Environmental conditions rather than microbial inoculum composition determine the bacterial composition, microbial biomass and enzymatic activity of reconstructed soil microbial communities

Soil Biology and Biochemistry

Volumn 90, Issue , 2015, Pages 10-18

  Xun, Weibing ^a,b   Huang, Ting ^a   Zhao, Jun ^a   Ran, Wei ^a   Wang, Boren ^b   Shen, Qirong ^a   Zhang, Ruifu ^a,b  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

^b INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

Bacterial community; Enzymatic activity; Microbial biomass; Soil incubation; ray sterilization

Indexed keywords

BACTERIA; BIOMASS; FERTILIZERS; GAMMA RAYS; PHOSPHATASES; PHYSICOCHEMICAL PROPERTIES; RNA; SOIL SURVEYS;

BACTERIAL COMMUNITY; ENVIRONMENTAL CONDITIONS; ENZYMATIC ACTIVITIES; MICROBIAL BIOMASS; POTASSIUM CONCENTRATIONS; SOIL BACTERIAL COMMUNITY; SOIL INCUBATION; SOIL MICROBIAL COMMUNITY;

SOILS;

ABUNDANCE; BIOMASS; ENVIRONMENTAL CONDITIONS; ENZYME ACTIVITY; GENETIC ANALYSIS; INOCULATION; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; ORGANIC MATTER; PHOSPHORUS; PHYSICOCHEMICAL PROPERTY; POTASSIUM; SOIL AMENDMENT; SOIL MICROORGANISM; SOIL QUALITY; SPECIES DIVERSITY;

BACTERIA (MICROORGANISMS);

EID: 84938915782     PISSN: 00380717     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.soilbio.2015.07.018     Document Type: Article

References (52)

1. Alef K., Nannipieri P. Methods in Applied Soil Microbiology and Biochemistry 1995, Acad. Press.
2. Beijerinck M.W. De infusies en de ontdekking der backteriën 1913, 1-28. Jaarb. Van K. Akad. Van Wet.
3. Borneman J., Triplett E.W. Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Applied and Environmental Microbiology 1997, 63:2647-2653.
4. Braker G., Fesefeldt A., Witzel K.P. Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples. Applied and Environmental Microbiology 1998, 64:3769-3775.
5. Bremner J.M., Mulvaney C.S. Methods of Soil Analysis. Part 2. Chemical and Microbiological Properties 1982, 595-624. Methods Soil Anal.
6. Buckley D.H., Schmidt T.M. Exploring the biodiversity of soil-a microbial rain forest. Biodivers. Microb. Life 2002, Wiley-Liss Inc.
7. Chen L., Xun W., Sun L., Zhang N., Shen Q., Zhang R. Effect of different long-term fertilization regimes on the viral community in an agricultural soil of Southern China. European Journal of Soil Biology 2014, 62:121-126.
8. Cruz-Martínez K., Suttle K.B., Brodie E.L., Power M.E., Andersen G.L., Banfield J.F. Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland. ISME Journal 2009, 3:738-744.
9. Dahnke W.C. Recommended Chemical Soil Test Procedures for the North Central Region 1988, Bulletin 499.
10. Daily G. Nature's Services: Societal Dependence on Natural Ecosystems 1997, Island Press.
11. Delmont T.O., Francioli D., Jacquesson S., Laoudi S., Mathieu A., Nesme J., Ceccherini M.T., Nannipieri P., Simonet P., Vogel T.M. Microbial community development and unseen diversity recovery in inoculated sterile soil. Biology and Fertility of Soils 2014, 50:1069-1076.
12. Dethlefsen L., Huse S., Sogin M.L., Relman D.A. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biology 2008, 6:e280.
13. Dick R.P., Rasmussen P.E., Kerle E.A. Influence of long-term residue management on soil enzyme activities in relation to soil chemical properties of a wheat-fallow system. Biology and Fertility of Soils 1988, 6:159-164.
14. Dixon P. VEGAN, a package of R functions for community ecology. Journal of Vegetation Science 2003, 14:927-930.
15. Fierer N., Jackson R.B. The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences 2006, 103:626-631.
16. Girvan M.S., Bullimore J., Pretty J.N., Osborn A.M., Ball A.S. Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Applied and Environmental Microbiology 2003, 69:1800-1809.
17. Gómez J.P., Bravo G.A., Brumfield R.T., Tello J.G., Cadena C.D. A phylogenetic approach to disentangling the role of competition and habitat filtering in community assembly of Neotropical forest birds. Journal of Animal Ecology 2010, 79:1181-1192.
18. Griffiths B.S., Hallett P.D., Kuan H.L., Gregory A.S., Watts C.W., Whitmore A.P. Functional resilience of soil microbial communities depends on both soil structure and microbial community composition. Biology and Fertility of Soils 2008, 44:745-754.
19. Hassett D.J., Cohen M.S. Bacterial adaptation to oxidative stress: implications for pathogenesis and interaction with phagocytic cells. FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology 1989, 3:2574-2582.
20. Hill M.O., Gauch H.G. Detrended correspondence analysis: an improved ordination technique. Vegetatio 1980, 42:47-58.
21. Horn D.J.V., Okie J.G., Buelow H.N., Gooseff M.N., Barrett J.E., Takacs-Vesbach C.D. Soil microbial responses to increased moisture and organic resources along a salinity gradient in a polar desert. Applied and Environmental Microbiology 2014, 80:3034-3043.
22. Huse S.M., Dethlefsen L., Huber J.A., Welch D.M., Relman D.A., Sogin M.L. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genetics 2008, 4:e1000255.
23. Jackson M.L. Soil Chemical Analysis 1958, Prentice Hall, Englewood Cliffs, NJ.
24. Jones S.E., Lennon J.T. Dormancy contributes to the maintenance of microbial diversity. Proceedings of the National Academy of Sciences 2010, 107:5881-5886.
25. Justice S.S., Hunstad D.A., Cegelski L., Hultgren S.J. Morphological plasticity as a bacterial survival strategy. Nature Reviews Microbiology 2008, 6:162-168.
26. Lennon J.T., Jones S.E. Microbial seed banks: the ecological and evolutionary implications of dormancy. Nature Reviews Microbiology 2011, 9:119-130.
27. Lensi R., Lescure C., Steinberg C., Savoie J.-M., Faurie G. Dynamics of residual enzyme activities, denitrification potential, and physico-chemical properties in a γ-sterilized soil. Soil Biology and Biochemistry 1991, 23:367-373.
28. Liu Z., Lozupone C., Hamady M., Bushman F.D., Knight R. Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Research 2007, 35. e120-e120.
29. Marquis R.E., Bender G.R., Murray D.R., Wong A. Arginine deiminase system and bacterial adaptation to acid environments. Applied and Environmental Microbiology 1987, 53:198-200.
30. McLaren A.D., Luse R.A., Skujins J.J. Sterilization of soil by irradiation and some further observations on soil enzyme activity 1. Soil Science Society of America Journal 1962, 26:371.
31. Nakatsu C.H., Carmosini N., Baldwin B., Beasley F., Kourtev P., Konopka A. Soil microbial community responses to additions of organic carbon substrates and heavy metals (Pb and Cr). Applied and Environmental Microbiology 2005, 71:7679-7689.
32. Nannipieri P., Muccini L., Ciardi C. Microbial biomass and enzyme activities: production and persistence. Soil Biology and Biochemistry 1983, 15:679-685.
33. Olsen S.R., Cole C.V., Watanabe F.S., Dean L.A. Estimation of Available Phosphorus in Soils by Extraction with Sodium Bicarbonate 1954, US Department of Agriculture, Washington, DC.
34. Philippot L., Piutti S., Martin-Laurent F., Hallet S., Germon J.C. Molecular analysis of the nitrate-reducing community from unplanted and maize-planted soils. Applied and Environmental Microbiology 2002, 68:6121-6128.
35. Poly F., Ranjard L., Nazaret S., Gourbière F., Monrozier L.J. Comparison of nifH gene pools in soils and soil microenvironments with contrasting properties. Applied and Environmental Microbiology 2001, 67:2255-2262.
36. Pruesse E., Quast C., Knittel K., Fuchs B.M., Ludwig W., Peplies J., Glöckner F.O. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Research 2007, 35:7188-7196.
37. Quince C., Lanzen A., Davenport R.J., Turnbaugh P.J. Removing noise from pyrosequenced amplicons. BMC Bioinformatics 2011, 12:38.
38. Ramette A., Tiedje J.M. Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem. Proceedings of the National Academy of Sciences 2007, 104:2761-2766.
39. Ramsay A.J., Bawden A.D. Effects of sterilization and storage on respiration, nitrogen status and direct counts of soil bacteria using acridine orange. Soil Biology and Biochemistry 1983, 15:263-268.
40. Roesch L.F.W., Fulthorpe R.R., Riva A., Casella G., Hadwin A.K.M., Kent A.D., Daroub S.H., Camargo F.A.O., Farmerie W.G., Triplett E.W. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME Journal 2007, 1:283-290.
41. 2-fixing, and total-community bacteria by terminal restriction fragment length polymorphism analysis using multiple restriction enzymes. Applied and Environmental Microbiology 2005, 71:2026-2035.
42. Rotthauwe J.H., Witzel K.P., Liesack W. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Applied and Environmental Microbiology 1997, 63:4704-4712.
43. Rousk J., Bååth E., Brookes P.C., Lauber C.L., Lozupone C., Caporaso J.G., Knight R., Fierer N. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME Journal 2010, 4:1340-1351.
44. Schloss P.D., Gevers D., Westcott S.L. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One 2011, 6:e27310.
45. Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., Lesniewski R.A., Oakley B.B., Parks D.H., Robinson C.J., Sahl J.W., Stres B., Thallinger G.G., Horn D.J.V., Weber C.F. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 2009, 75:7537-7541.
46. Schollenberger C.J. Determination of soil organic matter. Soil Science 1931, 31:483-486.
47. Shen C., Xiong J., Zhang H., Feng Y., Lin X., Li X., Liang W., Chu H. Soil pH drives the spatial distribution of bacterial communities along elevation on Changbai mountain. Soil Biology and Biochemistry 2013, 57:204-211.
48. Shih K.L., Souza K.A. Degradation of biochemical activity in soil sterilized by dry heat and gamma radiation. Origin of Life 1978, 9:51-63.
49. Throbäck I.N., Enwall K., Jarvis A., Hallin S. Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiology Ecology 2004, 49:401-417.
50. Vance E.D., Brookes P.C., Jenkinson D.S. An extraction method for measuring soil microbial biomass C. Soil Biology and Biochemistry 1987, 19:703-707.
51. Wang Q., Garrity G.M., Tiedje J.M., Cole J.R. Naïve bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology 2007, 73:5261-5267.
52. Weyhenmeyer G.A., Peter H., Willén E. Shifts in phytoplankton species richness and biomass along a latitudinal gradient - consequences for relationships between biodiversity and ecosystem functioning. Freshwater Biology 2013, 58:612-623.