Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession

Proceedings of the National Academy of Sciences of the United States of America

Volumn 112, Issue 11, 2015, Pages E1326-E1332

  Dini Andreote, Francisco ^a,b   Stegen, James C ^b   Van Elsas, Jan Dirk ^a   Salles, Joana Falcão ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

Community assembly; Evolutionary niche conservatism; Neutral theory; Niche theory; Simulation model

Indexed keywords

SOIL ORGANIC MATTER;

ARTICLE; CHRONOSEQUENCE; COMMUNITY SUCCESSION; CONCEPTUAL FRAMEWORK; DETERMINISTIC MODEL; ECOSYSTEM; ENVIRONMENTAL ASPECTS AND RELATED PHENOMENA; ENVIRONMENTAL CHANGE; MATHEMATICAL MODEL; MICROBIAL COLONIZATION; MICROBIAL COMMUNITY; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SECONDARY SUCCESSION (COMMUNITY); SIMULATION; SPATIOTEMPORAL ANALYSIS; STOCHASTIC MODEL; BIOLOGICAL MODEL; COMPUTER SIMULATION; MARKOV CHAIN; MICROBIOLOGY;

BACTERIA (MICROORGANISMS);

COMPUTER SIMULATION; ECOSYSTEM; MODELS, BIOLOGICAL; SOIL MICROBIOLOGY; STOCHASTIC PROCESSES;

EID: 84925237232     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1414261112     Document Type: Article

References (58)

1. Dumbrell AJ, Nelson M, Helgason T, Dytham C, Fitter AH (2010) Relative roles of niche and neutral processes in structuring a soil microbial community. ISME J 4(3):337-345.
2. Zhou J, et al. (2014) Stochasticity, succession, and environmental perturbations in a fluidic ecosystem. Proc Natl Acad Sci USA 111(9):E836-E845.
3. Stegen JC, et al. (2013) Quantifying community assembly processes and identifying features that impose them. ISME J 7(11):2069-2079.
4. Vellend M (2010) Conceptual synthesis in community ecology. Q Rev Biol 85(2):183-206.
5. Hubbell SP (2001) The Unified Neutral Theory of Biodiversity and Biogeography (Princeton Univ Press, Princeton, NJ).
6. Chase JM, Myers JA (2011) Disentangling the importance of ecological niches from stochastic processes across scales. Philos Trans R Soc Lond B Biol Sci 366(1576):2351-2363.
7. Baath E (1996) Adaptation of soil bacterial communities to prevailing pH in different soils. FEMS Microbiol Ecol 19(4):227-237.
8. Torsvik V, Øvreås L, Thingstad TF (2002) Prokaryotic diversity-Magnitude, dynamics, and controlling factors. Science 296(5570):1064-1066.
9. Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103(3):626-631.
10. Lozupone CA, Knight R (2007) Global patterns in bacterial diversity. Proc Natl Acad Sci USA 104(27):11436-11440.
11. Caruso T, et al. (2011) Stochastic and deterministic processes interact in the assembly of desert microbial communities on a global scale. ISME J 5(9):1406-1413.
12. Chisholm RA, Pacala SW (2011) Theory predicts a rapid transition from niche-structured to neutral biodiversity patterns across a speciation-rate gradient. Theor Ecol 4(2):195-200.
13. Langenheder S, Székely AJ (2011) Species sorting and neutral processes are both important during the initial assembly of bacterial communities. ISME J 5(7):1086-1094.
14. Chase JM (2007) Drought mediates the importance of stochastic community assembly. Proc Natl Acad Sci USA 104(44):17430-17434.
15. Myers JA, Harms KE (2011) Seed arrival and ecological filters interact to assemble high-diversity plant communities. Ecology 92(3):676-686.
16. Fierer N, Nemergut D, Knight R, Craine JM (2010) Changes through time: Integrating microorganisms into the study of succession. Res Microbiol 161(8):635-642.
17. Jackson CR, Churchill PF, Roden EE (2001) Successional changes in bacterial assemblage structure during epilithic biofilm development. Ecology 82(2):555-566.
18. Tscherko D, Rustemeier J, Richter A, Wanek W, Kandeler E (2003) Functional diversity of the soil microflora in primary succession across two glacier forelands in the Central Alps. Eur J Soil Sci 54(4):685-696.
19. Schütte UM, et al. (2009) Bacterial succession in a glacier foreland of the High Arctic. ISME J 3(11):1258-1268.
20. Ferrenberg S, et al. (2013) Changes in assembly processes in soil bacterial communities following a wildfire disturbance. ISME J 7(6):1102-1111.
21. Bengtsson MM, Sjøtun K, Lanzén A, Ovreås L (2012) Bacterial diversity in relation to secondary production and succession on surfaces of the kelp Laminaria hyperborea. ISME J 6(12):2188-2198.
22. Olff H, De Leeuw J, Bakker JP, Platerink RJ, van Wijnen HJ (1997) Vegetation succession and herbivory in a salt marsh: Changes induced by sea level rise and silt deposition along an elevational gradient. J Ecol 85(6):799-814.
23. Sigler WV, Zeyer J (2002) Microbial diversity and activity along the forefields of two receding glaciers. Microb Ecol 43(4):397-407.
24. Nicol GW, Tscherko D, Embley TM, Prosser JI (2005) Primary succession of soil Crenarchaeota across a receding glacier foreland. Environ Microbiol 7(3):337-347.
25. Deiglmayr K, Philippot L, Tscherko D, Kandeler E (2006) Microbial succession of ni-trate-reducing bacteria in the rhizosphere of Poa alpina across a glacier foreland in the Central Alps. Environ Microbiol 8(9):1600-1612.
26. Nemergut DR, et al. (2007) Microbial community succession in an unvegetated, recently deglaciated soil. Microb Ecol 53(1):110-122.
27. Zumsteg A, et al. (2012) Bacterial, archaeal and fungal succession in the forefield of a receding glacier. Microb Ecol 63(3):552-564.
28. Jackson CR (2003) Changes in community properties during microbial succession. Oikos 101(2):444-448.
29. Martiny AC, Jørgensen TM, Albrechtsen H-J, Arvin E, Molin S (2003) Long-term succession of structure and diversity of a biofilm formed in a model drinking water distribution system. Appl Environ Microbiol 69(11):6899-6907.
30. Revetta RP, et al. (2013) Establishment and early succession of bacterial communities in monochloramine-treated drinking water biofilms. FEMS Microbiol Ecol 86(3):404-414.
31. Mahaffee WF, Kloepper JW (1997) Temporal changes in the bacterial communities of soil, rhizosphere, and endorhiza associated with field grown cucumber (Cucumis sativus L.). Microb Ecol 34(3):210-223.
32. Wieland G, Neumann R, Backhaus H (2001) Variation of microbial communities in soil, rhizosphere, and rhizoplane in response to crop species, soil type, and crop development. Appl Environ Microbiol 67(12):5849-5854.
33. Marschner P, Neumann G, Kania A, Weiskopf L, Lieberei R (2002) Spatial and temporal dynamics of the microbial community structure in the rhizosphere of cluster roots of white lupin (Lupinus albus L.). Plant Soil 246(2):167-174.
34. Chaparro JM, Badri DV, Vivanco JM (2014) Rhizosphere microbiome assemblage is affected by plant development. ISME J 8(4):790-803.
35. Sigler WV, Crivii S, Zeyer J (2002) Bacterial succession in glacial forefield soils characterized by community structure, activity and opportunistic growth dynamics. Microb Ecol 44(4):306-316.
36. Badri DV, Chaparro JM, Zhang R, Shen Q, Vivanco JM (2013) Application of natural blends of phytochemicals derived from the root exudates of Arabidopsis to the soil reveal that phenolic-related compounds predominantly modulate the soil microbiome. J Biol Chem 288(7):4502-4512.
37. Chaparro JM, et al. (2013) Root exudation of phytochemicals in Arabidopsis follows specific patterns that are developmentally programmed and correlate with soil microbial functions. PLoS ONE 8(2):e55731.
38. Inceoʇlu Ö, Al-Soud WA, Salles JF, Semenov AV, van Elsas JD (2011) Comparative analysis of bacterial communities in a potato field as determined by pyrosequencing. PLoS ONE 6(8):e23321.
39. Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75(15):5111-5120.
40. Rousk J, et al. (2010) Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J 4(10):1340-1351.
41. Graham CH, Fine PV (2008) Phylogenetic beta diversity: Linking ecological and evolutionary processes across space in time. Ecol Lett 11(12):1265-1277.
42. Stegen JC, Lin X, Konopka AE, Fredrickson JK (2012) Stochastic and deterministic assembly processes in subsurface microbial communities. ISME J 6(9):1653-1664.
43. Losos JB (2008) Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecol Lett 11(10):995-1003.
44. Wang J, et al. (2013) Phylogenetic beta diversity in bacterial assemblages across ecosystems: Deterministic versus stochastic processes. ISME J 7(7):1310-1321.
45. Lindemann SR, et al. (2013) The epsomitic phototrophic microbial mat of Hot Lake, Washington: Community structural responses to seasonal cycling. Front Microbiol 4:323.
46. Hardy OJ (2008) Testing the spatial phylogenetic structure of local communities: Statistical performances of different null models and test statistics on a locally neutral community. J Ecol 96(5):914-926.
47. Dini-Andreote F, et al. (2014) Dynamics of bacterial community succession in a salt marsh chronosequence: Evidences for temporal niche partitioning. ISME J 8(10):1989-2001.
48. Chase JM (2010) Stochastic community assembly causes higher biodiversity in more productive environments. Science 328(5984):1388-1391.
49. McGenity TJ, Gemmell RT, Grant WD, Stan-Lotter H (2000) Origins of halophilic microorganisms in ancient salt deposits. Environ Microbiol 2(3):243-250.
50. Oren A (2008) Microbial life at high salt concentrations: Phylogenetic and metabolic diversity. Saline Syst 4:2.
51. Oren A (2002) Halophilic Microorganisms and Their Environments (Kluwer, Dordrecht, The Netherlands).
52. Morrissey EM, Gillespie JL, Morina JC, Franklin RB (2014) Salinity affects microbial activity and soil organic matter content in tidal wetlands. Glob Change Biol 20(4):1351-1362.
53. Herlemann DP, et al. (2011) Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J 5(10):1571-1579.
54. Chase JM (2003) Community assembly: When should history matter? Oecologia 136(4):489-498.
55. Bianchi TS (2011) The role of terrestrially derived organic carbon in the coastal ocean: A changing paradigm and the priming effect. Proc Natl Acad Sci USA 108(49):19473-19481.
56. Jorgensen SL, et al. (2012) Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge. Proc Natl Acad Sci USA 109(42):E2846-E2855.
57. Martiny JB, Eisen JA, Penn K, Allison SD, Horner-Devine MC (2011) Drivers of bacterial beta-diversity depend on spatial scale. Proc Natl Acad Sci USA 108(19):7850-7854.
58. Caporaso JG, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7(5):335-336.