Shifts in the bacterial community structure and function along a vegetation gradient in the Great Xing’an Mountains

References

• Acosta-Martinez V, Dowd S, Sun Y, Allen V. 2008. Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol Biochem. 40:2762–2770. doi: 10.1016/j.soilbio.2008.07.022
   Web of Science ®Google Scholar
• Amato KR, Yeoman CJ, Kent A, Righini N, Carbonero F, Estrada A, Gaskins HR, Stumpf RM, Yildirim S, Torralba M. 2013. Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. Isme J. 7:1344–1353. doi: 10.1038/ismej.2013.16
   PubMed Web of Science ®Google Scholar
• An SS, Huang YM, Zheng FL. 2009. Evaluation of soil microbial indices along a revegetation chronosequence in grassland soils on the Loess Plateau, Northwest China. Appl Soil Ecol. 41:286–292. doi: 10.1016/j.apsoil.2008.12.001
   Web of Science ®Google Scholar
• Andruschkewitsch M, Wachendorf C, Sradnick A, Hensgen F, Joergensen RG, Wachendorf M. 2014. Soil substrate utilization pattern and relation of functional evenness of plant groups and soil microbial community in five low mountain natura 2000. Plant Soil. 383:275–289. doi: 10.1007/s11104-014-2167-9
   Web of Science ®Google Scholar
• Atkinson D, Watson CA. 2000. The beneficial rhizosphere: a dynamic entity. Appl Soil Ecol. 15:99–104. doi: 10.1016/S0929-1393(00)00084-6
   Web of Science ®Google Scholar
• Bell CW, Acosta-Martinez V, Mcintyre NE, Cox S, Tissue DT, Zak JC. 2009. Linking microbial community structure and function to seasonal differences in soil moisture and temperature in a Chihuahuan desert grassland. Microbial Ecol. 58:827–842. doi: 10.1007/s00248-009-9529-5
   PubMed Web of Science ®Google Scholar
• Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 456:53–59. doi: 10.1038/nature07517
   PubMed Web of Science ®Google Scholar
• Berard A, Bouchet T, Sévenier G, Pablo AL, Gros R. 2011. Resilience of soil microbial communities impacted by severe drought and high temperature in the context of Mediterranean heat waves. Eur J Soil Biol. 47:333–342. doi: 10.1016/j.ejsobi.2011.08.004
   Web of Science ®Google Scholar
• Bowman JP, Nichols DS. 2005. Novel members of the family Flavobacteriaceae from Antarctic maritime habitats including Subsaximicrobium wynnwilliamsii gen. nov., sp. nov., Subsaximicrobium saxinquilinus sp. nov., Subsaxibacter broadyi gen. nov., sp. nov., Lacinutrix copepodicola gen. nov., sp. nov., and novel species of the genera Bizionia, Gelidibacter and Gillisia. Int J Syst Evol Microbiol. 55:1471–1486. doi: 10.1099/ijs.0.63527-0
   PubMed Web of Science ®Google Scholar
• Carney KM, Matson PA. 2005. Plant communities, soil microorganisms, and soil carbon cycling: does altering the world belowground matter to ecosystem functioning? Ecosystems. 8:928–940. doi: 10.1007/s10021-005-0047-0
   Web of Science ®Google Scholar
• Davinic M, Fultz LM, Acosta-Martinez V, Calderón FJ, Cox SB, Dowd SE, Allen VG, Zak JC, Moore-Kucera J. 2012. Pyrosequencing and mid-infrared spectroscopy reveal distinct aggregate stratification of soil bacterial communities and organic matter composition. Soil Biol Biochem. 46:63–72. doi: 10.1016/j.soilbio.2011.11.012
   Web of Science ®Google Scholar
• de Castro VHL, Schroeder LF, Quirino BF, Kruger RH, Barreto CC. 2013. Acidobacteria from oligotrophic soil from the cerrado can grow in a wide range of carbon source concentrations. Can J Microbiol. 59:746–753. doi: 10.1139/cjm-2013-0331
   PubMed Web of Science ®Google Scholar
• Degens BP, Vojvodić-Vuković M. 1999. A sampling strategy to assess the effects of land use on microbial functional diversity in soils. Soil Res. 37:593–602.
   Web of Science ®Google Scholar
• Eichorst SA, Breznak JA, Schmidt TM. 2007. Isolation and characterization of soil bacteria that define Teniglobus gen. nov., in the phylum Acidobacteria. Appl Environ Microb. 73:2708–2717. doi: 10.1128/AEM.02140-06
   PubMed Web of Science ®Google Scholar
• Eisenhauer N, Yee K, Johnson EA, Maraun M, Parkinson D, Straube D, Scheu S. 2011. Positive relationship between herbaceous layer diversity and the performance of soil biota in a temperate forest. Soil Biol Biochem. 43:462–465. doi: 10.1016/j.soilbio.2010.10.018
   Web of Science ®Google Scholar
• Fierer N, Bradford MA, Jackson RB. 2007. Toward an ecological classification of soil bacteria. Ecology. 88:1354–1364. doi: 10.1890/05-1839
   PubMed Web of Science ®Google Scholar
• Fierer N, Jackson RB. 2006. The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA. 103:626–631. doi: 10.1073/pnas.0507535103
   PubMed Web of Science ®Google Scholar
• Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, Knight R. 2012. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J. 6:1007–1017. doi: 10.1038/ismej.2011.159
   PubMed Web of Science ®Google Scholar
• Fu WG, Li PP, Wu YY, Bian XM. 2006. Diurnal dynamics of microclimate at different succession stages of vegetation communities in inner-river wetland of Zhenjiang city. Chinese J Appl Ecol. 17:1699–1704.
   Google Scholar
• Gan QM. 2013. Nutrients stoichiometry of soil and plant at different vegetation degradation stages in the northern greater Xing’an mountains. Harbin: Northeast Forestry University.
   Google Scholar
• Gan QM, Sun HL, Zheng H, Hao LF, Liu TY. 2013. Concentrations of C, N, P and stoichiometry of soil and plant at the different vegetation degradation stages in great Xing’an mountains. Forest Eng. 29:1–5.
   Google Scholar
• Garcia C, Roldan A, Hernandez T. 2005. Ability of different plant species to promote microbiological processes in semiarid soil. Geoderma. 124:193–202. doi: 10.1016/j.geoderma.2004.04.013
   Web of Science ®Google Scholar
• Gardner T, Acostamartinez V, Senwo Z, Dowd SE. 2011. Soil rhizosphere microbial communities and enzyme activities under organic farming in Alabama. Diversity. 3:308–328. doi: 10.3390/d3030308
   Google Scholar
• Garland JL. 1996. Analytical approaches to the characterization of samples of microbial communities using patterns of potential C source utilization. Soil Biol Biochem. 28:213–221. doi: 10.1016/0038-0717(95)00112-3
   Web of Science ®Google Scholar
• Garland JL. 1997. Analysis and interpretation of community-level physiological profiles in microbial ecology. Fems Microbiol Ecol. 24:289–300. doi: 10.1111/j.1574-6941.1997.tb00446.x
   Web of Science ®Google Scholar
• Garland JL, Mills AL. 1991. Classification and characterization of heterotrophic microbial communities on the basis of patterns of community level sole carbon source utilization. Appl Environ Microb. 57:2351–2359.
   PubMed Web of Science ®Google Scholar
• Grayston SJ, Griffith GS, Mawdsley JL, Campbell CD, Bardgett RD. 2001. Accounting for variability in soil microbial communities of temperate upland grassland ecosystems. Soil Biol Biochem. 33:533–551. doi: 10.1016/S0038-0717(00)00194-2
   Web of Science ®Google Scholar
• He F, Yang B, Wang H, Yan Q, Cao Y, He X. 2016. Changes in composition and diversity of fungal communities along Quercus mongolica forests developments in Northeast China. Appl Soil Ecol. 100:162–171. doi: 10.1016/j.apsoil.2015.12.014
   Web of Science ®Google Scholar
• Helal HM, Sauerbeck D. 1989. Carbon turnover in the rhizosphere. J Plant Nutr Soil Sc. 152:211–216.
   Web of Science ®Google Scholar
• Hobbie SE, Oleksyn J, Eissenstat DM, Reich PB. 2010. Fine root decomposition rates do not mirror those of leaf litter among temperate tree species. Oecologia. 162:505–513. doi: 10.1007/s00442-009-1479-6
   PubMed Web of Science ®Google Scholar
• Huang X, Liu L, Wen T, Zhu R, Zhang J, Cai Z. 2015. Illumina MiSeq investigations on the changes of microbial community in the Fusarium oxysporum f.sp. cubense infected soil during and after reductive soil disinfestation. Microbiol Res. 181:33–42. doi: 10.1016/j.micres.2015.08.004
   PubMed Web of Science ®Google Scholar
• Jangid K, Williams MA, Franzluebbers AJ, Schmidt TM, Coleman DC, Whitman WB. 2011. Land-use history has a stronger impact on soil microbial community composition than aboveground vegetation and soil properties. Soil Biol Biochem. 42:162–168.
   Google Scholar
• Jones RT, Robeson MS, Lauber CL, Hamady M, Knight R, Fierer N. 2009. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J. 3:442–453. doi: 10.1038/ismej.2008.127
   PubMed Web of Science ®Google Scholar
• Joos FIC, Prentice S, Sitch R, Meyer G, Hoos GK, Plattner S, Hasselmann K. 2001. Global warming feedbacks on terrestrial carbon uptake under the intergovernmental panel on climate change (IPCC) emission scenarios. Global Biogeochem Cycle.15:891–907. doi: 10.1029/2000GB001375
   Web of Science ®Google Scholar
• Kara Ö, Bolat I, Çakıroğlu K, Öztürk M. 2008. Plant canopy effects on litter accumulation and soil microbial biomass in two temperate forests. Biol Fert Soils. 43:2184–2193.
   Google Scholar
• Kirchman DL. 2002. The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol Ecol. 39:91–100.
   PubMed Web of Science ®Google Scholar
• Klopatek CC, De Bano LF, Klopatek JM. 1988. Effects of simulated fire on vesicular-arbuscular mycorrhizae in pinyon-juniper woodland soil. Plant Soil. 109:245–249. doi: 10.1007/BF02202090
   Web of Science ®Google Scholar
• Kuramae EE, Yergeau E, Wong LC, Pijl AS, van Veen JA, Kowalchuk GA. 2012. Soil characteristics more strongly influence soil bacterial communities than land-use type. FEMS Microbiol Ecol. 79:12–24. doi: 10.1111/j.1574-6941.2011.01192.x
   PubMed Web of Science ®Google Scholar
• Ladygina N, Hedlund K. 2010. Plant species influence microbial diversity and carbon allocation in the rhizosphere. Soil Biol Biochem. 42:162–168. doi: 10.1016/j.soilbio.2009.10.009
   Web of Science ®Google Scholar
• LaMontagne MG, Schimel JP, Holden PA. 2003. Comparison of subsurface and surface soil bacterial communities in California grassland as assessed by terminal restriction fragment length polymorphisms of PCR amplified 16S rRNA genes. Microb Ecol. 46:216–227. doi: 10.1007/s00248-003-1006-y
   PubMed Web of Science ®Google Scholar
• Lewandowski TE, Forrester JA, Mladenoff DJ, D’Amato AW, Palik BJ. 2016. Response of the soil microbial community and soil nutrient bioavailability to biomass harvesting and reserve tree retention in northern Minnesota aspen-dominated forests. Appl Soil Ecol. 99:110–117. doi: 10.1016/j.apsoil.2015.11.001
   Web of Science ®Google Scholar
• Liu JJ, Sui YY, Yu ZH, Yao Q, Shi Y, Chu HY, Jin J, Liu XB, Wang GH. 2016. Diversity and distribution patterns of acidobacterial communities in the black soil zone of northeast China. Soil Biol Biochem. 95:212–222. doi: 10.1016/j.soilbio.2015.12.021
   Web of Science ®Google Scholar
• Li X, Sun ML, Zhang HH, Xu N, Sun GY. 2016. Use of mulberry-soybean intercropping in salt-alkali soil impacts the diversity of the soil bacterial community. Microb Biotechnol. 9:293–304. doi: 10.1111/1751-7915.12342
   PubMed Web of Science ®Google Scholar
• Lynch JM, Whipps JM. 1990. Substrate flow in the rhizosphere. Plant Soil. 129:1–10. doi: 10.1007/BF00011685
   Web of Science ®Google Scholar
• Marschner P, Yang CH, Lieberei R, Crowley DE. 2001. Soil and plant specific effects on bacterial community composition in the rhizosphere. Soil Biol Biochem. 33:1437–1445. doi: 10.1016/S0038-0717(01)00052-9
   Web of Science ®Google Scholar
• Marshall CB, McLaren JR, Turkington R. 2011. Soil microbial communities resistant to changes in plant functional group composition. Soil Biol Biochem. 43:78–85. doi: 10.1016/j.soilbio.2010.09.016
   Web of Science ®Google Scholar
• Meharg AA, Killham K. 1990. The effect of soil pH on rhizosphere carbon flow of Lolium perenne. Plant Soil. 123:1–7. doi: 10.1007/BF00009920
   Web of Science ®Google Scholar
• Mitchell RJ, Keith AM, Potts JM, Ross J, Reid E, Dawson LA. 2012. Overstory and understory vegetation interact to alter soil community composition and activity. Plant Soil. 352:65–84. doi: 10.1007/s11104-011-0980-y
   Web of Science ®Google Scholar
• Mu C, Lu H, Wang B, Bao X, Cui W. 2013. Short-term effects of harvesting on carbon storage of boreal Larix gmelinii-Carex schmidtii forested wetlands in Daxing’anling, northeast China. Forest Ecol Manag. 293:140–148. doi: 10.1016/j.foreco.2012.12.031
   Web of Science ®Google Scholar
• Naether A, Foesel BU, Naegele V, Wüst PK, Weinert J, Bonkowski M, Alt F, Oelmann Y, Polle A, Lohaus G, et al. 2012. Environmental factors affect acidobacterial communities below the subgroup level in grassland and forest soils. Appl Environ Microb. 7:7398–7406. doi: 10.1128/AEM.01325-12
   Web of Science ®Google Scholar
• Navarrete AA, Kuramae EE, de Hollander M, Pijl AS, van Veen JA, Tsai SM. 2013. Acidobacterial community responses to agricultural management of soybean in Amazon forest soils. FEMS Microbiol Ecol. 83:607–621. doi: 10.1111/1574-6941.12018
   PubMed Web of Science ®Google Scholar
• Nemergut DR, Cleveland CC, Wieder WR, Washenberger CL, Townsend AR. 2010. Plot-scale manipulations of organic matter inputs to soils correlate with shifts in microbial community composition in a lowland tropical rain forest. Soil Biol Biochem. 42:2153–2160. doi: 10.1016/j.soilbio.2010.08.011
   Web of Science ®Google Scholar
• Pettit NM, Smith ARJ, Freedman RB, Burns RG. 1976. Soil urease: activity, stability and kinetic properties. Soil Biol Biochem. 8:479–484. doi: 10.1016/0038-0717(76)90089-4
   Web of Science ®Google Scholar
• Rayment G, Higginson FR. 1992. Australian laboratory hand book of soil and water chemical methods. Melbourne: Inkata Press.
   Google Scholar
• Roesch LFW, Fulthorpe RR, Riva A, Casella G, Hadwin AKM, Kent AD, Daroub SH, Camargo FAO, Farmerie WG, Triplett EW. 2007. Pyrosequencing enumerates and contrasts soil microbial diversity. Isme J. 1:283–290. doi: 10.1038/ismej.2007.53
   PubMed Web of Science ®Google Scholar
• Rutgers M, Breure AM, Insam H, Bloem J, Benedetti A, Hopkins DW. 2006. Substrate utilization in Biolog^TM plates for analysis of CLPP. Wallington: CABI Publishing; p. 212–227.
   Google Scholar
• Saiya-Cork KR, Sinsabaugh RL, Zak DR. 2002. The effects of long term nitrogen deposition on extracellular enzyme activity in an Acer saccharum forest soil. Soil Biol Biochem. 34:1309–1315. doi: 10.1016/S0038-0717(02)00074-3
   Web of Science ®Google Scholar
• Salomo S, Münch C, Röske I. 2009. Evaluation of the metabolic diversity of microbial communities in four different filter layers of a constructed wetland with vertical flow by Biolog™ analysis. Water Res. 43:4569–4578. doi: 10.1016/j.watres.2009.08.009
   PubMed Web of Science ®Google Scholar
• Shi JY, Yuan XF, Lin HR, Yang YQ, Li ZY. 2011. Differences in soil properties and bacterial communities between the rhizosphere and bulk soil and among different production areas of the medicinal plant Fritillaria thunbergii. Int J Mol Sci. 12:3770–3785. doi: 10.3390/ijms12063770
   PubMed Web of Science ®Google Scholar
• Silver MCR, Nkwiine C. 2007. A review of studies on decomposer microbiota in Uganda. Afr J Ecol. 45:36–44. doi: 10.1111/j.0141-6707.2007.00804.x
   Web of Science ®Google Scholar
• Singleton DR, Furlong MA, Rathbun SL, Whitman WB. 2001. Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl Environ Microb. 67:4374–4376. doi: 10.1128/AEM.67.9.4374-4376.2001
   PubMed Web of Science ®Google Scholar
• Song YN, Zhang FS, Marschner P, Fan FL, Gao HM, Bao XG, Sun JH, Li L. 2007. Effect of intercropping on crop yield and chemical and microbiological properties in rhizosphere of wheat (Triticum aestivum L.), maize (Zea mays L.), and faba bean (Vicia faba L.). Biol Fert Soils. 43:565–574. doi: 10.1007/s00374-006-0139-9
   Web of Science ®Google Scholar
• Spohn M, Kuzyakov Y. 2014. Spatial and temporal dynamics of hotspots of enzyme activity in soil as affected by living and dead roots-a soil zymography analysis. Plant Soil. 379:67–77. doi: 10.1007/s11104-014-2041-9
   Web of Science ®Google Scholar
• Sradnick A, Murugan R, Oltmanns M, Raupp J, Joergensen RG. 2013. Changes in functional diversity of the soil microbial community in a heterogeneous sandy soil after long-term fertilization with cattle manure and mineral fertilizer. Appl Soil Ecol. 63:23–28. doi: 10.1016/j.apsoil.2012.09.011
   Web of Science ®Google Scholar
• Stursova M, Sinsabaugh RL. 2008. Stabilization of oxidative enzymes in desert soil may limit organic matter accumulation. Soil Biol Biochem. 40:550–553. doi: 10.1016/j.soilbio.2007.09.002
   Web of Science ®Google Scholar
• Tabatabai MA. 1994. Soil enzymes. In: RW Weaver, JS Angle, PS Bottomley, editors. Methods of soil analysis: part 2-microbiological and biochemical properties. Madison: Soil Science Society of America; p. 775–833.
   Google Scholar
• Venkatesan S, Senthurpandian VK. 2006. Comparison of enzyme activity with depth under tea plantations and forested sites in south India. Geoderma. 137:212–216. doi: 10.1016/j.geoderma.2006.08.011
   Web of Science ®Google Scholar
• Walkley AJ, Blank IA. 1933. An examination of degradation method for determining soil organic matter: A proposed modification of the chromic acid titration method. Soil Sci. 37:29–38. doi: 10.1097/00010694-193401000-00003
   Google Scholar
• Wang XH, Hu M, Xia Y, Wen XH, Ding K. 2012. Pyrosequencing analysis of bacterial diversity in 14 wastewater treatment systems in China. Appl Environ Microbiol. 78:7042–7047. doi: 10.1128/AEM.01617-12
   PubMed Web of Science ®Google Scholar
• Wang ZL. 2005. The change analyses of the forest resource in Daxinganling. Forest By Product and Speciality in China. 3:61–62.
   Google Scholar
• 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 Microb. 67:5849–5854. doi: 10.1128/AEM.67.12.5849-5854.2001
   PubMed Web of Science ®Google Scholar
• Zak DR, Holmes WE, White DC, Peacock AD, Tilman D. 2003. Plant diversity, soil microbial communities, and ecosystem function: are there any links? Ecology. 84:2042–2050. doi: 10.1890/02-0433
   Web of Science ®Google Scholar
• Zelles L. 1999. Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: a review. Biol Fert Soils. 29:111–129. doi: 10.1007/s003740050533
   Web of Science ®Google Scholar
• Zhang B, Deng H, Wang HL, Yin R, Hallett PD, Griffiths BS, Daniell TJ. 2010. Does microbial habitat or community structure drive the functional stability of microbes to stresses following re-vegetation of a severely degraded soil? Soil Biol Biochem. 42:850–859. doi: 10.1016/j.soilbio.2010.02.004
   Web of Science ®Google Scholar
• Zhang B, Wang H, Yao S, Bi L. 2013. Litter quantity confers soil functional resilience through mediating soil biophysical habitat and microbial community structure on an eroded bare land restored with mono Pinus massoniana. Soil Biol Biochem. 57:556–567. doi: 10.1016/j.soilbio.2012.07.024
   Web of Science ®Google Scholar
• Zhang YG, Cong J, Lu H, Yang CY, Yang YF, Zhou JZ, Li DQ. 2014. An integrated study to analyze soil microbial community structure and metabolic potential in Two forest types. Plos One. 9:e93773. doi: 10.1371/journal.pone.0093773
   PubMed Web of Science ®Google Scholar
• Zhou J, Zhou X, Li Y, Xing J. 2015. Bacterial communities in haloalkaliphilic sulfate-reducing bioreactors under different electron donors revealed by 16S rRNA MiSeq sequencing. J Hazard Mater. 295:176–184. doi: 10.1016/j.jhazmat.2015.04.010
   PubMed Web of Science ®Google Scholar
• Zul D, Denzel S, A, Overmann J. 2007. Effects of plant biomass, plant diversity, and water content on bacterial communities in soil lysimeters: implications for the determinants of bacterial diversity. Appl Environ Microb. 73:6916–6929. doi: 10.1128/AEM.01533-07
   PubMed Web of Science ®Google Scholar