Soil bacterial community dynamics reflect changes in plant community and soil properties during the secondary succession of abandoned farmland in the Loess Plateau

Soil Biology and Biochemistry

Volumn 97, Issue , 2016, Pages 40-49

  Zhang, Chao ^a   Liu, Guobin ^a,b   Xue, Sha ^a   Wang, Guoliang ^a  

^a NORTHWEST A F UNIVERSITY   (China)

^b INSTITUTE OF SOIL AND WATER CONSERVATION   (China)

Author keywords

16S rRNA sequencing; Bacterial diversity; Loess Plateau; Plant community; Secondary succession

Indexed keywords

BACTERIA; CARBON; FORESTRY; LANDFORMS; MICROORGANISMS; ORGANIC CARBON; RNA; SEDIMENTS; SOILS;

16S RRNA SEQUENCING; BACTERIAL DIVERSITY; LOESS PLATEAU; PLANT COMMUNITIES; SECONDARY SUCCESSION;

FARMS;

ABANDONED LAND; AGRICULTURAL LAND; BACTERIUM; CHRONOSEQUENCE; COMMUNITY RESPONSE; DIVERSITY INDEX; PLANT COMMUNITY; SECONDARY SUCCESSION; SOIL CARBON; SOIL MICROORGANISM; SOIL NITROGEN; SOIL PROPERTY;

CHINA; LOESS PLATEAU;

ACIDOBACTERIA; ACTINOBACTERIA; BACTERIA (MICROORGANISMS); PROTEOBACTERIA;

EID: 84960092184     PISSN: 00380717     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.soilbio.2016.02.013     Document Type: Article

References (67)

1. Abella S. Disturbance and plant succession in the Mojave and Sonoran deserts of the American southwest. International Journal of Environmental Research and Public Health 2010, 7:1248-1284.
2. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. Journal of Molecular Biology 1990, 215:403-410.
3. An S.S., Huang Y.M., Zheng F.L. Evaluation of soil microbial indices along a revegetation chronosequence in grassland soils on the Loess Plateau, Northwest China. Applied Soil Ecology 2009, 41:286-292.
4. An S.S., Huang Y.M., Zheng F.L., Yang J.G. Aggregate characteristics during natural revegetation on the Loess Plateau. Pedosphere 2008, 18:809-816.
5. Arroyo A.I., Pueyo Y., Saiz H., Alados C.L. Plant-plant interactions as a mechanism structuring plant diversity in a Mediterranean semi-arid ecosystem. Ecology and Evolution 2015, 5(22):5305-5317.
6. Bailly J., Fraissinet-Tachet L., Verner M.C., Debaud J.C., Lemaire M., Wesolowski-Louvel M., Marmeisse R. Soil eukaryotic functional diversity, a metatranscriptomic approach. ISME Journal 2007, 1:632-642.
7. 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. Applied and Environmental Microbiology 2011, 77:6158-6164.
8. Bergmann G.T., Bates S.T., Eilers K.G., Lauber C.L., Caporaso J.G., Walters W.A., Knight R., Fierer N. The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biology & Biochemistry 2011, 43:1450-1455.
9. Bissett A., Richardson A.E., Baker G., Thrall P.H. Long-term land use effects on soil microbial community structure and function. Applied Soil Ecology 2011, 51:66-78.
10. Blaalid R., Carlsen T.O.R., Kumar S., Halvorsen R., Ugland K.I., Fontana G., Kauserud H. Changes in the root-associated fungal communities along a primary succession gradient analysed by 454 pyrosequencing. Molecular Ecology 2012, 21:1897-1908.
11. Bremner J.M., Mulvaney C.S. Nitrogen-total. Methods of Soil Analysis, Part 2, Chemical and Microbial Properties 1982, 595-624. Agronomy Society of America, Agronomy Monograph 9, Madison, Wisconsin. A.L. Page, R.H. Miller, D.R. Keeney (Eds.).
12. Caporaso J.G., Bittinger K., Bushman F.D., DeSantis T.Z., Andersen G.L., Knight R. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 2010, 26:266-267.
13. Caporaso J.G., Kuczynski J., Stombaugh J., Bittinger K., Bushman F.D., Costello E.K., Fierer N., Peña A.G., Goodrich J.K., Gordon J.I., Huttley G.A., Kelley S.T., Knights D., Koenig J.E., Ley R.E., Lozupone C.A., McDonald D., Muegge B.D., Pirrung M., Reeder J., Sevinsky J.R., Turnbaugh P.J., Walters W.A., Widmann J., Yatsunenko T., Zaneveld J., Knight R. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 2010, 7:335-336.
14. Chan C.O., Casper P., Sha L.Q., Feng Z.L., Fu Y., Yang X.D., Ulrich A., Zou X.M. Vegetation cover of forest, shrub and pasture strongly influences soil bacterial community structure as revealed by 16S rRNA gene T-RFLP analysis. FEMS Microbiology Ecology 2008, 64:449-458.
15. Edgar R.C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26:2460-2461.
16. Edgar R.C., Haas B.J., Clemente J.C., Quince C., Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 27:2194-2200.
17. Erlacher A., Cernava T., Cardinale M., Soh J., Sensen C.W., Grube M., Berg G. Rhizobiales as functional and endosymbiontic members in the lichen symbiosis of Lobaria pulmonaria L. Frontiers in Microbiology 2015, 6.
18. Felske A., Wolterink A., Van Lis R., De Vos W.M., Akkermans A.D.L. Response of a soil bacterial community to grassland succession as monitored by 16S rRNA levels of the predominant ribotypes. Applied and Enviornmental Microbiology 2000, 66:3998-4003.
19. Fierer N., Bradford M.A., Jackson R.B. Toward an ecological classification of soil bacteria. Ecology 2007, 88:1354-1364.
20. Goldfarb K.C., Karaoz U., Hanson C.A., Santee C.A., Bradford M.A., Treseder K.K., Wallenstein M.D., Brodie E.L. Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance. Frontiers in Microbiology 2011, 2:94.
21. Grime J.P. Competitive exclusion in herbaceous vegetation. Nature 1973, 242:344-347.
22. Hossain Z., Sugiyama S. Geographical structure of soil microbial communities in northern Japan: effects of distance, land use type and soil properties. European Journal of Soil Biology 2011, 47:88-97.
23. Huston M. A general hypothesis of species diversity. American Naturalist 1979, 113:81-101.
24. Jangid K., Whitman W.B., Condron L.M., Turner B.L., Williams M.A. Soil bacterial community succession during long-term ecosystem development. Molecular Ecology 2013, 22:3415-3424.
25. Jiao F., Wen Z.M., An S.S. Changes in soil properties across a chronosequence of vegetation restoration on the Loess Plateau of China. Catena 2011, 86:110-116.
26. Jones R.T., Robeson M.S., Lauber C.L., Hamady M., Knight R., Fierer N. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. The ISME Journal 2009, 3:442-453.
27. Kardol P., Bezemer T.M., van der Putten W.H. Temporal variation in plant-soil feedback controls succession. Ecology Letters 2006, 9(9):1080-1088.
28. Kim H.M., Jung J.Y., Yergeau E., Hwang C.Y., Hinzman L., Nam S., Hong S.G., Kim O.S., Chun J., Lee Y.K. Bacterial community structure and soil properties of a subarctic tundra soil in council, Alaska. FEMS Microbiology Ecology 2014, 89:465-475.
29. Knelman J.E., Legg T.M., O'Neill S.P., Washenberger C.L., González A., Cleveland C.C., Nemergut D.R. Bacterial community structure and function change in association with colonizer plants during early primary succession in a glacier forefield. Soil Biology & Biochemistry 2012, 46:172-180.
30. Kolton M., Harel Y.M., Pasternak Z., Graber E.R., Elad Y., Cytryn E. Impact of biochar application to soil on the root-associated bacterial community structure of fully developed greenhouse pepper plants. Applied and Environmental Microbiology 2011, 77:4924-4930.
31. Koranda M., Schnecker J., Kaiser C., Fuchslueger L., Kitzler B., Stange C.F., Sessitsch A., Sophie Z.B., Richter A. Microbial processes and community composition in the rhizosphere of European beech-the influence of plant C exudates. Soil Biology and Biochemistry 2011, 43:551-558.
32. Kuramae E., Gamper H., Van Veen J., Kowalchuk G. Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with a neutral pH. FEMS Microbiology Ecology 2011, 77:285-294.
33. Li C.H., Ma B.L., Zhang T.Q. Soil bulk density effects on microbial populations and enzyme activities during the growth of Maize (Zea Mays L) planted in large pots under field exposure. Canadian Journal of Soil Science 2002, 82(2):1024-1032.
34. Li C.H., Yan K., Tang L.S., Jia Z.J., Li Y. Change in deep soil microbial communities due to long-term fertilization. Soil Biology & Biochemistry 2014, 75:264-272.
35. Li C.H., Zhou S. Soil bulk density effects on the seedling growth of maize. North China Agronomy 1994, 9:22-28. (in Chinese).
36. Li J., Hu H.W., Ma Y.B., Wang J.T., Liu Y.R., He J.Z. Long-term nickel exposure altered the bacterial community composition but not diversity in two contrasting agricultural soils. Environmental Science and Pollution Research 2015, 22:10496-10505.
37. Li X.Z., Rui J.P., Mao Y.J., Yannarell A., Mackie R. Dynamics of the bacterial community structure in the rhizosphere of a maize cultivar. Soil Biology & Biochemistry 2014, 68:392-401.
38. Li Y., Wen H., Chen L., Yin T. Succession of bacterial community structure and diversity in soil along a chronosequence of reclamation and re-vegetation on coal mine spoils in China. PLoS One 2014, 9:e115024.
39. Liang J., Wang X.A., Yu Z.D., Dong Z.M., Wang J.C. Effects of vegetation succession on soil fertility within farming-plantation ecotone in Ziwuling Mountains of the Loess Plateau in China. Agricultural Sciences in China 2010, 9:1481-1491.
40. Lin Y.T., Whitman W.B., Coleman D.C., Chiu C.Y. Comparison of soil bacterial communities between coastal and inland forests in a subtropical area. Applied Soil Ecology 2012, 60:49-55.
41. Lin Y.T., Whitman W.B., Coleman D.C., Chen T.H., Chiu C.Y. Composition of bacterial communities in sand dunes of subtropical coastal forests. Biology and Fertility of Soils 2014, 50:809-814.
42. Lozano Y.M., Hortal S., Armas C., Pugnaire F.I. Interactions among soil, plants, and microorganisms drive secondary succession in a dry environment. Soil Biology & Biochemistry 2014, 78:298-306.
43. Mahnert A., Moissl-Eichinger C., Berg G. Microbiome interplay: plants alter microbial abundance and diversity within the built environment. Frontiers in Microbiology 2015, 6:887.
44. Nelson D.W., Sommers L.E. Total carbon, organic carbon, and organic matter. Methods of Soil Analysis, Part 2. Chemical and Microbial Properties 1982, 539-552. Agronomy Society of America, Agronomy Monograph 9, Madison, Wisconsin. A.L. Page, R.H. Miller, D.R. Keeney (Eds.).
45. Nemergut D.R., Cleveland C.C., Wieder W.R., Washenberger C.L., Townsend A.R. Plot-scale manipulations of organic matter inputs to soils correlate with shifts in microbial community composition in a lowland tropical rain forest. Soil Biology and Biochemistry 2010, 42:2153-2160.
46. Oh Y.M., Kim M., Lee-Cruz L., Lai-Hoe A., Go R., Ainuddin N., Rahim R.A., Shukor N., Adams J.M. Distinctive bacterial communities in the rhizoplane of four tropical tree species. Microbial Ecology 2012, 64:1018-1027.
47. Olsen S.R., Sommers L.E. Phosphorous. Methods of Soil Analysis, Part 2, Chemical and Microbial Properties 1982, 403-430. Agronomy Society of America, Agronomy Monograph 9, Madison, Wisconsin. A.L. Page, R.H. Miller, D.R. Keeney (Eds.).
48. Peiffer J.A., Spor A., Koren O., Zhao J., Tringe S.G., Dangl J.L., Buckler E.S., Ley R.E. Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proceedings of the National Academy of Sciences 2013, 110:6548-6553.
49. Prosser J.I. Molecular and functional diversity in soil micro-organisms. Plant Soil 2002, 244:9-17.
50. 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., Van Horn D.J., 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.
51. Schütte U.M.E., Abdo Z., Foster J., Ravel J., Bunge J., Solheim B., Forney L.J. Bacterial diversity in a glacier foreland of the high Arctic. Molecular Ecology 2010, 19:54-66.
52. 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.
53. Singh B.K., Millard P., Whiteley A.S., Murrell J.C. Unravelling rhizosphere-microbial interactions: opportunities and limitations. Trends in Microbiology 2004, 12:386-393.
54. Suleiman A.K.A., Manoeli L., Boldo J.T., Pereira M.G., Roesch L.F.W. Shifts in soil bacterial community after eight years of land-use change. Systematic and Applied Microbiology 2013, 36:137-144.
55. Tscherko D., Ute H., Marie-Claude M., Ellen K. Shifts in rhizosphere microbial communities and enzyme activity of Poa alpina across an alpine chronosequence. Soil Biology & Biochemistry 2004, 36:1685-1698.
56. Urbanová M., Kopecký J., Valášková V., Ságová-Marečková M., Elhottová D., Kyselková M., Moënne-Loccoz Y., Baldrian P. Development of bacterial community during spontaneous succession on spoil heaps after brown coal mining. FEMS Microbiology Ecology 2011, 78:59-69.
57. Walker L.R., Walker J., Hobbs R.J. Linking Restoration and Ecological Succession 2007, 5-21. Springer, The Netherlands.
58. Walker L.R., Wardle D.A., Bardgett R.D., Clarkson B.D. The use of chronosequences in studies of ecological succession and soil development. Journal of Ecology 2010, 98:725-736.
59. Wang B., Liu G.B., Xue S., Zhu B.B. Changes in soil physico-chemical and microbiological properties during natural succession on abandoned farmland in the Loess Plateau. Environmental Earth Sciences 2010, 62:915-925.
60. Wang G.L., Liu G.B., Xu M.X. Above and belowground dynamics of plant community succession following abandonment of farmland on the Loess Plateau, China. Plant Soil 2009, 316:227-239.
61. Wang Q., Garrity G.M., Tiedje J.M., Cole J.R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology 2007, 73:5261-5267.
62. Williams M.A., Jangid K., Shanmugam S.G., Whitman W.B. Bacterial communities in soil mimic patterns of vegetative succession and ecosystem climax but are resilient to change between seasons. Soil Biology & Biochemistry 2013, 57:749-757.
63. Xu L.h., Ravnskov Sabine, Larsen J., Nilsson R.H., Nicolaisen M. Soil fungal community structure along a soil health gradient in pea fields examined using deep amplicon sequencing. Soil Biology & Biochemistry 2012, 46:26-32.
64. Yao M.J., Rui J.P., Li J.B., Dai Y.M., Bai Y.F., Hedenec P., Wang J.M., Zhang S.H., Pei K.Q., Liu C., Wang Y.F., He Z.L., Frouz J., Li X.Z. Rate-specific responses of prokaryotic diversity and structure to nitrogen deposition in the Leymus chinensis steppe. Soil Biology & Biochemistry 2014, 79:81-90.
65. Yuan Y.L., Si G.C., Wang J., Luo T.X., Zhang G.X. Bacterial community in alpine grasslands along an altitudinal gradient on the Tibetan Plateau. FEMS Microbiology Ecology 2014, 87:121-132.
66. Zhang C., Liu G.B., Xue S., Wang G.L. Changes in rhizospheric microbial community structure and function during the natural recovery of abandoned cropland on the Loess Plateau, China. Ecological Engineering 2015, 75:161-171.
67. Zhang J.T. Succession analysis of plant communities in abandoned croplands in the eastern Loess Plateau of China. Journal of Arid Environments 2005, 63:458-474.