Soil carbon content drives the biogeographical distribution of fungal communities in the black soil zone of northeast China

Soil Biology and Biochemistry - Tập 83 - Trang 29-39 - 2015
Junjie Liu1, Yueyu Sui1, Guanghua Wang1, Yu Shi2, Haiyan Chu2, Jian Jin1, Xiaobing Liu1
1Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
2State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China

Tóm tắt

Từ khóa


Tài liệu tham khảo

Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, 25, 3389, 10.1093/nar/25.17.3389

Anderson, 2004, Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques, Environmental Microbiology, 6, 769, 10.1111/j.1462-2920.2004.00675.x

Baker, 2009, Environmental and spatial characterisation of bacterial community composition in soil to inform sampling strategies, Soil Biology & Biochemistry, 41, 2292, 10.1016/j.soilbio.2009.08.010

Bates, 2013, Meeting report: fungal ITS workshop (October 2012), Stands in Genomic Sciences, 8, 118, 10.4056/sigs.3737409

Brown, 2014, Contrasting primary successional trajectories of fungi and bacteria in retreating glacier soils, Molecular Ecology, 23, 481, 10.1111/mec.12487

Buée, 2009, 454 pyrosequencing analyses of forest soils reveal an unexpectedly fungal diversity, New Phytologist, 184, 449, 10.1111/j.1469-8137.2009.03003.x

Caporaso, 2010, QIIME allows integration and analysis of high-throughput community sequencing data, Nature Methods, 7, 335, 10.1038/nmeth.f.303

Chao, 1984, Non-parametric estimation of the number of classes in a population, Scandinavian Journal of Statistics, 11, 265

Christensen, 1989, A view of fungal ecology, Mycologia, 81, 1, 10.1080/00275514.1989.12025620

Chu, 2010, Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes, Environmental Microbiology, 12, 2998, 10.1111/j.1462-2920.2010.02277.x

Clarke, 2001, A further biodiversity index applicable to species lists: variation in taxonomic distinctness, Marine Ecology-progress Series, 216, 265, 10.3354/meps216265

Davis, 2009, Assessment of the diversity, abundance, and ecological distribution of candidate division SR1 reveals a high level of phylogenetic diversity but limited morphotypic diversity, Applied and Environmental Microbiololgy, 75, 4139, 10.1128/AEM.00137-09

de Boer, 2005, Living in a fungal world: impact of fungi on soil bacterial niche development, FEMS Microbiology Reviews, 29, 795, 10.1016/j.femsre.2004.11.005

DeSantis, 2006, NAST, a multiple sequence alignment server for comparative analysis of 16S rRNA genes, Nucleic Acids Research, 34, 394, 10.1093/nar/gkl244

Faith, 2009, The cladistic basis for the phylogenetic diversity (PD) measure links evolutionary features to environmental gradients and supports broad applications of microbial ecology's “phylogenetic beta diversity” framework, The International Journal of Molecular Sciences, 10, 4723, 10.3390/ijms10114723

Faith, 1992, Conservation evaluation and phylogenetic diversity, Biological Conservation, 61, 1, 10.1016/0006-3207(92)91201-3

Fierer, 2005, Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays, Applied and Environmental Microbiololgy, 71, 4117, 10.1128/AEM.71.7.4117-4120.2005

Fierer, 2006, The diversity and biogeography of soil bacterial communities, Proceedings of the National Academy of Sciences of the United States of America, 103, 626, 10.1073/pnas.0507535103

Fierer, 2013, Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States, Science, 342, 621, 10.1126/science.1243768

Fierer, 2008, Microbial biogeography: patterns in microbial diversity across space and time, 95

Finlay, 2002, Global dispersal of free-living microbial eukaryote species, Science, 296, 1061, 10.1126/science.1070710

Fuhrman, 2008, A latitudinal diversity gradient in planktonic marine bacteria, Proceedings of the National Academy of Sciences of the United States of America, 105, 7774, 10.1073/pnas.0803070105

Ganderton, 2005

García-Salamanca, 2012, Bacterial diversity in the rhizosphere of maize and the surrounding carbonate-rich bulk soil, Microbial Biotechnology, 6, 36, 10.1111/j.1751-7915.2012.00358.x

Ge, 2008, Differences in soil bacterial diversity: driven by contemporary disturbances or historical contingencies?, ISME Journal, 2, 254, 10.1038/ismej.2008.2

Green, 2004, Spatial scaling of microbial eukaryote diversity, Nature, 432, 747, 10.1038/nature03034

Griffiths, 2011, The bacterial biogeography of British soils, Environmental Microbiology, 13, 1642, 10.1111/j.1462-2920.2011.02480.x

Hamady, 2009, Microbial community profiling for human microbiome projects: tools, techniques, and challenges, Genome Research, 19, 1141, 10.1101/gr.085464.108

Hendrix, 1986, Detritus food webs in conventional and no-tillage agroecosystems, Bioscience, 36, 374, 10.2307/1310259

Hollister, 2010, Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments, ISME Journal, 4, 829, 10.1038/ismej.2010.3

Jenkins, 2009, Actinobacterial community dynamics in long term managed grasslands, Antonie Van Leeuwenhoek, 95, 319, 10.1007/s10482-009-9317-8

Jones, 2009, A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses, ISME Journal, 3, 442, 10.1038/ismej.2008.127

Kivlin, 2014, Environmental filtering affects soil fungal community composition more than dispersal limitation at regional scales, Fungal Ecology, 12, 14, 10.1016/j.funeco.2014.04.004

Ladau, 2013, Global marine bacterial diversity peaks at high latitudes in winter, ISME Journal, 7, 1669, 10.1038/ismej.2013.37

Lauber, 2009, Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale, Applied and Environmental Microbiololgy, 75, 5111, 10.1128/AEM.00335-09

Lauber, 2008, The influence of soil properties on the structure of bacterial and fungal communities across land-use types, Soil Biology & Biochemistry, 40, 2407, 10.1016/j.soilbio.2008.05.021

Levin, 1992, The problem of pattern and scale in ecology, Ecology, 73, 1943, 10.2307/1941447

Li, 2006, Cd-hit, a fast program for clustering and comparing large sets of protein or nucleotide sequences, Bioinformatics, 22, 1658, 10.1093/bioinformatics/btl158

Liu, 2014, High throughput sequencing analysis of biogeographical distribution of bacterial communities in the black soils of northeast China, Soil Biology & Biochemistry, 70, 113, 10.1016/j.soilbio.2013.12.014

Liu, 2014, The interactive effects of soil transplant into colder regions and cropping on soil microbiology and biogeochemistry, Environmental Microbiology

Liu, 2012, Overview of mollisols in the word: distribution, land use and management, Candian Journal of Soil Science, 92, 383, 10.4141/cjss2010-058

Liu, 2008, Distribution of soil enzyme activities and microbial biomass along a latitudinal gradient in farmlands of Songliao plain, Northeast China, Pedosphere, 18, 431, 10.1016/S1002-0160(08)60034-X

Lomolino, 2006

Lozupone, 2005, UniFrac: a new phylogenetic method for comparing microbial communities, Applied and Environmental Microbiololgy, 71, 8228, 10.1128/AEM.71.12.8228-8235.2005

Marilley, 1998, Bacterial diversity in the bulk soil and rhizosphere fractions of Lolium perenne and Trifolium repens as revealed by PCR restriction analysis of 16S rDNA, Plant and Soil, 198, 219, 10.1023/A:1004309008799

Martiny, 2006, Microbial biogeography: putting microorganisms on the map, Nature, 4, 102

Meiser, 2014, Meta-analysis of deep-sequenced fungal communities indicates limited taxon sharing between studies and the presence of biogeographic patterns, New Phytologist, 201, 623, 10.1111/nph.12532

Nevarez, 2009, Physiological traits of Penicillium glabrum strain LCP 08.5568, a filamentous fungus isolated from bottled aromatised mineral water, International Journal of Food Microbiology, 130, 166, 10.1016/j.ijfoodmicro.2009.01.013

Nicol, 2008, The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria, Environmental Microbiology, 10, 2966, 10.1111/j.1462-2920.2008.01701.x

Pautasso, 2013, Fungal under-representation is (slowly) diminishing in the life sciences, Fungal Ecology, 6, 129, 10.1016/j.funeco.2012.04.004

Peay, 2013, Strong coupling of plant and fungal community structure across western Amazonian rainforests, ISME Journal, 7, 1852, 10.1038/ismej.2013.66

Pereira e Silva, 2012, Spatial and temporal variation of archaeal, bacterial and fungal communities in agricultural soils, PLoS One, 7, e51554, 10.1371/journal.pone.0051554

Polme, 2013, Biogeography of ectomycorrhizal fungi associated with alders (Alnus spp.) in relation to biotic and abiotic variables at the global scale, New Phytologist, 198, 1239, 10.1111/nph.12170

Price, 2009, FastTree: computing large minimum evolution trees with profiles instead of a distance matrix, Molecular Biology and Evolution, 26, 1641, 10.1093/molbev/msp077

R Development Core Team, 2006

Rousk, 2010, Soil bacterial and fungal communities across a pH gradient in an arable soil, ISME Journal, 4, 1340, 10.1038/ismej.2010.58

Rousk, 2009, Contrasting soil pH effects on fungal and bacterial growth suggests functional redundancy in carbon mineralisation, Applied and Environmental Microbiololgy, 75, 1589, 10.1128/AEM.02775-08

Schmidt, 2013, Illumina metabarcoding of a soil fungal community, Soil Biology & Biochemistry, 65, 128, 10.1016/j.soilbio.2013.05.014

Schmidt, 2014, Do bacterial and fungal communities assemble differently during primary succession?, Molecular Ecology, 23, 254, 10.1111/mec.12589

Shen, 2014, Contrasting elevational diversity patterns between eukaryotic soil microbes and plants, Ecology, 10.1890/14-0310.1

Shen, 2013, Soil pH drives the spatial distribution of bacterial communities along elevation on Changbai Mountain, Soil Biology & Biochemistry, 57, 204, 10.1016/j.soilbio.2012.07.013

Shi, 2014, Variation in forest soil fungal diversity along a latitudinal gradient, Fungal Diversity, 64, 305, 10.1007/s13225-013-0270-5

Sul, 2013, Tropical agricultural land management influences on soil microbial communities through its effect on soil organic carbon, Soil Biology & Biochemistry, 65, 33, 10.1016/j.soilbio.2013.05.007

van der Wal, 2006, Fungal biomass development in a chronosequence of land abandonment, Soil Biology & Biochemistry, 38, 51, 10.1016/j.soilbio.2005.04.017

Wheeler, 1991, Influence of pH on the growth of some toxigenic species of Aspergillus, Penicillium and Fusarium, International Journal of Food Microbiology, 12, 141, 10.1016/0168-1605(91)90063-U

White, 1990, PCR protocols a guide to methods and applications, 315

Willig, 2003, Latitudinal gradients of biodiversity: pattern, process, scale, and synthesis, Annual Review of Ecology Evolution and Systematics, 34, 273, 10.1146/annurev.ecolsys.34.012103.144032

Wu, 2013, The biogeography of fungal communities in wetland sediments along the Changjiang River and other sites in China, ISME Journal, 7, 1299, 10.1038/ismej.2013.29

Xiong, 2012, Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau, Environmental Microbiology, 14, 2457, 10.1111/j.1462-2920.2012.02799.x

Yergeau, 2007, Size and structure of bacterial, fungal and nematode communities along an Antarctic environmental gradient, FEMS Microbiology Ecology, 59, 436, 10.1111/j.1574-6941.2006.00200.x

Yuan, 2014, Bacterial community in alpine grasslands along an altitudinal gradient on the Tibetan Plateau, FEMS Microbiology Ecology, 87, 121, 10.1111/1574-6941.12197

Zhang, 2007, Spatial variability of nutrient properties in black soil of Northeast China, Pedosphere, 17, 19, 10.1016/S1002-0160(07)60003-4