Determinants of the biodiversity patterns of ammonia-oxidizing archaea community in two contrasting forest stands
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  • 作者:Jie Chen ; Yichao Rui ; Xuan Zhou ; Wanhui Ye ; Wei Liu
  • 关键词:Ammonia ; oxidizing archaea ; Beta diversity ; Forest succession ; Genetic distance ; MRM ; Subtropical forests
  • 刊名:Journal of Soils and Sediments
  • 出版年:2016
  • 出版时间:March 2016
  • 年:2016
  • 卷:16
  • 期:3
  • 页码:878-888
  • 全文大小:992 KB
  • 参考文献:Bahram M, Koljalg U, Courty PE et al (2013) The distance decay of similarity in communities of ectomycorrhizal fungi in different ecosystems and scales. J Ecol 101:1335–1344CrossRef
    Borcard D, Legendre P (1994) Environmental control and spatial structure in ecological communities: an example using oribatid mites (Acari, Oribatei). Environ Ecol Stat 1:37–61CrossRef
    Brant JB, Myrold DD, Sulzman EW (2006) Root controls on soil microbial community structure in forest soils. Oecologia 148:650–659CrossRef
    Bru D, Ramette A, Saby NPA et al (2011) Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale. ISME J 5:532–542CrossRef
    Chen XF, Li ZP, Liu M et al (2015) Microbial community and functional diversity associated with different aggregate fractions of a paddy soil fertilized with organic manure and/or NPK fertilizer for 20 years. J Soil Sediment 15:292–301CrossRef
    Dang H, Li J, Zhang X et al (2009) Diversity and spatial distribution ofamoA-encoding archaea in the deep-sea sediments of the tropical West Pacific Continental Margin. J Appl Microbiol 106:1482–1493CrossRef
    de Gannes V, Eudoxie G, Hickey WJ (2014) Impacts of edaphic factors on communities of ammonia-oxidizing archaea, ammonia-oxidizing bacteria and nitrification in tropical soils. PLoS One 9(2):e89568CrossRef
    Di HJ, Cameron KC, Shen JP et al (2010) Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions. FEMS Microbiol Ecol 72:386–394CrossRef
    Dray S, Legendre P, Peres-Neto PR (2006) Spatial modelling: a comprehensive framework for principal coordinate analysis of neighbour matrices (PCNM). Ecol Model 196:483–493CrossRef
    Dumbrell AJ, Nelson M, Helgason T et al (2010) Relative roles of niche and neutral processes in structuring a soil microbial community. ISME J 4:1078–1078CrossRef
    Fang YT, Yoh M, Koba K et al (2011) Nitrogen deposition and forest nitrogen cycling along an urban–rural transect in southern China. Glob Change Biol 17:872–885CrossRef
    Flinn KM, Lechowicz MJ, Waterway MJ (2008) Plant species diversity and composition of wetlands within an upland forest. Am J Bot 95:1216–1224CrossRef
    Florencio M, Diaz-Paniagua C, Gomez-Rodriguez C, Serrano L (2014) Biodiversity patterns in a macroinvertebrate community of a temporary pond network. Insect Conserv Diver 7:4–21CrossRef
    Fu QL, Liu C, Ding NF et al (2012) Soil microbial communities and enzyme activities in a reclaimed coastal soil chronosequence under rice-barley cropping. J Soil Sediment 12:1134–1144CrossRef
    Gilbert B, Bennett JR (2010) Partitioning variation in ecological communities: do the numbers add up? J Appl Ecol 47:1071–1082CrossRef
    Goslee SC, Urban DL (2007) The ecodist package for dissimilarity-based analysis of ecological data. J Stat Softw 22:1–19CrossRef
    Haichar FE, Marol C, Berge O et al (2008) Plant host habitat and root exudates shape soil bacterial community structure. ISME J 2:1221–1230CrossRef
    Hatzenpichler R (2012) Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea. Appl Environ Microb 78:7501–7510CrossRef
    Hedin LO, Vitousek PM, Matson PA (2003) Nutrient losses over four million years of tropical forest development. Ecology 84:2231–2255CrossRef
    Hooper DU, Bignell DE, Brown VK et al (2000) Interactions between aboveground and belowground biodiversity in terrestrial ecosystems: patterns, mechanisms, and feedbacks. Bioscience 50:1049–1061CrossRef
    Hu CJ, Fu BJ, Liu GH et al (2010) Vegetation patterns influence on soil microbial biomass and functional diversity in a hilly area of the Loess Plateau, China. J Soil Sediment 10:1082–1091CrossRef
    Huang WJ, Liu JX, Tang XL et al (2009) Inorganic nitrogen and available phosphorus concentrations in the soils of five forests at Dinghushan, China*. Chinese J of Appplied Environ Biol 2009:441–447 (in Chinese)CrossRef
    Isobe K, Koba K, Suwa Y et al (2012) High abundance of ammonia-oxidizing archaea in acidified subtropical forest soils in southern China after long-term N deposition. Fems Microbiol Ecol 80:193–203CrossRef
    Keiser AD, Strickland MS, Fierer N, Bradford MA (2011) The effect of resource history on the functioning of soil microbial communities is maintained across time. Biogeosciences 8:1477–1486CrossRef
    Koleff P, Gaston KJ, Lennon JJ (2003) Measuring beta diversity for presence-absence data. J Anim Ecol 72:367–382CrossRef
    Konneke M, Bernhard AE, de la Torre JR et al (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437:543–546CrossRef
    Krsek M, Wellington EMH (1999) Comparison of different methods for the isolation and purification of total community DNA from soil. J Microbiol Meth 39:1–16CrossRef
    Legendre P, Lapointe FJ, Casgrain P (1994) Modelling brain evolution from behavior: a permutational regression approach. Evolution 48:1487–1499CrossRef
    Li JJ, Zheng YM, Yan JX et al (2013) Succession of plant and soil microbial communities with restoration of abandoned land in the Loess Plateau, China. J Soil Sediment 13:760–769CrossRef
    Liang Y, He X, Liang S et al (2014) Community structure analysis of soil ammonia oxidizers during vegetation restoration in southwest China. J Basic Microb 54:180–189CrossRef
    Lichstein JW (2007) Multiple regression on distance matrices: a multivariate spatial analysis tool. Plant Ecol 188:117–131CrossRef
    Liu GS, Jiang NH, Zhang LD, Liu ZL (1996) Soil physical and chemical analysis and description of soil profiles. China Standards Press, Beijing
    Liu J, Yan HF, Newmaster SG et al (2015) The use of DNA barcoding as a tool for the conservation biogeography of subtropical forests in China. Divers Distrib 21:188–199CrossRef
    Liu KH, Fang YT, Yu FM et al (2010) Soil acidification in response to acid deposition in three subtropical forests of subtropical China. Pedosphere 20:399–408CrossRef
    Liu L, Zhang T, Gilliam FS et al (2013) Interactive effects of nitrogen and phosphorus on soil microbial communities in a tropical forest. PLoS One 8(4):e61188CrossRef
    Liu WP, Cao HL, Liu W et al (2011) Study on diversity of monsoon evergreen broad leaved forest in different kinds of habitat in Dinghushan. J of Anhui Agri Sci 39:16159–16163 (in Chinese)
    Lu L, Jia Z (2013) Urease gene-containing Archaeadominate autotrophic ammonia oxidation in two acid soils. Environ Microbiol 15:1795–1809CrossRef
    Ma L, Chen C, Shen Y et al (2014) Determinants of tree survival at local scale in a sub-tropical forest. Ecol Res 29:69–80CrossRef
    Madritch MD, Hunter MD (2002) Phenotypic diversity influences ecosystem functioning in an oak sandhills community. Ecology 83:2084–2090CrossRef
    Martiny JBH, Bohannan BJM, Brown JH et al (2006) Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4:102–112CrossRef
    Martiny JBH, Eisen JA, Penn K et al (2011) Drivers of bacterial beta-diversity depend on spatial scale. Proc Natl Acad Sci U S A 108:7850–7854CrossRef
    McArthur JV, Kovacic DA, Smith MH (1988) Genetic diversity in natural populations of a soil bacterium across a landscape gradient. Proc Natl Acad Sci U S A 85:9621–9624
    McCaig AE, Glover LA, Prosser JI (2001) Numerical analysis of grassland bacterial community structure under different land management regimens by using 16S ribosomal DNA sequence data and denaturing gradient gel electrophoresis banding patterns. Appl Environ Microb 67:4554–4559CrossRef
    Merila P, Malmivaara-Lamsa M, Spetz P et al (2010) Soil organic matter quality as a link between microbial community structure and vegetation composition along a successional gradient in a boreal forest. Appl Soil Ecol 46:259–267CrossRef
    Muyzer G, Dewaal EC, Uitterlinden AG (1993) Profiling of complex microbial-populations by denaturing gradient gel-electrophoresis analysis of polymerase chain reaction-amplified genes-coding for 16s ribosomal-RNA. Appl Environ Microb 59:695–700
    Nicol GW, Leininger S, Schleper C, Prosser JI (2008) The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ Microbiol 10:2966–2978CrossRef
    O’Hanlon R, Harrington TJ (2012) Macrofungal diversity and ecology in four Irish forest types. Fungal Ecol 5:499–508CrossRef
    Peres-Neto PR, Legendre P, Dray S, Borcard D (2006) Variation partitioning of species data matrices: estimation and comparison of fractions. Ecology 87:2614–2625CrossRef
    Prosser JI, Nicol GW (2012) Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation. Trends Microbiol 20:523–531CrossRef
    Ramette A, Tiedje JM (2007) Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem. Proc Natl Acad Sci U S A 104:2761–2766CrossRef
    Saetre P (1999) Spatial patterns of ground vegetation, soil microbial biomass and activity in a mixed spruce-birch stand. Ecography 22:183–192CrossRef
    Schweitzer JA, Bailey JK, Fischer DG et al (2008) Plant-soil-microorganism interactions: heritable relationship between plant genotype and associated soil microorganisms. Ecology 89:773–781CrossRef
    Southwood TRE, Henderson PA (2000) Ecological methods. Blackwell Science, Oxford
    Tamura K, Peterson D, Peterson N et al (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739CrossRef
    Tourna M, Freitag TE, Nicol GW, Prosser JI (2008) Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms. Environ Microbiol 10:1357–1364CrossRef
    Treusch AH, Leininger S, Kletzin A et al (2005) Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environ Microbiol 7:1985–1995CrossRef
    Wang JJ, Wu YC, Jiang HC et al (2008) High beta diversity of bacteria in the shallow terrestrial subsurface. Environ Microbiol 10:2537–2549CrossRef
    Wang JT, Zheng YM, Hu HW et al (2015) Soil pH determines the alpha diversity but not beta diversity of soil fungal community along altitude in a typical Tibetan forest ecosystem. J Soil Sediment 15:1224–1232CrossRef
    Wardle DA, Bardgett RD, Klironomos JN et al (2004) Ecological linkages between aboveground and belowground biota. Science 304:1629–1633CrossRef
    Wessen E, Soderstrom M, Stenberg M et al (2011) Spatial distribution of ammonia-oxidizing bacteria and archaea across a 44-hectare farm related to ecosystem functioning. ISEM J 5:1213–1225CrossRef
    Yan ER, Wang XH, Huang JJ et al (2007) Long-lasting legacy of forest succession and forest management: Characteristics of coarse woody debris in an evergreen broad-leaved forest of Eastern China. Forest Ecol Manag 252:98–107CrossRef
    Zhalnina K, de Quadros PD, Camargo FA, Triplett EW (2012) Drivers of archaeal ammonia-oxidizing communities in soil. Front Microbiol 3:210CrossRef
    Zhang LM, Hu HW, Shen JP, He JZ (2012) Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils. ISEM J 6:1032–1045CrossRef
    Zhao Y, Zhou ZH, Li W et al (2005) DNA extraction from soil for molecular microbial community analysis. J of Agro-Environ sci 24:854–860 (in Chinese)
  • 作者单位:Jie Chen (1) (2)
    Yichao Rui (3)
    Xuan Zhou (1) (2)
    Wanhui Ye (1)
    Wei Liu (1)

    1. Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xinke Rd. Tianhe District, Guangzhou, 510650, China
    2. University of Chinese Academy of Sciences, Beijing, China
    3. Soil Biology and Molecular Ecology Group, School of Earth and Environment, the University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
  • 刊物类别:Earth and Environmental Science
  • 刊物主题:Environment
    Soil Science and Conservation
    Environment
    Environmental Physics
  • 出版者:Springer Berlin / Heidelberg
  • ISSN:1614-7480
文摘
Purpose The variation in soil microbial community patterns is primarily influenced by ecological processes associated with spatial distance and environmental heterogeneities. However, the relative importance of these processes in determining the patterns of soil microbial biodiversity in different successional forests remains unclear.

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