Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly

Llorens–Marès, Tomàs; Liu, Zhenfeng; Allen, Lisa Zeigler; Rusch, Douglas B.; Craig, Matthew T.; Dupont, Chris L.; Bryant, Donald A.; Casamayor, Emilio O.

doi:10.1038/ismej.2016.93

Title: Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly

Journal Article · Fri Jul 08 00:00:00 EDT 2016 · The ISME Journal

DOI:https://doi.org/10.1038/ismej.2016.93· OSTI ID:1535036

Llorens–Marès, Tomàs; Liu, Zhenfeng; Allen, Lisa Zeigler; Rusch, Douglas B.; Craig, Matthew T.; Dupont, Chris L.; Bryant, Donald A.; Casamayor, Emilio O.

Not provided.

Cite

Export

Save

Research Organization:: Pennsylvania State Univ., University Park, PA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

DOE Contract Number:: FG02-94ER20137

OSTI ID:: 1535036

Journal Information:: The ISME Journal, Vol. 11, Issue 1; ISSN 1751-7362

Publisher:: Nature Publishing Group

Country of Publication:: United States

Language:: English

References (66)

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes Albertsen, Mads; Hugenholtz, Philip; Skarshewski, Adam Nature Biotechnology, Vol. 31, Issue 6 https://doi.org/10.1038/nbt.2579	journal	May 2013
Horizontal Gene Exchange in Environmental Microbiota Aminov, Rustam I. Frontiers in Microbiology, Vol. 2 https://doi.org/10.3389/fmicb.2011.00158	journal	January 2011
Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities Andersson, A. F.; Banfield, J. F. Science, Vol. 320, Issue 5879 https://doi.org/10.1126/science.1157358	journal	May 2008
Bacterial iron homeostasis Andrews, Simon C.; Robinson, Andrea K.; Rodríguez-Quiñones, Francisco FEMS Microbiology Reviews, Vol. 27, Issue 2-3 https://doi.org/10.1016/S0168-6445(03)00055-X	journal	June 2003
Euxinic Freshwater Hypolimnia Promote Bacterial Endemicity in Continental Areas Barberán, Albert; Casamayor, Emilio O. Microbial Ecology, Vol. 61, Issue 2 https://doi.org/10.1007/s00248-010-9775-6	journal	November 2010
Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analyses Bhaya, Devaki; Grossman, Arthur R.; Steunou, Anne-Soisig The ISME Journal, Vol. 1, Issue 8 https://doi.org/10.1038/ismej.2007.46	journal	October 2007
Prochlorococcus: the structure and function of collective diversity Biller, Steven J.; Berube, Paul M.; Lindell, Debbie Nature Reviews Microbiology, Vol. 13, Issue 1 https://doi.org/10.1038/nrmicro3378	journal	December 2014
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data Carver, T.; Harris, S. R.; Berriman, M. Bioinformatics, Vol. 28, Issue 4 https://doi.org/10.1093/bioinformatics/btr703	journal	December 2011
DNAPlotter: circular and linear interactive genome visualization Carver, T.; Thomson, N.; Bleasby, A. Bioinformatics, Vol. 25, Issue 1 https://doi.org/10.1093/bioinformatics/btn578	journal	November 2008
Identification of and Spatio-Temporal Differences between Microbial Assemblages from Two Neighboring Sulfurous Lakes: Comparison by Microscopy and Denaturing Gradient Gel Electrophoresis Casamayor, E. O.; Schafer, H.; Baneras, L. Applied and Environmental Microbiology, Vol. 66, Issue 2 https://doi.org/10.1128/AEM.66.2.499-508.2000	journal	February 2000
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis Castresana, J. Molecular Biology and Evolution, Vol. 17, Issue 4 https://doi.org/10.1093/oxfordjournals.molbev.a026334	journal	April 2000
A Novel Photosynthetic Strategy for Adaptation to Low-Iron Aquatic Environments Chauhan, Devendra; Folea, I. Mihaela; Jolley, Craig C. Biochemistry, Vol. 50, Issue 5 https://doi.org/10.1021/bi1009425	journal	February 2011
The Origins of Ecological Diversity in Prokaryotes Cohan, Frederick M.; Koeppel, Alexander F. Current Biology, Vol. 18, Issue 21 https://doi.org/10.1016/j.cub.2008.09.014	journal	November 2008
Discovery of a protein phosphatase activity encoded in the genome of bacteriophage λ. Probable identity with open reading frame 221 Cohen, P. T. W.; Cohen, P. Biochemical Journal, Vol. 260, Issue 3 https://doi.org/10.1042/bj2600931	journal	June 1989
Evidence for cyanophages active against bloom-forming freshwater cyanobacteria Deng, Li; Hayes, Paul K. Freshwater Biology, Vol. 53, Issue 6 https://doi.org/10.1111/j.1365-2427.2007.01947.x	journal	June 2008
Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage Dupont, Chris L.; Rusch, Douglas B.; Yooseph, Shibu The ISME Journal, Vol. 6, Issue 6 https://doi.org/10.1038/ismej.2011.189	journal	December 2011
MUSCLE: multiple sequence alignment with high accuracy and high throughput Edgar, R. C. Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797 https://doi.org/10.1093/nar/gkh340	journal	March 2004
Phylogeny of the genus Chlorobium based on 16S rDNA sequence Figueras, Jordi B.; Garcia-Gil, L. Jesus; Abella, Carles A. FEMS Microbiology Letters, Vol. 152, Issue 1 https://doi.org/10.1111/j.1574-6968.1997.tb10405.x	journal	July 1997
Marine viruses and their biogeochemical and ecological effects Fuhrman, Jed A. Nature, Vol. 399, Issue 6736 https://doi.org/10.1038/21119	journal	June 1999
Consed: A Graphical Tool for Sequence Finishing Gordon, David; Abajian, Chris; Green, Phil Genome Research, Vol. 8, Issue 3 https://doi.org/10.1101/gr.8.3.195	journal	March 1998
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats Grissa, I.; Vergnaud, G.; Pourcel, C. Nucleic Acids Research, Vol. 35, Issue Web Server https://doi.org/10.1093/nar/gkm360	journal	May 2007
Dominance of a clonal green sulfur bacterial population in a stratified lake: Clonal dominance in microbial lake community Gregersen, Lea H.; Habicht, Kirsten S.; Peduzzi, Sandro FEMS Microbiology Ecology, Vol. 70, Issue 1 https://doi.org/10.1111/j.1574-6941.2009.00737.x	journal	October 2009
genoPlotR: comparative gene and genome visualization in R Guy, L.; Roat Kultima, J.; Andersson, S. G. E. Bioinformatics, Vol. 26, Issue 18 https://doi.org/10.1093/bioinformatics/btq413	journal	July 2010
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood Guindon, Stéphane; Gascuel, Olivier Systematic Biology, Vol. 52, Issue 5 https://doi.org/10.1080/10635150390235520	journal	October 2003
Comparative proteomics and activity of a green sulfur bacterium through the water column of Lake Cadagno, Switzerland: Comparative proteomics in Lake Cadagno Habicht, Kirsten S.; Miller, Mette; Cox, Raymond P. Environmental Microbiology, Vol. 13, Issue 1 https://doi.org/10.1111/j.1462-2920.2010.02321.x	journal	August 2010
phyloXML: XML for evolutionary biology and comparative genomics Han, Mira V.; Zmasek, Christian M. BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-356	journal	October 2009
Specific Gene bciD for C7-Methyl Oxidation in Bacteriochlorophyll e Biosynthesis of Brown-Colored Green Sulfur Bacteria Harada, Jiro; Mizoguchi, Tadashi; Satoh, Souichirou PLoS ONE, Vol. 8, Issue 4 https://doi.org/10.1371/journal.pone.0060026	journal	April 2013
Delineation of the virulence-related locus (vrl) of Dichelobacter nodosus Haring, V.; Billington, S. J.; Wright, C. L. Microbiology, Vol. 141, Issue 9 https://doi.org/10.1099/13500872-141-9-2081	journal	September 1995
Characterization of the ferrous iron uptake system of Escherichia coli. Kammler, M.; Schön, C.; Hantke, K. Journal of Bacteriology, Vol. 175, Issue 19 https://doi.org/10.1128/jb.175.19.6212-6219.1993	journal	October 1993
Genomic analysis of bacteriophage PBECO4 infecting Escherichia coli O157:H7 Kim, Min Soo; Hong, Sung Sik; Park, Kwangseo Archives of Virology, Vol. 158, Issue 11 https://doi.org/10.1007/s00705-013-1718-3	journal	May 2013
Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential Klatt, Christian G.; Wood, Jason M.; Rusch, Douglas B. The ISME Journal, Vol. 5, Issue 8 https://doi.org/10.1038/ismej.2011.73	journal	June 2011
Analyses of the <i>vrl</i> Gene Cluster in <i>Desulfococcus multivorans</i>: Homologous to the Virulence-Associated Locus of the Ovine Footrot Pathogen <i>Dichelobacter nodosus</i> Strain A198 Knaust, Florian; Kube, Michael; Reinhardt, Richard Journal of Molecular Microbiology and Biotechnology, Vol. 13, Issue 1-3 https://doi.org/10.1159/000103607	journal	January 2007
PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses Lanfear, R.; Calcott, B.; Ho, S. Y. W. Molecular Biology and Evolution, Vol. 29, Issue 6 https://doi.org/10.1093/molbev/mss020	journal	January 2012
Transfer of photosynthesis genes to and from Prochlorococcus viruses Lindell, D.; Sullivan, M. B.; Johnson, Z. I. Proceedings of the National Academy of Sciences, Vol. 101, Issue 30 https://doi.org/10.1073/pnas.0401526101	journal	July 2004
Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics Llorens-Marès, Tomàs; Yooseph, Shibu; Goll, Johannes The ISME Journal, Vol. 9, Issue 7 https://doi.org/10.1038/ismej.2014.254	journal	January 2015
High Bacterial Diversity and Phylogenetic Novelty in Dark Euxinic Freshwaters Analyzed by 16S Tag Community Profiling Llorens-Marès, Tomàs; Triadó-Margarit, Xavier; Borrego, Carles M. Microbial Ecology, Vol. 71, Issue 3 https://doi.org/10.1007/s00248-015-0696-2	journal	November 2015
Insights derived from the structures of the Ser/Thr phosphatases calcineurin and protein phosphatase 1 Lohse, Dl; Denu, Jm; Dixon, Je Structure, Vol. 3, Issue 10 https://doi.org/10.1016/S0969-2126(01)00234-9	journal	October 1995
TheViral MetaGenome Annotation Pipeline (VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data Lorenzi, Hernan A.; Hoover, Jeff; Inman, Jason Standards in Genomic Sciences, Vol. 4, Issue 3 https://doi.org/10.4056/sigs.1694706	journal	June 2011
Individual genome assembly from complex community short-read metagenomic datasets Luo, Chengwei; Tsementzi, Despina; Kyrpides, Nikos C. The ISME Journal, Vol. 6, Issue 4 https://doi.org/10.1038/ismej.2011.147	journal	October 2011
The biochemical basis for structural diversity in the carotenoids of chlorophototrophic bacteria Maresca, Julia A.; Graham, Joel E.; Bryant, Donald A. Photosynthesis Research, Vol. 97, Issue 2 https://doi.org/10.1007/s11120-008-9312-3	journal	June 2008
Isorenieratene Biosynthesis in Green Sulfur Bacteria Requires the Cooperative Actions of Two Carotenoid Cyclases Maresca, J. A.; Romberger, S. P.; Bryant, D. A. Journal of Bacteriology, Vol. 190, Issue 19 https://doi.org/10.1128/JB.00758-08	journal	August 2008
Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities Martín, Héctor García; Ivanova, Natalia; Kunin, Victor Nature Biotechnology, Vol. 24, Issue 10 https://doi.org/10.1038/nbt1247	journal	September 2006
Occurrence of phosphate acquisition genes in Prochlorococcus cells from different ocean regions Martiny, Adam C.; Huang, Ying; Li, Weizhong Environmental Microbiology, Vol. 11, Issue 6 https://doi.org/10.1111/j.1462-2920.2009.01860.x	journal	June 2009
Biased biological functions of horizontally transferred genes in prokaryotic genomes Nakamura, Yoji; Itoh, Takeshi; Matsuda, Hideo Nature Genetics, Vol. 36, Issue 7 https://doi.org/10.1038/ng1381	journal	June 2004
SyntTax: a web server linking synteny to prokaryotic taxonomy Oberto, Jacques BMC Bioinformatics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2105-14-4	journal	January 2013
Lateral gene transfer and the nature of bacterial innovation Ochman, Howard; Lawrence, Jeffrey G.; Groisman, Eduardo A. Nature, Vol. 405, Issue 6784 https://doi.org/10.1038/35012500	journal	May 2000
GenomeMatcher: A graphical user interface for DNA sequence comparison Ohtsubo, Yoshiyuki; Ikeda-Ohtsubo, Wakako; Nagata, Yuji BMC Bioinformatics, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2105-9-376	journal	September 2008
Phylogeny and molecular fingerprinting of green sulfur bacteria Overmann, J.; Tuschak, Christian Archives of Microbiology, Vol. 167, Issue 5 https://doi.org/10.1007/s002030050448	journal	April 1997
Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity Palenik, B.; Ren, Q.; Tai, V. Environmental Microbiology, Vol. 11, Issue 2 https://doi.org/10.1111/j.1462-2920.2008.01772.x	journal	February 2009
Horizontal gene transfer and the evolution of bacterial and archaeal population structure Polz, Martin F.; Alm, Eric J.; Hanage, William P. Trends in Genetics, Vol. 29, Issue 3 https://doi.org/10.1016/j.tig.2012.12.006	journal	March 2013
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes Pruesse, Elmar; Peplies, Jörg; Glöckner, Frank Oliver Bioinformatics, Vol. 28, Issue 14 https://doi.org/10.1093/bioinformatics/bts252	journal	May 2012
Shifting the genomic gold standard for the prokaryotic species definition Richter, Michael; Rosselló-Móra, Ramon Proceedings of the National Academy of Sciences, Vol. 106, Issue 45 https://doi.org/10.1073/pnas.0906412106	journal	October 2009
Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation Rocap, Gabrielle; Larimer, Frank W.; Lamerdin, Jane Nature, Vol. 424, Issue 6952 https://doi.org/10.1038/nature01947	journal	August 2003
Viruses manipulate the marine environment Rohwer, Forest; Thurber, Rebecca Vega Nature, Vol. 459, Issue 7244 https://doi.org/10.1038/nature08060	journal	May 2009
Characterization of Prochlorococcus clades from iron-depleted oceanic regions Rusch, D. B.; Martiny, A. C.; Dupont, C. L. Proceedings of the National Academy of Sciences, Vol. 107, Issue 37 https://doi.org/10.1073/pnas.1009513107	journal	August 2010
Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori Saunders, Nigel J.; Boonmee, Prawit; Peden, John F. BMC Genomics, Vol. 6, Issue 1 https://doi.org/10.1186/1471-2164-6-9	journal	January 2005
Photosystem I gene cassettes are present in marine virus genomes Sharon, Itai; Alperovitch, Ariella; Rohwer, Forest Nature, Vol. 461, Issue 7261 https://doi.org/10.1038/nature08284	journal	August 2009
Halotolerant Cyanobacterium Aphanothece halophytica Contains an Na ⁺ -dependent F ₁ F ₀ -ATP Synthase with a Potential Role in Salt-stress Tolerance Soontharapirakkul, Kanteera; Promden, Worrawat; Yamada, Nana Journal of Biological Chemistry, Vol. 286, Issue 12 https://doi.org/10.1074/jbc.M110.208892	journal	January 2011
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models Stamatakis, Alexandros Bioinformatics, Vol. 22, Issue 21 https://doi.org/10.1093/bioinformatics/btl446	journal	August 2006
Genetic Linkage and Horizontal Gene Transfer, the Roots of the Antibiotic Multi -Resistance Problem Summers, Anne O. Animal Biotechnology, Vol. 17, Issue 2 https://doi.org/10.1080/10495390600957217	journal	December 2006
Community structure and metabolism through reconstruction of microbial genomes from the environment Tyson, Gene W.; Chapman, Jarrod; Hugenholtz, Philip Nature, Vol. 428, Issue 6978 https://doi.org/10.1038/nature02340	journal	February 2004
Protein serine/threonine phosphatases Ernest Villafranca, J.; Kissinger, Charles R.; Parge, Hans E. Current Opinion in Biotechnology, Vol. 7, Issue 4 https://doi.org/10.1016/S0958-1669(96)80114-5	journal	August 1996
CRISPR–Cas systems: beyond adaptive immunity Westra, Edze R.; Buckling, Angus; Fineran, Peter C. Nature Reviews Microbiology, Vol. 12, Issue 5 https://doi.org/10.1038/nrmicro3241	journal	April 2014
Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches Wiedenbeck, Jane; Cohan, Frederick M. FEMS Microbiology Reviews, Vol. 35, Issue 5 https://doi.org/10.1111/j.1574-6976.2011.00292.x	journal	September 2011
Comparative genomics and functional analysis of niche-specific adaptation in Pseudomonas putida Wu, Xiao; Monchy, Sébastien; Taghavi, Safiyh FEMS Microbiology Reviews, Vol. 35, Issue 2 https://doi.org/10.1111/j.1574-6976.2010.00249.x	journal	March 2011
Abundant SAR11 viruses in the ocean Zhao, Yanlin; Temperton, Ben; Thrash, J. Cameron Nature, Vol. 494, Issue 7437 https://doi.org/10.1038/nature11921	journal	February 2013

Similar Records

A paralog of a bacteriochlorophyll biosynthesis enzyme catalyzes the formation of 1,2-dihydrocarotenoids in green sulfur bacteria

Journal Article · Sat Sep 01 00:00:00 EDT 2018 · Journal of Biological Chemistry · OSTI ID:1535036

Canniffe, Daniel P.; Thweatt, Jennifer L.; Gomez Maqueo Chew, Aline; +2 more

Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions

Journal Article · Fri Jan 15 00:00:00 EST 2021 · The ISME Journal · OSTI ID:1535036

Berg, Maureen; Goudeau, Danielle; Olmsted, Charles; +7 more

Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes

Journal Article · Tue Oct 15 00:00:00 EDT 2019 · Frontiers in Genetics · OSTI ID:1535036

Guo, Jiarong; Quensen, John F.; Sun, Yanni; +4 more

Related Subjects

Environmental Sciences & Ecology
Microbiology

Title: Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly

Citation Formats

References (66)

Similar Records

Related Subjects