions are available at https://cjneely10.github.io/year-archive/. MetaSanity is optimized for users with limited programing experience. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Elaina D Graham
- Department of Biological Sciences, Los Angeles, CA 90089, USA
| | - Benjamin J Tully
- Department of Biological Sciences, Los Angeles, CA 90089, USA
- Center for Dark Energy Biospheres Investigation, University of Southern California, Los Angeles, CA 90089, USA
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9
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Tully BJ, Graham ED, Heidelberg JF. The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans. Sci Data 2018; 5:170203. [PMID: 29337314 PMCID: PMC5769542 DOI: 10.1038/sdata.2017.203] [Citation(s) in RCA: 263] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 11/13/2017] [Indexed: 02/05/2023] Open
Abstract
Microorganisms play a crucial role in mediating global biogeochemical cycles in the marine environment. By reconstructing the genomes of environmental organisms through metagenomics, researchers are able to study the metabolic potential of Bacteria and Archaea that are resistant to isolation in the laboratory. Utilizing the large metagenomic dataset generated from 234 samples collected during the Tara Oceans circumnavigation expedition, we were able to assemble 102 billion paired-end reads into 562 million contigs, which in turn were co-assembled and consolidated in to 7.2 million contigs ≥2 kb in length. Approximately 1 million of these contigs were binned to reconstruct draft genomes. In total, 2,631 draft genomes with an estimated completion of ≥50% were generated (1,491 draft genomes >70% complete; 603 genomes >90% complete). A majority of the draft genomes were manually assigned phylogeny based on sets of concatenated phylogenetic marker genes and/or 16S rRNA gene sequences. The draft genomes are now publically available for the research community at-large.
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Affiliation(s)
- Benjamin J Tully
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA 90089, USA
| | - Elaina D Graham
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - John F Heidelberg
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA 90089, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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Tully BJ, Wheat CG, Glazer BT, Huber JA. A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer. ISME J 2017; 12:1-16. [PMID: 29099490 PMCID: PMC5739024 DOI: 10.1038/ismej.2017.187] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/19/2017] [Accepted: 09/22/2017] [Indexed: 11/29/2022]
Abstract
The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb3- and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer.
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Affiliation(s)
- Benjamin J Tully
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA
| | - C Geoff Wheat
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Brain T Glazer
- Department of Oceanography, University of Hawaii, Honolulu, HI, USA
| | - Julie A Huber
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA.,Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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Tully BJ, Sachdeva R, Graham ED, Heidelberg JF. 290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology. PeerJ 2017; 5:e3558. [PMID: 28713657 PMCID: PMC5507172 DOI: 10.7717/peerj.3558] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 06/19/2017] [Indexed: 12/05/2022] Open
Abstract
The Tara Oceans Expedition has provided large, publicly-accessible microbial metagenomic datasets from a circumnavigation of the globe. Utilizing several size fractions from the samples originating in the Mediterranean Sea, we have used current assembly and binning techniques to reconstruct 290 putative draft metagenome-assembled bacterial and archaeal genomes, with an estimated completion of ≥50%, and an additional 2,786 bins, with estimated completion of 0–50%. We have submitted our results, including initial taxonomic and phylogenetic assignments, for the putative draft genomes to open-access repositories for the scientific community to use in ongoing research.
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Affiliation(s)
- Benjamin J Tully
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA
| | - Rohan Sachdeva
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States of America
| | - Elaina D Graham
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States of America
| | - John F Heidelberg
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States of America
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12
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Graham ED, Heidelberg JF, Tully BJ. BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation. PeerJ 2017; 5:e3035. [PMID: 28289564 PMCID: PMC5345454 DOI: 10.7717/peerj.3035] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 01/26/2017] [Indexed: 12/20/2022] Open
Abstract
Metagenomics has become an integral part of defining microbial diversity in various environments. Many ecosystems have characteristically low biomass and few cultured representatives. Linking potential metabolisms to phylogeny in environmental microorganisms is important for interpreting microbial community functions and the impacts these communities have on geochemical cycles. However, with metagenomic studies there is the computational hurdle of ‘binning’ contigs into phylogenetically related units or putative genomes. Binning methods have been implemented with varying approaches such as k-means clustering, Gaussian mixture models, hierarchical clustering, neural networks, and two-way clustering; however, many of these suffer from biases against low coverage/abundance organisms and closely related taxa/strains. We are introducing a new binning method, BinSanity, that utilizes the clustering algorithm affinity propagation (AP), to cluster assemblies using coverage with compositional based refinement (tetranucleotide frequency and percent GC content) to optimize bins containing multiple source organisms. This separation of composition and coverage based clustering reduces bias for closely related taxa. BinSanity was developed and tested on artificial metagenomes varying in size and complexity. Results indicate that BinSanity has a higher precision, recall, and Adjusted Rand Index compared to five commonly implemented methods. When tested on a previously published environmental metagenome, BinSanity generated high completion and low redundancy bins corresponding with the published metagenome-assembled genomes.
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Affiliation(s)
- Elaina D Graham
- Department of Biological Sciences, University of Southern California , Los Angeles , CA , USA
| | - John F Heidelberg
- Department of Biological Sciences, University of Southern California , Los Angeles , CA , USA
| | - Benjamin J Tully
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA; Center for Dark Energy Biosphere Investigations, Los Angeles, CA, USA
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Meyer JL, Jaekel U, Tully BJ, Glazer BT, Wheat CG, Lin HT, Hsieh CC, Cowen JP, Hulme SM, Girguis PR, Huber JA. A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge. Sci Rep 2016; 6:22541. [PMID: 26935537 PMCID: PMC4776111 DOI: 10.1038/srep22541] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/15/2016] [Indexed: 11/23/2022] Open
Abstract
The rock-hosted, oceanic crustal aquifer is one of the largest ecosystems on Earth, yet little is known about its indigenous microorganisms. Here we provide the first phylogenetic and functional description of an active microbial community residing in the cold oxic crustal aquifer. Using subseafloor observatories, we recovered crustal fluids and found that the geochemical composition is similar to bottom seawater, as are cell abundances. However, based on relative abundances and functional potential of key bacterial groups, the crustal fluid microbial community is heterogeneous and markedly distinct from seawater. Potential rates of autotrophy and heterotrophy in the crust exceeded those of seawater, especially at elevated temperatures (25 °C) and deeper in the crust. Together, these results reveal an active, distinct, and diverse bacterial community engaged in both heterotrophy and autotrophy in the oxygenated crustal aquifer, providing key insight into the role of microbial communities in the ubiquitous cold dark subseafloor biosphere.
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Affiliation(s)
- Julie L Meyer
- Josephine Bay Paul Center, Marine Biological Laboratory, 7 MBL St., Woods Hole, MA 02543
| | - Ulrike Jaekel
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA 02138
| | - Benjamin J Tully
- Center for Dark Energy Biosphere Investigations, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089
| | - Brian T Glazer
- Department of Oceanography, University of Hawai'i at Mānoa, 1000 Pope Rd., Honolulu, HI 96822
| | - C Geoffrey Wheat
- Global Undersea Research Unit, University of Alaska Fairbanks, P.O. Box 475, Moss Landing, CA 95039
| | - Huei-Ting Lin
- Department of Oceanography, University of Hawai'i at Mānoa, 1000 Pope Rd., Honolulu, HI 96822
| | - Chih-Chiang Hsieh
- Department of Oceanography, University of Hawai'i at Mānoa, 1000 Pope Rd., Honolulu, HI 96822
| | - James P Cowen
- Department of Oceanography, University of Hawai'i at Mānoa, 1000 Pope Rd., Honolulu, HI 96822
| | - Samuel M Hulme
- Moss Landing Marine Laboratory, 8272 Moss Landing Road, Moss Landing, CA 95039
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA 02138
| | - Julie A Huber
- Josephine Bay Paul Center, Marine Biological Laboratory, 7 MBL St., Woods Hole, MA 02543
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Vardakis J, Tully BJ, Guo L, Ventikos Y, Chou D. Investigating hydrocephalus using Multiple-network Poroelastic Theory. Fluids Barriers CNS 2015. [PMCID: PMC4582815 DOI: 10.1186/2045-8118-12-s1-p54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Tully BJ, Sachdeva R, Heidelberg KB, Heidelberg JF. Comparative genomics of planktonic Flavobacteriaceae from the Gulf of Maine using metagenomic data. Microbiome 2014; 2:34. [PMID: 25258679 PMCID: PMC4164334 DOI: 10.1186/2049-2618-2-34] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 08/20/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND The Gulf of Maine is an important biological province of the Northwest Atlantic with high productivity year round. From an environmental Sanger-based metagenome, sampled in summer and winter, we were able to assemble and explore the partial environmental genomes of uncultured members of the class Flavobacteria. Each of the environmental genomes represents organisms that compose less than 1% of the total microbial metagenome. RESULTS Four partial environmental genomes were assembled with varying degrees of estimated completeness (37%-84% complete) and were analyzed from a perspective of gathering information regarding niche partitioning between co-occurring organisms. Comparative genomics revealed potentially important niche partitioning genomic variations, including iron transporters and genes associated with cell attachment and polymer degradation. Analysis of large syntenic regions helped reveal potentially ecologically relevant variations for Flavobacteriaceae in the Gulf of Maine, such as arginine biosynthesis, and identify a putative genomic island incorporating novel exogenous genes from the environment. CONCLUSIONS Biogeographic analysis revealed flavobacteria species with distinct abundance patterns suggesting the presence of local blooms relative to the other species, as well as seasonally selected organisms. The analysis of genomic content for the Gulf of Maine Flavobacteria supports the hypothesis of a particle-associated lifestyle and specifically highlights a number of putative coding sequences that may play a role in the remineralization of particulate organic matter. And lastly, analysis of the underlying sequences for each assembled genome revealed seasonal and nonseasonal variants of specific genes implicating a dynamic interaction between individuals within the species.
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Affiliation(s)
- Benjamin J Tully
- Biological Science, Marine & Environmental Biology, Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles CA 90089, USA
| | - Rohan Sachdeva
- Biological Science, Marine & Environmental Biology, Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles CA 90089, USA
| | - Karla B Heidelberg
- Biological Science, Marine & Environmental Biology, Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles CA 90089, USA
| | - John F Heidelberg
- Biological Science, Marine & Environmental Biology, Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles CA 90089, USA
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Tully BJ, Heidelberg JF. Microbial communities associated with ferromanganese nodules and the surrounding sediments. Front Microbiol 2013; 4:161. [PMID: 23805131 PMCID: PMC3691505 DOI: 10.3389/fmicb.2013.00161] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Accepted: 05/31/2013] [Indexed: 11/16/2022] Open
Abstract
The formation and maintenance of deep-sea ferromanganese/polymetallic nodules still remains a mystery 140 years after their discovery. The wealth of rare metals concentrated in these nodules has spurred global interest in exploring the mining potential of these resources. The prevailing theory of abiotic formation has been called into question and the role of microbial metabolisms in nodule development is now an area of active research. To understand the community structure of microbes associated with nodules and their surrounding sediment, we performed targeted sequencing of the V4 hypervariable region of the 16S rRNA gene from three nodules collected from the central South Pacific. Results have shown that the microbial communities of the nodules are significantly distinct from the communities in the surrounding sediments, and that the interiors of the nodules harbor communities different from the exterior. This suggests not only differences in potential metabolisms between the nodule and sediment communities, but also differences in the dominant metabolisms of interior and exterior communities. We identified several operational taxonomic units (OTUs) unique to both the nodule and sediment environments. The identified OTUs were assigned putative taxonomic identifications, including two OTUs only found associated with the nodules, which were assigned to the α-Proteobacteria. Finally, we explored the diversity of the most assigned taxonomic group, the Thaumarchaea MG-1, which revealed novel OTUs compared to previous research from the region and suggests a potential role as a source of fixed carbon for ammonia oxidizing archaea in the environment.
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Affiliation(s)
- Benjamin J Tully
- Department of Biological Science, Marine and Environmental Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California Los Angeles, CA, USA
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Biddle JF, Sylvan JB, Brazelton WJ, Tully BJ, Edwards KJ, Moyer CL, Heidelberg JF, Nelson WC. Prospects for the study of evolution in the deep biosphere. Front Microbiol 2012; 2:285. [PMID: 22319515 PMCID: PMC3265032 DOI: 10.3389/fmicb.2011.00285] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 12/31/2011] [Indexed: 11/18/2022] Open
Abstract
Since the days of Darwin, scientists have used the framework of the theory of evolution to explore the interconnectedness of life on Earth and adaptation of organisms to the ever-changing environment. The advent of molecular biology has advanced and accelerated the study of evolution by allowing direct examination of the genetic material that ultimately determines the phenotypes upon which selection acts. The study of evolution has been furthered through examination of microbial evolution, with large population numbers, short generation times, and easily extractable DNA. Such work has spawned the study of microbial biogeography, with the realization that concepts developed in population genetics may be applicable to microbial genomes (Martiny et al., 2006; Manhes and Velicer, 2011). Microbial biogeography and adaptation has been examined in many different environments. Here we argue that the deep biosphere is a unique environment for the study of evolution and list specific factors that can be considered and where the studies may be performed. This publication is the result of the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) theme team on Evolution (www.darkenergybiosphere.org).
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Affiliation(s)
- Jennifer F Biddle
- College of Earth, Ocean and the Environment, University of Delaware Lewes, DE, USA
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Abstract
Thaumarchaea, which represent as much as 20% of prokaryotic biomass in the open ocean, have been linked to environmentally relevant biogeochemical processes, such as ammonia oxidation (nitrification) and inorganic carbon fixation. We have used culture-independent methods to study this group because current cultivation limitations have proved a hindrance in studying these organisms. From a metagenomic data set obtained from surface waters from the Gulf of Maine, we have identified 36,111 sequence reads (containing 30 Mbp) likely derived from environmental planktonic Thaumarchaea. Metabolic analysis of the raw sequences and assemblies identified copies of the catalytic subunit required in aerobic ammonia oxidation. In addition, genes that comprise a nearly complete carbon assimilation pathway in the form of the 3-hyroxypropionate/4-hydroxybutyrate cycle were identified. Comparative genomics contrasting the putative environmental thaumarchaeal sequences and 'Candidatus Nitrosopumilus maritimus SCM1' revealed a number of genomic islands absent in the Gulf of Maine population. Analysis of these genomic islands revealed an integrase-associated island also found in distantly related microbial species, variations in the abundance of genes predicted to be important in thaumarchaeal respiratory chain, and the absence of a high-affinity phosphate uptake operon. Analysis of the underlying sequence diversity suggests the presence of at least two dominant environmental populations. Attempts to assemble complete environmental genomes were unsuccessful, but analysis of scaffolds revealed two diverging populations, including a thaumarchaeal-related scaffold with the full urease operon. Ultimately, the analysis revealed a number of insights into the metabolic potential of a predominantly uncultivated lineage of organisms. The predicted functions in the thaumarchaeal metagenomic sequences are directly supported by historic measurements of nutrient concentrations and provide new avenues of research in regards to understanding the role Thaumarchaea play in the environment.
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Affiliation(s)
- Benjamin J Tully
- Department of Biological Sciences, David and Dana Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA.
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