Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

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

Volumn 111, Issue 9, 2014, Pages

  Zhou, Jizhong ^a,b,c   Deng, Ye ^b,d   Zhang, Ping ^b   Xue, Kai ^b   Liang, Yuting ^a,b   Van Nostrand, Joy D ^b   Yang, Yunfeng ^a   He, Zhili ^b   Wu, Liyou ^b   Stahl, David A ^e   Hazen, Terry C ^f,g   Tiedje, James M ^h   Arkin, Adam P ^c  

^a TSINGHUA UNIVERSITY   (China)

^b UNIVERSITY OF OKLAHOMA   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^d RESEARCH CENTER FOR ECO ENVIRONMENTAL SCIENCES   (China)

^e University of Washington   (United States)

^f University of Tennessee   (United States)

^g OAK RIDGE NATIONAL LABORATORY   (United States)

^h MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

Community assembly; Disturbances; GeoChip; Metagenomics; Remediation

Indexed keywords

ARTICLE; CONCEPTUAL FRAMEWORK; ECOSYSTEM; ENVIRONMENTAL CHANGE; MICROBIAL COMMUNITY; PRIORITY JOURNAL; STATISTICS;

COMMUNITY ASSEMBLY; DISTURBANCES; GEOCHIP; METAGENOMICS; REMEDIATION;

ECOSYSTEM; GROUNDWATER; MICROBIOTA; MODELS, BIOLOGICAL; PLANT OILS; POPULATION DYNAMICS; SPECIES SPECIFICITY; STOCHASTIC PROCESSES; TIME FACTORS; WATER MICROBIOLOGY;

EID: 84895808319     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1324044111     Document Type: Article

References (63)

1. Chase JM (2003) Community assembly: When should history matter? Oecologia 136 (4):489-498.
2. 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.
3. Holyoak M, Leibold MA, Holt RD (2005) Metacommunities: Spatial Dynamics and Ecological Communities (Univ of Chicago Press, Chicago).
4. Orrock JL, Watling JI (2010) Local community size mediates ecological drift and competition in metacommunities. Proc Biol Sci 277(1691):2185-2191.
5. 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.
6. Hubbell SP (2001) The Unified Neutral Theory of Biodiversity and Biogeography (Princeton Univ Press, Princeton, NJ).
7. Tilman D (2004) Niche tradeoffs, neutrality, and community structure: A stochastic theory of resource competition, invasion, and community assembly. Proc Natl Acad Sci USA 101(30):10854-10861.
8. Chesson P (2000) Mechanisms of maintenance of species diversity. Annu Rev Ecol Syst 31:343.
9. Fargione J, Brown CS, Tilman D (2003) Community assembly and invasion: An experimental test of neutral versus niche processes. Proc Natl Acad Sci USA 100(15): 8916-8920.
10. Chase JM, Biro EG, Ryberg WA, Smith KG (2009) Predators temper the relative importance of stochastic processes in the assembly of prey metacommunities. Ecol Lett 12(11):1210-1218.
11. Chave J (2004) Neutral theory and community ecology. Ecol Lett 7(3):241-253.
12. Fukami T, Bezemer TM, Mortimer SR, van der Putten WH (2005) Species divergence and trait convergence in experimental plant community assembly. Ecol Lett 8(12): 1283-1290.
13. Chase JM(2007) Drought mediates the importance of stochastic community assembly. Proc Natl Acad Sci USA 104(44):17430-17434.
14. Zhou J, et al. (2013) Stochastic assembly leads to alternative communities with distinct functions in a bioreactor microbial community. MBio 4(2) e00584-12.
15. Chase JM (2010) Stochastic community assembly causes higher biodiversity in more productive environments. Science 328(5984):1388-1391.
16. Ofiteru ID, et al. (2010) Combined niche and neutral effects in a microbial wastewater treatment community. Proc Natl Acad Sci USA 107(35):15345-15350.
17. Kardol P, Souza L, Classen AT (2013) Resource availability mediates the importance of priority effects in plant community assembly and ecosystem function. Oikos 122(1):84-94.
18. Ellwood MDF, Manica A, Foster WA (2009) Stochastic and deterministic processes jointly structure tropical arthropod communities. Ecol Lett 12(4):277-284.
19. Kraft NJB, et al. (2011) Disentangling the drivers of β diversity along latitudinal and elevational gradients. Science 333(6050):1755-1758.
20. 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.
21. Stegen JC, Lin XJ, Konopka AE, Fredrickson JK (2012) Stochastic and deterministic assembly processes in subsurface microbial communities. ISME J 6(9):1653-1664.
22. Kreyling J, Jentsch A, Beierkuhnlein C (2011) Stochastic trajectories of succession initiated by extreme climatic events. Ecol Lett 14(8):758-764.
23. Prach K, Walker LR (2011) Four opportunities for studies of ecological succession. Trends Ecol Evol 26(3):119-123.
24. Connell JH, Slatyer RO (1977) Mechanisms of succession in natural communities and their role in community stability and organization. Am Nat 111(982):1119-1144.
25. Houseman GR, Mittelbach GG, Reynolds HL, Gross KL (2008) Perturbations alter community convergence, divergence, and formation of multiple community states. Ecology 89(8):2172-2180.
26. Shade A, et al. (2012) Fundamentals of microbial community resistance and resilience. Front Microbiol 3:417.
27. Ley RE, Turnbaugh PJ, Klein S, Gordon JI (2006) Microbial ecology: Human gut microbes associated with obesity. Nature 444(7122):1022-1023.
28. Werner JJ, et al. (2011) Bacterial community structures are unique and resilient in fullscale bioenergy systems. Proc Natl Acad Sci USA 108(10):4158-4163.
29. Xu MY, et al. (2010) Responses of microbial community functional structures to pilotscale uranium in situ bioremediation. ISME J 4(8):1060-1070.
30. Curtis TP, Head IM, Graham DW (2003) Theoretical ecology for engineering biology. Environ Sci Technol 37(3):64A-70A.
31. Kennedy AC, Smith KL (1995) Soil microbial diversity and the sustainability of agricultural soils. Plant Soil 170(1):75-86.
32. Gihring TM, et al. (2011) A limited microbial consortium is responsible for extended bioreduction of uranium in a contaminated aquifer. Appl EnvironMicrobiol 77(17):5955-5965.
33. Vellend M (2010) Conceptual synthesis in community ecology. Q Rev Biol 85(2): 183-206.
34. He Z, et al. (2010) GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity. ISME J 4(9):1167-1179.
35. Zhou JZ, et al. (2012) Microbial mediation of carbon-cycle feedbacks to climate warming. Nat Clim Change 2(2):106-110.
36. Connell JH (1978) Diversity in tropical rain forests and coral reefs. Science 199(4335): 1302-1310.
37. Svensson JR, Lindegarth M, Jonsson PR, Pavia H (2012) Disturbance-diversity models: What do they really predict and how are they tested? Philos Trans R Soc Lond B Biol Sci 279(1736):2163-2170.
38. Miller AD, Roxburgh SH, Shea K (2011) How frequency and intensity shape diversitydisturbance relationships. Proc Natl Acad Sci USA 108(14):5643-5648.
39. Li J, Loneragan WA, Duggin JA, Grant CD (2004) Issues affecting the measurement of disturbance response patterns in herbaceous vegetation: A test of the intermediate disturbance hypothesis. Plant Ecol 172(1):11-26.
40. Chase JM, Kraft NJB, Smith KG, Vellend M, Inouye BD (2011) Using null models to disentangle variation in community dissimilarity from variation in α-diversity. Ecosphere 2(2):art24.
41. Ulrich W, Gotelli NJ (2010) Null model analysis of species associations using abundance data. Ecology 91(11):3384-3397.
42. Gotelli NJ (2000) Null model analysis of species co-occurrence patterns. Ecology 81(9): 2606-2621.
43. Gotelli NJ, Entsminger GL (2009) EcoSim: Null models software for ecology. Version 7.
44. Lindström ES, Langenheder S (2012) Local and regional factors influencing bacterial community assembly. Environ Microbiol Rep 4(1):1-9.
45. Wu WM, et al. (2006) Pilot-scale in situ bioremediation of uranium in a highly contaminated aquifer. 1. Conditioning of a treatment zone. Environ Sci Technol 40(12): 3978-3985.
46. Hazen TC, et al. (2010) Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 330(6001):204-208.
47. Lu Z, et al. (2012) Microbial gene functions enriched in the Deepwater Horizon deepsea oil plume. ISME J 6(2):451-460.
48. Gonzalez A, et al. (2012) Characterizing microbial communities through space and time. Curr Opin Biotechnol 23(3):431-436.
49. Jones SE, et al. (2008) Typhoons initiate predictable change in aquatic bacterial communities. Limnol Oceanogr 53(4):1319-1326.
50. Shade A, et al. (2011) Resistance, resilience and recovery: Aquatic bacterial dynamics after water column disturbance. Environ Microbiol 13(10):2752-2767.
51. Shade A, et al. (2012) Lake microbial communities are resilient after a whole-ecosystem disturbance. ISME J 6(12):2153-2167.
52. Fries MR, Hopkins GD, McCarty PL, Forney LJ, Tiedje JM (1997) Microbial succession during a field evaluation of phenol and toluene as the primary substrates for trichloroethene cometabolism. Appl Environ Microbiol 63(4):1515-1522.
53. Blanco-Canqui H, Lal R (2008) No-tillage and soil-profile carbon sequestration: An onfarm assessment. Soil Sci Soc Am J 72(3):693-701.
54. Lal R (2004) Soil carbon sequestration impacts on global climate change and food security. Science 304(5677):1623-1627.
55. Martens DA (2001) Nitrogen cycling under different soil management systems. Adv Agron 70:143-192.
56. Herrick JE, et al. (2001) Field soil aggregate stability kit for soil quality and rangeland health evaluations. Catena 44(1):27-35.
57. Hartmann M, et al. (2012) Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests. ISME J 6(12):2199-2218.
58. Wu WM, et al. (2006) Pilot-scale in situ bioremedation of uranium in a highly contaminated aquifer. 2. Reduction of U(VI) and geochemical control of U(VI) bioavailability. Environ Sci Technol 40(12):3986-3995.
59. Wu WM, et al. (2007) In situ bioreduction of uranium (VI) to submicromolar levels and reoxidation by dissolved oxygen. Environ Sci Technol 41(16):5716-5723.
60. Zhou JZ, Bruns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62(2):316-322.
61. He Z, et al. (2007) GeoChip: A comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J 1(1):67-77.
62. Dixon P (2003) VEGAN, a package of R functions for community ecology. J Veg Sci 14(6):927-930.
63. Bardgett RD, Bowman WD, Kaufmann R, Schmidt SK (2005) A temporal approach to linking aboveground and belowground ecology. Trends Ecol Evol 20(11):634-641.