Niche distribution and influence of environmental parameters in marine microbial communities: A systematic review

PeerJ

Volumn 2015, Issue 6, 2015, Pages

  Coutinho, Felipe H ^a,b   Meirelles, Pedro M ^a   Moreira, Ana Paula B ^a   Paranhos, Rodolfo P ^a   Dutilh, Bas E ^a,b,c   Thompson, Fabiano L ^a  

^a FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^b RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^c UTRECHT UNIVERSITY   (Netherlands)

Author keywords

Community ecology; Global ocean; Metagenomics; Microbial ecology; Species interactions

Indexed keywords

CHLOROPHYLL A;

CYANOBACTERIUM; DIAZOTIZATION; ECOLOGICAL NICHE; ENVIRONMENTAL PARAMETERS; GAMMAPROTEOBACTERIA; MARINE SPECIES; MARINOMONAS; META ANALYSIS (TOPIC); METAGENOME; MICROBIAL COMMUNITY; NONHUMAN; PROKARYOTE; REVIEW; SYSTEMATIC REVIEW;

EID: 84945191979     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.1008     Document Type: Review

References (64)

1. Abraham WR, Strompl C, Meyer H, Lindholst S, Moore ER, Christ R, Vancanneyt M, Tindall BJ, Bennasar A, Smit J, Tesar M. 1999. Phylogeny and polyphasic taxonomy of Caulobacter species. Proposal of Maricaulis gen. nov. with Maricaulis maris (Poindexter) comb. nov. as the type species, and emended description of the genera Brevundimonas and Caulobacter. International Journal of Systematic Bacteriology 49(Pt 3):1053-1073 DOI 10.1099/00207713-49-3-1053.
2. Albert S, O'Neil JM, Udy JW, Ahern KS, O'Sullivan CM, Dennison WC. 2005. Blooms of the cyanobacterium Lyngbya majuscula in coastal Queensland, Australia: disparate sites, common factors. Marine Pollution Bulletin 51:428-437 DOI 10.1016/j.marpolbul.2004.10.016.
3. Allison SD, Martiny JB. 2008. Colloquium paper: resistance, resilience, and redundancy in microbial communities. Proceedings of the National Academy of Sciences of the United States of America 105(Suppl):11512-11519 DOI 10.1073/pnas.0801925105.
4. Alves Jr N, Meirelles PM, de Oliveira Santos E, Dutilh B, Silva GG, Paranhos R, Cabral AS, Rezende C, Iida T, deMoura RL, Kruger RH, Pereira RC, Valle R, Sawabe T, Thompson C, Thompson F. 2014. Microbial community diversity and physical-chemical features of the Southwestern Atlantic Ocean. Archives of Microbiology 197(2):165-179 DOI 10.1007/s00203-014-1035-6.
5. Angel R, Matthies D, Conrad R. 2011. Activation of methanogenesis in arid biological soil crusts despite the presence of oxygen. PLoS ONE 6:e20453 DOI 10.1371/journal.pone.0020453.
6. Barberan A, Bates ST, Casamayor EO, Fierer N. 2012. Using network analysis to explore co-occurrence patterns in soil microbial communities. The ISME Journal 6:343-351 DOI 10.1038/ismej.2011.119.
7. Beman JM, Steele JA, Fuhrman JA. 2011. Co-occurrence patterns for abundant marine archaeal and bacterial lineages in the deep chlorophyll maximum of coastal California. The ISME Journal 5:1077-1085 DOI 10.1038/ismej.2010.204.
8. Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B (Methodological) 289-300.
9. Bergman B, Sandh G, Lin S, Larsson J, Carpenter EJ. 2013. Trichodesmium-a widespread marine cyanobacterium with unusual nitrogen fixation properties. FEMS Microbiology Reviews 37:286-302 DOI 10.1111/j.1574-6976.2012.00352.x.
10. Bruce T, Meirelles PM, Garcia G, Paranhos R, Rezende CE, deMoura RL, Filho RF, Coni EO, Vasconcelos AT, Amado Filho G, Hatay M, Schmieder R, Edwards R, Dinsdale E, Thompson FL. 2012. Abrolhos bank reef health evaluated by means of water quality, microbial diversity, benthic cover, and fish biomass data. PLoS ONE 7:e36687 DOI 10.1371/journal.pone.0036687.
11. Carini P, Steindler L, Beszteri S, Giovannoni SJ. 2013. Nutrient requirements for growth of the extreme oligotroph "Candidatus Pelagibacter ubique" HTCC1062 on a defined medium. The ISME Journal 7:592-602 DOI 10.1038/ismej.2012.122.
12. Chaffron S, Rehrauer H, Pernthaler J, von Mering C. 2010. A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Research 20:947-959 DOI 10.1101/gr.104521.109.
13. Danhorn T, Young CR, Delong EF. 2012. Comparison of large-insert, small-insert and pyrosequencing libraries for metagenomic analysis. The ISME Journal 6:2056-2066 DOI 10.1038/ismej.2012.35.
14. Del CarmenMuñoz-Marín M, Luque I, Zubkov MV, Hill PG, Diez J, García-Fernández JM. 2013. Prochlorococcus can use the Pro1404 transporter to take up glucose at nanomolar concentrations in the Atlantic Ocean. Proceedings of the National Academy of Sciences of the United States of America 110:8597-8602 DOI 10.1073/pnas.1221775110.
15. Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM, Furlan M, Desnues C, Haynes M, Li L, McDaniel L, Moran MA, Nelson KE, Nilsson C, Olson R, Paul J, Brito BR, Ruan Y, Swan BK, Stevens R, Valentine DL, Thurber RV, Wegley L, White BA, Rohwer F. 2008. Functional metagenomic profiling of nine biomes. Nature 452:629-632 DOI 10.1038/nature06810.
16. Dumbrell AJ, Nelson M, Helgason T, Dytham C, Fitter AH. 2010. Relative roles of niche and neutral processes in structuring a soil microbial community. The ISME Journal 4:337-345 DOI 10.1038/ismej.2009.122.
17. Eiler A, Heinrich F, Bertilsson S. 2012. Coherent dynamics and association networks among lake bacterioplankton taxa. The ISME Journal 6:330-342 DOI 10.1038/ismej.2011.113.
18. Faust K, Raes J. 2012. Microbial interactions: from networks to models. Nature Reviews Microbiology 10:538-550 DOI 10.1038/nrmicro2832.
19. Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, Raes J, Huttenhower C. 2012. Microbial co-occurence relationships in the human microbiome. PLoS Computational Biology 8:e1002606 DOI 10.1371/journal.pcbi.1002606.
20. Foster KR, Bell T. 2012. Competition, not cooperation, dominates interactions among culturable microbial species. Current Biology 22:1845-1850 DOI 10.1016/j.cub.2012.08.005.
21. Freilich S, Kreimer A, Meilijson I, Gophna U, Sharan R, Ruppin E. 2010. The large-scale organization of the bacterial network of ecological co-occurrence interactions. Nucleic Acids Research 38:3857-3868 DOI 10.1093/nar/gkq118.
22. Friedman J, Alm EJ. 2012. Inferring correlation networks from genomic survey data. PLoS Computational Biology 8:e1002687 DOI 10.1371/journal.pcbi.1002687.
23. Fuhrman J, Steele J. 2008. Community structure of marine bacterioplankton: patterns, networks, and relationships to function. Aquatic Microbial Ecology 53:69-81 DOI 10.3354/ame01222.
24. Gifford SM, Sharma S, Booth M, Moran MA. 2012. Expression patterns reveal niche diversification in a marine microbial assemblage. The ISME Journal 7:281-298 DOI 10.1038/ismej.2012.96.
25. Gilbert JA, Field D, Swift P, Thomas S, Cummings D, Temperton B, Weynberg K, Huse S, Hughes M, Joint I, Somerfield PJ, Muhling M. 2010. The taxonomic and functional diversity of microbes at a temperate coastal site: a "multi-omic" study of seasonal and diel temporal variation. PLoS ONE 5:e15545 DOI 10.1371/journal.pone.0015545.
26. Gilbert JA, Steele JA, Caporaso JG, Steinbrück L, Reeder J, Temperton B, Huse S, McHardy AC, Knight R, Joint I, Somerfield P, Fuhrman JA, Field D. 2012. Defining seasonal marine microbial community dynamics. The ISME Journal 6:298-308 DOI 10.1038/ismej.2011.107.
27. Grasshoff K, Kremling K, Ehrhardt M (eds.) 2009. Methods of seawater analysis. John Wiley & Sons.
28. Gregoracci GB, Nascimento JR, Cabral AS, Paranhos R, Valentin JL, Thompson CC, Thompson FL. 2012. Structuring of bacterioplankton diversity in a large tropical bay. PLoS ONE 7:e31408 DOI 10.1371/journal.pone.0031408.
29. Horner-Devine MC, Silver JM, Leibold MA, Bohannan BJM, Colwell RK, Fuhrman JA, Green JL, Kuske CR, Martiny JBH, Muyzer G, Øvreås L, Reysenbach AL, Smith VH. 2007. A comparison of taxon co-occurrence patterns for macro-and microorganisms. Ecology 88:1345-1353 DOI 10.1890/06-0286.
30. Jeraldo P, Sipos M, Chia N, Brulc JM, Dhillon AS, Konkel ME, Larson CL, Nelson KE, Qu A, Schook LB, Yang F, White BA, Goldenfeld N. 2012. Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes. Proceedings of the National Academy of Sciences of the United States of America 109:9692-9698 DOI 10.1073/pnas.1206721109.
31. Johnson ZI, Zinser ER, Coe A, McNulty NP, Woodward EM, Chisholm SW. 2006. Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science 311:1737-1740 DOI 10.1126/science.1118052.
32. Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, Ding H, Marttinen P, MalmstromRR, Stocker R, Follows MJ, Stepanauskas R, Chisholm SW. 2014. Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science 344:416-420 DOI 10.1126/science.1248575.
33. Langenheder S, Szekely AJ. 2011. Species sorting and neutral processes are both important during the initial assembly of bacterial communities. The ISME Journal 5:1086-1094 DOI 10.1038/ismej.2010.207.
34. Lauro FM, McDougald D, Thomas T, Williams TJ, Egan S, Rice S, Demaere MZ, Ting L, Ertan H, Johnson J, Ferriera S, Lapidus A, Anderson I, Kyrpides N, Munk AC, Detter C, Han CS, Brown MV, Robb FT, Kjelleberg S, Cavicchioli R. 2009. The genomic basis of trophic strategy in marine bacteria. Proceedings of the National Academy of Sciences of the United States of America 106:15527-15533 DOI 10.1073/pnas.0903507106.
35. Levy R, Borenstein E. 2013. Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules. Proceedings of the National Academy of Sciences of the United States of America 110:12804-12809 DOI 10.1073/pnas.1300926110.
36. Luo C, Tsementzi D, Kyrpides N, Read T, Konstantinidis KT. 2012. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS ONE 7:e30087 DOI 10.1371/journal.pone.0030087.
37. Macalady JL, Dattagupta S, Schaperdoth I, Jones DS, Druschel GK, Eastman D. 2008. Niche differentiation among sulfur-oxidizing bacterial populations in cave waters. The ISME Journal 2:590-601 DOI 10.1038/ismej.2008.25.
38. Maire V, Gross N, Börger L, Proulx R, Wirth C, Pontes LDS, Soussana JF, Louault F. 2012. Habitat filtering and niche differentiation jointly explain species relative abundance within grassland communities along fertility and disturbance gradients. New Phytologist 196:497-509 DOI 10.1111/j.1469-8137.2012.04287.x.
39. Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA. 2008. The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386 DOI 10.1186/1471-2105-9-386.
40. Mohagheghi A, Grohmann K, Himmel M, Leighton L, Updegraff DM. 1986. Isolation and characterization of acidothermus-cellulolyticus Gen-Nov, Sp-Nov, a new genus of thermophilic, acidophilic, cellulolytic bacteria. International Journal of Systematic Bacteriology 36:435-443 DOI 10.1099/00207713-36-3-435.
41. Omoregie EO, Crumbliss LL, Bebout BM, Zehr JP. 2004. Determination of nitrogen-fixing phylotypes in Lyngbya sp. and Microcoleus chthonoplastes cyanobacterial mats from Guerrero Negro, Baja California, Mexico. Applied and Environmental Microbiology 70:2119-2128 DOI 10.1128/AEM.70.4.2119-2128.2004.
42. Palla G, Barabasi AL, Vicsek T. 2007. Quantifying social group evolution. Nature 446:664-667 DOI 10.1038/nature05670.
43. Partensky F, Blanchot J, Vaulot D. 1999. Differential distribution and ecology of Prochlorococcus and Synechococcus in oceanic waters: a review. Bulletin-Institut Oceanographique Monaco-Numero Special 19:457-476.
44. Partensky F, Garczarek L. 2010. Prochlorococcus: advantages and limits of minimalism. Annual Review of Marine Science 2:305-331 DOI 10.1146/annurev-marine-120308-081034.
45. Paul D, Bridges S, Burgess SC, Dandass Y, Lawrence ML. 2008. Genome sequence of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5T. Journal of Bacteriology 190:5531-5532 DOI 10.1128/JB.00614-08.
46. Peng J, Lu Z, Rui J, Lu Y. 2008. Dynamics of the methanogenic archaeal community during plant residue decomposition in an anoxic rice field soil. Applied and Environmental Microbiology 74:2894-2901 DOI 10.1128/AEM.00070-08.
47. Pontarp M, Canback B, Tunlid A, Lundberg P. 2012. Phylogenetic analysis suggests that habitat filtering is structuring marine bacterial communities across the globe. Microbial Ecology 64:8-17 DOI 10.1007/s00248-011-0005-7.
48. Reddy KJ, Haskell JB, Sherman DM, Sherman LA. 1993. Unicellular, aerobic nitrogen-fixing cyanobacteria of the genus Cyanothece. Journal of Bacteriology 175:1284-1292.
49. Rice D, Mazur BJ, Haselkorn R. 1982. Isolation and physical mapping of nitrogen fixation genes from the cyanobacterium Anabaena 7120. Journal of Biological Chemistry 257:13157-13163.
50. Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, Arellano A, Coleman M, Hauser L, Hess WR, Johnson ZI, Land M, Lindell D, Post AF, Regala W, Shah M, Shaw SL, Steglich C, Sullivan MB, Ting CS, Tolonen A, Webb EA, Zinser ER, Chisholm SW. 2003. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424:1042-1047 DOI 10.1038/nature01947.
51. Ruan Q, Dutta D, Schwalbach MS, Steele JA, Fuhrman JA, Sun F. 2006. Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors. Bioinformatics 22:2532-2538 DOI 10.1093/bioinformatics/btl417.
52. Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T. 2012. A travel guide to Cytoscape plugins. Nature Methods 9:1069-1076 DOI 10.1038/nmeth.2212.
53. Sanudo-Wilhelmy SA, Kustka AB, Gobler CJ, Hutchins DA, Yang M, Lwiza K, Burns J, Capone DG, Raven JA, Carpenter EJ. 2001. Phosphorus limitation of nitrogen fixation by Trichodesmium in the central Atlantic Ocean. Nature 411:66-69 DOI 10.1038/35075041.
54. Scanlan DJ, Ostrowski M, Mazard S, Dufresne A, Garczarek L, Hess WR, Post AF, Hagemann M, Paulsen I, Partensky F. 2009. Ecological genomics of marine picocyanobacteria. Microbiology and Molecular Biology Reviews 73:249-299 DOI 10.1128/MMBR.00035-08.
55. Solonenko SA, Ignacio-Espinoza JC, Alberti A, Cruaud C, Hallam S, Konstantinidis K, Tyson G, Wincker P, Sullivan MB. 2013. Sequencing platform and library preparation choices impact viral metagenomes. BMC Genomics 14:320 DOI 10.1186/1471-2164-14-320.
56. Steele JA, Countway PD, Xia L, Vigil PD, Beman JM, Kim DY, Chow C-EET, Sachdeva R, Jones AC, Schwalbach MS, Rose JM, Hewson I, Patel A, Sun FZ, Caron DA, Fuhrman JA. 2011. Marine bacterial, archaeal and protistan association networks reveal ecological linkages. The ISME Journal 5:1414-1425 DOI 10.1038/ismej.2011.24.
57. Stegen JC, Lin X, Konopka AE, Fredrickson JK. 2012. Stochastic and deterministic assembly processes in subsurface microbial communities. The ISME Journal 6:1653-1664 DOI 10.1038/ismej.2012.22.
58. Thompson CC, Silva GG, Vieira NM, Edwards R, Vicente AC, Thompson FL. 2013. Genomic taxonomy of the genus Prochlorococcus. Microbial Ecology 66:752-762 DOI 10.1007/s00248-013-0270-8.
59. Tripp HJ. 2013. The unique metabolism of SAR11 aquatic bacteria. Journal of Microbiology 51:147-153 DOI 10.1007/s12275-013-2671-2.
60. Ulrich W, Hajdamowicz I, Zalewski M, Stańska M, Ciurzycki W, Tykarski P. 2009. Species assortment or habitat filtering: a case study of spider communities on lake islands. Ecological Research 25:375-381 DOI 10.1007/s11284-009-0661-y.
61. Willner D, Thurber RV, Rohwer F. 2009. Metagenomic signatures of 86 microbial and viral metagenomes. Environmental Microbiology 11(7):1752-1766 DOI 10.1111/j.1462-2920.2009.01901.x.
62. Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, Bryant DA, Robb F, Colman A, Tallon LJ, Badger JH, Madupu R, Ward NL, Eisen JA. 2009. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS ONE 4:e4207 DOI 10.1371/journal.pone.0004207.
63. Yachi S, Loreau M. 1999. Biodiversity and ecosystem productivity in a fluctuating environment: the insurance hypothesis. Proceedings of the National Academy of Sciences of the United States of America 96:1463-1468 DOI 10.1073/pnas.96.4.1463.
64. Zubkov MV, Fuchs BM, Tarran GA, Burkill PH, Amann R. 2003. High rate of uptake of organic nitrogen compounds by Prochlorococcus cyanobacteria as a key to their dominance in oligotrophic oceanic waters. Applied and Environmental Microbiology 69:1299-1304 DOI 10.1128/AEM.69.2.1299-1304.2003.