Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents

FEMS Microbiology Ecology

Volumn 91, Issue 1, 2015, Pages 1-11

  Anderson, Rika E ^a,b   Sogin, Mitchell L ^c   Baross, John A ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^c MARINE BIOLOGICAL LABORATORY   (United States)

Author keywords

Biogeography; Hydrothermal vents; Rare biosphere

Indexed keywords

ABUNDANCE; BIOGEOGRAPHY; BIOSPHERE; COMMUNITY STRUCTURE; DEEP SEA; EUKARYOTE; HYDROTHERMAL VENT; MICROBIAL COMMUNITY; RARE SPECIES; SULFIDE;

ARCHAEA; BACTERIA (MICROORGANISMS);

RNA 16S; SEA WATER;

ARCHAEON; BACTERIUM; BIODIVERSITY; DNA SEQUENCE; ECOLOGY; ECOSYSTEM; GENETICS; HEAT; HYDROTHERMAL VENT; MICROBIAL CONSORTIUM; MICROBIOLOGY; NUCLEOTIDE SEQUENCE; PHYLOGENY;

ARCHAEA; BACTERIA; BASE SEQUENCE; BIODIVERSITY; ECOLOGY; ECOSYSTEM; HOT TEMPERATURE; HYDROTHERMAL VENTS; MICROBIAL CONSORTIA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEAWATER; SEQUENCE ANALYSIS, DNA;

EID: 84940386185     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1093/femsec/fiu016     Document Type: Article

References (49)

1. Allen EE, Tyson GW, Whitaker RJ, et al. Genome dynamics in a natural archaeal population. P Natl Acad Sci USA 2007;104:1883-8.
2. Aller JY, Kemp PF. Are Archaea inherently less diverse than Bacteria in the same environments? FEMS Microbiol Ecol 2008;65:74-87.
3. Anderson RE, Beltrán MT, Hallam SJ, et al. Microbial community structure across fluid gradients in the Juan de Fuca Ridge hydrothermal system. FEMS Microbiol Ecol 2013;83:324-39.
4. Anderson RE, Brazelton WJ, Baross JA. Using CRISPRs as a metagenomic tool to identify microbial hosts of a diffuse flow hydrothermal vent viral assemblage. FEMS Microbiol Ecol 2011;77:120-33.
5. Baas Becking L. Geobiologie of Inleiding Tot de Milieukunde [Geobiology or Introduction to the Science of the Environment]. The Hague, Netherlands: W.P. Van Stockum & Zoon, 1934.
6. Beiko RG, Harlow TJ, Ragan MA. Highways of gene sharing in prokaryotes. P Natl Acad Sci USA 2005;102:14332-7.
7. Berger SA, Krompass D, Stamatakis A. Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood. Syst Biol 2011;60:291-302.
8. Brown JH. On the relationship between abundance and distribution of species. Am Nat 1984;124:255-79.
9. Clarke KR, Gorley RN. PRIMER v6: User Manual/tutorial. Plymouth, UK: Primer-E Ltd, 2006.
10. Deming J, Baross J. Deep-sea smokers: windows to a subsurface biosphere? Geochim Cosmochim Ac 1993;57:3219-30.
11. Edgar RC. Search and clustering orders ofmagnitude faster than BLAST. Bioinformatics 2010;26:2460-1.
12. Embley RW, Baker ET, Chadwick WW, et al. Explorations of Mariana Arc volcanoes reveal new hydrothermal systems. Eos T Am Geophys Un 2004;85:37.
13. Flores GE, Campbell JH, Kirshtein JD, et al. Microbial community structure of hydrothermal deposits from geochemically different vent fields along the Mid-Atlantic Ridge. EnvironMicrobiol 2011;13:2158-71.
14. Flores GE, Shakya M, Meneghin J, et al. Inter-field variability in the microbial communities of hydrothermal vent deposits from a back-arc basin. Geobiology 2012;10:333-46.
15. Frigaard N-U, Martinez A, Mincer TJ, et al. Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea. Nature 2006;439:847-50.
16. Fuhrman JA. Microbial community structure and its functional implications. Nature 2009;459:193-9.
17. Galand PE, Casamayor EO, Kirchman DL, et al. Ecology of the rare microbial biosphere of the Arctic Ocean. P Natl Acad Sci USA 2009;106:22427-32.
18. Gibbons SM, Caporaso JG, Pirrung M, et al. Evidence for a persistent microbial seed bank throughout the global ocean. P Natl Acad Sci USA 2013;110:4651-5.
19. Hanson CA, Fuhrman JA, Horner-Devine MC, et al. Beyond biogeographic patterns: processes shaping the microbial landscape. Nat Rev Microbiol 2012;10:497-506.
20. Holden JF, Takai K, Summit M, et al. Diversity among three novel groups of hyperthermophilic deep-sea Thermococcus species from three sites in the northeastern Pacific Ocean. FEMS Microbiol Ecol 2001;36:51-60.
21. Huber JA, Butterfield DA, Baross JA. Temporal changes in archaeal diversity and chemistry in a mid-ocean ridge subseafloor habitat. Appl Environ Microb 2002;68: 1585-94.
22. Huber JA, Butterfield DA, Baross JA. Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption. FEMS Microbiol Ecol 2003;43:393-409.
23. Huber JA, Butterfield DA, Baross JA. Diversity and distribution of subseafloor Thermococcales populations in diffuse hydrothermal vents at an active deep-sea volcano in the northeast Pacific Ocean. J Geophys Res 2006;111:G04016.
24. Huber JA, Cantin H V, Huse SM, et al. Isolated communities of Epsilonproteobacteria in hydrothermal vent fluids of the Mariana Arc seamounts. FEMS Microbiol Ecol 2010;73:538-49.
25. Huber JA, Johnson HP, Butterfield DA, et al. Microbial life in ridge flank crustal fluids. Environ Microbiol 2006;8:88-99.
26. Huber JA, Mark Welch DB, Morrison HG, et al. Microbial population structures in the deep marine biosphere. Science 2007;318:97-100.
27. Huse SM, Dethlefsen L, Huber JA, et al. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet 2008;4:e1000255.
28. Huse SM, Huber JA, Morrison HG, et al. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 2007;8:R143.
29. Kelley DS, Baross JA, Delaney JR. Volcanoes, fluids, and life at mid-ocean ridge spreading centers. Annu Rev Earth Pl Sc 2002;30:385-491.
30. Koonin EV, Makarova KS, Aravind L. Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol 2001;55:709-42.
31. Kormas KA, Tivey MK, Von Damm K, et al. Bacterial and archaeal phylotypes associated with distinct mineralogical layers of a white smoker spire from a deep-sea hydrothermal vent site (9N, East Pacific Rise). Environ Microbiol 2006;8:909-20.
32. Martiny JBH, Bohannan BJ, Brown JH, et al. Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 2006;4:102-12.
33. Nemergut DR, Costello EK, Hamady M, et al. Global patterns in the biogeography of bacterial taxa. Environ Microbiol 2011;13:135-44.
34. Nercessian O, Reysenbach A-L, Prieur D, et al. Archaeal diversity associated with in situ samplers deployed on hydrothermal vents on the East Pacific Rise (13N). Environ Microbiol 2003;5:492-502.
35. Opatkiewicz AD, Butterfield DA, Baross JA. Individual hydrothermal vents at Axial Seamount harbor distinct subseafloor microbial communities. FEMS Microbiol Ecol 2009;70:81-92.
36. Pedrós-Alió C. Marine microbial diversity: can it be determined? Trends Microbiol 2006;14:257-63.
37. Pruesse E, Peplies J, Glöckner FO. SINA: accurate highthroughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012;28:1823-9.
38. Quast C, Pruesse E, Yilmaz P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 2013;41:D590-6.
39. R. Core Team. R: a language and environment for statistical computing, R Foundation for Statistical Computing, Vienna, Austria, 2014 http://www.R-project.org.
40. Schloss PD, Westcott SL, Ryabin T, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microb 2009;75:7537-41.
41. Schrenk MO, Kelley DS, Delaney JR, et al. Incidence and diversity of microorganisms within thewalls of an active deep-sea sulfide chimney. Appl Environ Microb 2003;69:3580-92.
42. Slobodkin A, Campbell B, Cary SC, et al. Evidence for the presence of thermophilic Fe(III)-reducing microorganisms in deep-sea hydrothermal vents at 13 degrees N (East Pacific Rise). FEMS Microbiol Ecol 2001;36:235-43.
43. Sogin ML, Morrison HG, Huber JA, et al. Microbial diversity in the deep sea and the underexplored 'rare biosphere'. P Natl Acad Sci USA 2006;103:12115-20.
44. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006;22:2688-90.
45. Sul WJ, Oliver TA, Ducklow HW, et al. Marine bacteria exhibit a bipolar distribution. P Natl Acad Sci USA 2013;110: 2342-7.
46. SummitM, Baross JA. A novel microbial habitat in themid-ocean ridge subseafloor. P Natl Acad Sci USA 2001;98:2158-63.
47. Takai K, Horikoshi K. Genetic diversity of archaea in deepsea hydrothermal vent environments. Genetics 1999;152: 1285-97.
48. Takai K, Komatsu T, Inagaki F, et al. Distribution of archaea in a black smoker chimney structure. Appl Environ Microb 2001;67:3618-29.
49. Vergin K, Done B, Carlson C, et al. Spatiotemporal distributions of rare bacterioplankton populations indicate adaptive strategies in the oligotrophic ocean. AquatMicrob Ecol 2013;71:1-13.