Characterizing microbial communities through space and time

Current Opinion in Biotechnology

Volumn 23, Issue 3, 2012, Pages 431-436

  Gonzalez, Antonio ^a   King, Andrew ^b   Robeson, Michael S ^c   Song, Sejin ^c   Shade, Ashley ^d   Metcalf, Jessica L ^c   Knight, Rob ^c,e  

^a UCB 450   (United States)

^b CSIRO   (Australia)

^c UNIVERSITY OF COLORADO   (United States)

^d YALE UNIVERSITY   (United States)

^e HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL TOOL; COMPUTATIONAL TOOLS; ENVIRONMENTAL HEALTH; HIGH-THROUGHPUT; MICROBIAL COMMUNITIES; MICROBIAL DIVERSITY; MODEL-BASED ANALYSIS; SPACE AND TIME; SPATIO-TEMPORAL; SPATIOTEMPORAL ANALYSIS; TEMPORAL SCALE;

BIOTECHNOLOGY;

MICROORGANISMS;

COMMUNITY STRUCTURE; DNA SEQUENCE; MICROBIAL COLONIZATION; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROBIOME; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; REVIEW;

BACTERIA; BIODIVERSITY; ENVIRONMENTAL MICROBIOLOGY; METAGENOMICS; MODELS, BIOLOGICAL; SPATIO-TEMPORAL ANALYSIS;

EID: 84861979991     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2011.11.017     Document Type: Review

References (62)

1. Colwell R.R. Microbial diversity: the importance of exploration and conservation. J Ind Microbiol Biotechnol 1997, 18:302-307.
2. DeLong E.F., Pace N.R. Environmental diversity of bacteria and archaea. Syst Biol 2001, 50:470-478.
3. Green J.L., Bohannan B.J., Whitaker R.J. Microbial biogeography: from taxonomy to traits. Science 2008, 320:1039-1043.
4. DeLong E.F. The microbial ocean from genomes to biomes. Nature 2009, 459:200-206.
5. Whitaker R.J., Grogan D.W., Taylor J.W. Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 2003, 301:976-978.
6. Paerl R.W., Turk K.A., Beinart R.A., Chavez F.P., Zehr J.P. Seasonal change in the abundance of Synechococcus and multiple distinct phylotypes in Monterey Bay determined by rbcL and narB quantitative PCR. Environ Microbiol 2011, doi:10.1111/j. 462-2920.2011.02594.x.
7. King A.J., Freeman K.R., McCormick K.F., Lynch R.C., Lozupone C., Knight R., Schmidt S.K. Biogeography and habitat modelling of high-alpine bacteria. Nat Commun 2010, 1:53.
8. Boucher D., Jardillier L., Debroas D. Succession of bacterial community composition over two consecutive years in two aquatic systems: a natural lake and a lake-reservoir. FEMS Microbiol Ecol 2006, 55:79-97.
9. Costello E.K., Lauber C.L., Hamady M., Fierer N., Gordon J.I., Knight R. Bacterial community variation in human body habitats across space and time. Science 2009, 326:1694-1697.
10. Fierer N., Jackson R.B. The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci U S A 2006, 103:626-631.
11. Martiny J.B., Bohannan B.J., Brown J.H., Colwell R.K., Fuhrman J.A., Green J.L., Horner-Devine M.C., Kane M., Krumins J.A., Kuske C.R., et al. Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 2006, 4:102-112.
12. Balser T.C., Firestone M.K. Linking microbial community composition and soil processes in a California annual grassland and mixed-conifer forest. Biogeochemistry 2005, 73:395-415.
13. Turnbaugh P.J., Hamady M., Yatsunenko T., Cantarel B.L., Duncan A., Ley R.E., Sogin M.L., Jones W.J., Roe B.A., Affourtit J.P., et al. A core gut microbiome in obese and lean twins. Nature 2009, 457:480-484.
14. Burke C., Steinberg P., Rusch D., Kjelleberg S., Thomas T. Bacterial community assembly based on functional genes rather than species. Proc Natl Acad Sci U S A 2011, 108:14288-14293.
15. Hamady M., Knight R. Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res 2009, 19:1141-1152.
16. Kuczynski J., Liu Z., Lozupone C., McDonald D., Fierer N., Knight R. Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Nat Methods 2010, 7:813-819.
17. Robeson M.S., King A.J., Freeman K.R., Birky C.W., Martin A.P., Schmidt S.K. Soil rotifer communities are extremely diverse globally but spatially autocorrelated locally. Proc Natl Acad Sci U S A 2011, 108:4406-4410.
18. Lozupone C.A., Knight R. Species divergence and the measurement of microbial diversity. FEMS Microbiol Rev 2008, 32:557-578.
19. Hamady M., Lozupone C., Knight R. Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 2010, 4:17-27.
20. Shivaji S., Pratibha M.S., Sailaja B., Hara Kishore K., Singh A.K., Begum Z., Anarasi U., Prabagaran S.R., Reddy G.S., Srinivas T.N. Bacterial diversity of soil in the vicinity of Pindari glacier, Himalayan mountain ranges, India, using culturable bacteria and soil 16S rRNA gene clones. Extremophiles 2011, 15:1-22.
21. Lacap D.C., Barraquio W., Pointing S.B. Thermophilic microbial mats in a tropical geothermal location display pronounced seasonal changes but appear resilient to stochastic disturbance. Environ Microbiol 2007, 9:3065-3076.
22. Zhou J., Kang S., Schadt C.W., Garten C.T. Spatial scaling of functional gene diversity across various microbial taxa. Proc Natl Acad Sci U S A 2008, 105:7768-7773.
23. O'Malley M.A. The nineteenth century roots of 'everything is everywhere'. Nat Rev Microbiol 2007, 5:647-651.
24. Nemergut D.R., Costello E.K., Hamady M., Lozupone C., Jiang L., Schmidt S.K., Fierer N., Townsend A.R., Cleveland C.C., Stanish L., et al. Global patterns in the biogeography of bacterial taxa. Environ Microbiol 2011, 13:135-144.
25. Fierer N., Strickland M.S., Liptzin D., Bradford M.A., Cleveland C.C. Global patterns in belowground communities. Ecol Lett 2009, 12:1238-1249.
26. Gilbert J.A., Steele J.A., Caporaso J.G., Steinbruck L., Reeder J., Temperton B., Huse S., McHardy A.C., Knight R., Joint I., et al. Defining seasonal marine microbial community dynamics. ISME J 2011, 10.1038/ismej.2011.107.
27. Steele J.A., Countway P.D., Xia L., Vigil P.D., Beman J.M., Kim D.Y., Chow C.E., Sachdeva R., Jones A.C., Schwalbach M.S., et al. Marine bacterial, archaeal and protistan association networks reveal ecological linkages. ISME J 2011, 5:1414-1425.
28. Bahl J., Lau M.C., Smith G.J., Vijaykrishna D., Cary S.C., Lacap D.C., Lee C.K., Papke R.T., Warren-Rhodes K.A., Wong F.K., et al. Ancient origins determine global biogeography of hot and cold desert cyanobacteria. Nat Commun 2011, 2:163.
29. Schmidt S.K., Lynch R.C., King A.J., Karki D., Robeson M.S., Nagy L., Williams M.W., Mitter M.S., Freeman K.R. Phylogeography of microbial phototrophs in the dry valleys of the high Himalayas and Antarctica. Proc Biol Sci 2011, 278:702-708.
30. Bryant J.A., Lamanna C., Morlon H., Kerkhoff A.J., Enquist B.J., Green J.L. Colloquium paper: microbes on mountainsides: contrasting elevational patterns of bacterial and plant diversity. Proc Natl Acad Sci U S A 2008, 105(Suppl. 1):11505-11511.
31. Schoener T.W., Spiller D.A., Losos J.B. Natural restoration of the species-area relation for a lizard after a hurricane. Science 2001, 294:1525-1528.
32. Fuhrman J.A., Steele J.A., Hewson I., Schwalbach M.S., Brown M.V., Green J.L., Brown J.H. A latitudinal diversity gradient in planktonic marine bacteria. Proc Natl Acad Sci U S A 2008, 105:7774-7778.
33. Fierer N., McCain C.M., Meir P., Zimmermann M., Rapp J.M., Silman M.R., Knight R. Microbes do not follow the elevational diversity patterns of plants and animals. Ecology 2011, 92:797-804.
34. Lauber C.L., Hamady M., Knight R., Fierer N. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 2009, 75:5111-5120.
35. Fierer N., Lauber C.L., Zhou N., McDonald D., Costello E.K., Knight R. Forensic identification using skin bacterial communities. Proc Natl Acad Sci U S A 2010, 107:6477-6481.
36. Mantel N. The detection of disease clustering and a generalized regression approach. Cancer Res 1967, 27:209-220.
37. Franklin R.B., Mills A.L. Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field. FEMS Microbiol Ecol 2003, 44:335-346.
38. Luc A. Under the hood: issues in the specification and interpretation of spatial regression models. Agric Econ 2002, 27:247-267.
39. Bru D., Ramette A., Saby N.P., Dequiedt S., Ranjard L., Jolivet C., Arrouays D., Philippot L. Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale. ISME J 2011, 5:532-542.
40. Hehemann J.H., Correc G., Barbeyron T., Helbert W., Czjzek M., Michel G. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 2010, 464:908-912.
41. Dale M.R.T., Dixon P., Fortin M.-J., Legendre P., Myers D.E., Rosenberg M.S. Conceptual and mathematical relationships among methods for spatial analysis. Ecography 2002, 25:558-577.
42. Harnstrom K., Ellegaard M., Andersen T.J., Godhe A. Hundred years of genetic structure in a sediment revived diatom population. Proc Natl Acad Sci U S A 2011, 108:4252-4257.
43. Koenig J.E., Spor A., Scalfone N., Fricker A.D., Stombaugh J., Knight R., Angenent L.T., Ley R.E. Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci U S A 2011, 108(Suppl. 1):4578-4585.
44. Caporaso J.G., Lauber C.L., Costello E.K., Berg-Lyons D., Gonzalez A., Stombaugh J., Knights D., Gajer P., Ravel J., Fierer N., et al. Moving pictures of the human microbiome. Genome Biol 2011, 12:R50.
45. Shade A., Jones S.E., McMahon K.D. The influence of habitat heterogeneity on freshwater bacterial community composition and dynamics. Environ Microbiol 2008, 10:1057-1067.
46. Eiler A., Heinrich F., Bertilsson S. Coherent dynamics and association networks among lake bacterioplankton taxa. ISME J 2011, 10.1038/ismej.2011.113.
47. Ruan Q., Dutta D., Schwalbach M.S., Steele J.A., Fuhrman J.A., Sun F. Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors. Bioinformatics 2006, 22:2532-2538.
48. Shade A., Chiu C.Y., McMahon K.D. Differential bacterial dynamics promote emergent community robustness to lake mixing: an epilimnion to hypolimnion transplant experiment. Environ Microbiol 2010, 12:455-466.
49. Crump B.C., Peterson B.J., Raymond P.A., Amon R.M., Rinehart A., McClelland J.W., Holmes R.M. Circumpolar synchrony in big river bacterioplankton. Proc Natl Acad Sci U S A 2009, 106:21208-21212.
50. Kent A.D., Yannarell A.C., Rusak J.A., Triplett E.W., McMahon K.D. Synchrony in aquatic microbial community dynamics. ISME J 2007, 1:38-47.
51. Clarke K.R., Somerfield P.J., Airoldi L., Warwick R.M. Exploring interactions by second-stage community analyses. J Exp Mar Biol Ecol 2006, 338:179-192.
52. Shade A., Read J.S., Welkie D.G., Kratz T.K., Wu C.H., McMahon K.D. Resistance, resilience and recovery: aquatic bacterial dynamics after water column disturbance. Environ Microbiol 2011, 13:2752-2767.
53. Werner J.J., Knights D., Garcia M.L., Scalfone N.B., Smith S., Yarasheski K., Cummings T.A., Beers A.R., Knight R., Angenent L.T. Bacterial community structures are unique and resilient in full-scale bioenergy systems. Proc Natl Acad Sci U S A 2011, 108:4158-4163.
54. He S., McMahon K.D. 'Candidatus Accumulibacter' gene expression in response to dynamic EBPR conditions. ISME J 2011, 5:329-340.
55. Bowers R.M., Sullivan A.P., Costello E.K., Collett J.L., Knight R., Fierer N. Sources of bacteria in outdoor air across cities in the Midwestern United States. Appl Environ Microbiol 2011, 77:6350-6356.
56. Jones S.E., Chiu C.-Y., Kratz T.K., Wu J.-T., Shade A., McMahon K.D. Typhoons initiate predictable change in aquatic bacterial communities. Limnol Oceanogr 2008, 53:1319-1326.
57. Dethlefsen L., Relman D.A. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A 2011, 108(Suppl. 1):4554-4561.
58. Schilling K.E., Zhang Y.-K., Hill D.R., Jones C.S., Wolter C.F. Temporal variations of Escherichia coli concentrations in a large Midwestern river. J Hydrol 2009, 365:79-85.
59. Trosvik P., Rudi K., Straetkvern K.O., Jakobsen K.S., Naes T., Stenseth N.C. Web of ecological interactions in an experimental gut microbiota. Environ Microbiol 2010, 12:2677-2687.
60. Banning N.C., Gleeson D.B., Grigg A.H., Grant C.D., Andersen G.L., Brodie E.L., Murphy D.V. Soil microbial community successional patterns during forest ecosystem restoration. Appl Environ Microbiol 2011, 77:6158-6164.
61. Sattin S.R., Cleveland C.C., Hood E., Reed S.C., King A.J., Schmidt S.K., Robeson M.S., Ascarrunz N., Nemergut D.R. Functional shifts in unvegetated, perhumid, recently-deglaciated soils do not correlate with shifts in soil bacterial community composition. J Microbiol 2009, 47:673-681.
62. Urbanova M., Kopecky J., Valaskova V., Sagova-Mareckova M., Elhottova D., Kyselkova M., Moënne-Loccoz Y., Baldrian P. Development of bacterial community during spontaneous succession on spoil heaps after brown coal mining. FEMS Microbiol Ecol 2011, 78:59-69.