Soil bacterial communities shaped by geochemical factors and land use in a less-explored area, Tibetan Plateau

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Guan, Xiangyu ^a,c   Wang, Jinfeng ^b   Zhao, Hui ^b   Wang, Jianjun ^d   Luo, Ximing ^c   Liu, Fei ^a   Zhao, Fangqing ^b  

^a CHINA UNIVERSITY OF GEOSCIENCES BEIJING   (China)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^c CHINA UNIVERSITY OF GEOSCIENCES   (China)

^d NANJING INSTITUTE OF GEOGRAPHY AND LIMNOLOGY   (China)

Author keywords

Bacterial community; Homogenization; Metagenomics; Soil; Tibetan Plateau

Indexed keywords

SULFUR;

ADAPTATION; AGRICULTURAL LAND; ALPINE MEADOW; ARTICLE; CHINA; CONTROLLED STUDY; CORRELATION ANALYSIS; ECOSYSTEM; ENVIRONMENTAL FACTOR; GEOCHEMISTRY; LAKE; LAND USE; LOW TEMPERATURE; METAGENOMICS; MICROORGANISM; NODULATION; NONHUMAN; PH; SOIL ANALYSIS; SOIL MICROFLORA; SOIL MOISTURE; TAXONOMY; THIOBACILLUS; ULTRAVIOLET RADIATION;

BACTERIA (MICROORGANISMS); THIOBACILLUS;

BACTERIA; ENVIRONMENT; GEOLOGICAL PHENOMENA; HUMANS; HYDROGEN-ION CONCENTRATION; SOIL; SOIL MICROBIOLOGY; TEMPERATURE; TIBET;

EID: 84887872054     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-820     Document Type: Article

References (70)

1. Delmont TO, Prestat E, Keegan KP, Faubladier M, Robe P, Clark IM, Pelletier E, Hirsch PR, Meyer F, Gilbert JA, et al. Structure, fluctuation and magnitude of a natural grassland soil metagenome. Isme J 2012, 6(9):1677-1687.
2. Wallenstein MD, McMahon S, Schimel J. Bacterial and fungal community structure in Arctic tundra tussock and shrub soils. Fems Microbiol Ecol 2007, 59(2):428-435.
3. Pointing SB, Chan Y, Lacap DC, Lau MC, Jurgens JA, Farrell RL. Highly specialized microbial diversity in hyper-arid polar desert. Proc Natl Acad Sci U S A 2009, 106(47):19964-19969.
4. Kuramae EE, Yergeau E, Wong LC, Pijl AS, van Veen JA, Kowalchuk GA. Soil characteristics more strongly influence soil bacterial communities than land-use type. Fems Microbiol Ecol 2012, 79(1):12-24.
5. Yergeau E, Hogues H, Whyte LG, Greer CW. The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses. Isme J 2010, 4(9):1206-1214.
6. Fierer N, Jackson RB. The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci U S A 2006, 103(3):626-631.
7. Nemergut DR, Costello EK, Hamady M, Lozupone C, Jiang L, Schmidt SK, Fierer N, Townsend AR, Cleveland CC, Stanish L, et al. Global patterns in the biogeography of bacterial taxa. Environ Microbiol 2011, 13(1):135-144.
8. Youssef NH, Elshahed MS. Diversity rankings among bacterial lineages in soil. Isme J 2009, 3:305-313.
9. Reith F, Brugger J, Zammit CM, Gregg AL, Goldfarb KC, Andersen GL, Desantis TZ, Piceno YM, Brodie EL, Lu Z, et al. Influence of geogenic factors on microbial communities in metallogenic Australian soils. Isme J 2012, 6:2107-2118.
10. Viles HA, Naylor LA, Carter NEA, Chaput D. Biogeomorphological disturbance regimes: progress in linking ecological and geornorphological systems. Earth Surf Proc Land 2008, 33(9):1419-1435.
11. Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, Knight R. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. Isme J 2012, 6(5):1007-1017.
12. Lauber CL, Hamady M, Knight R, Fierer N. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 2009, 75(15):5111-5120.
13. Ni J. A simulation of biomes on the Tibetan Plateau and their responses to global climate change. Mt Res Dev 2000, 20(1):80-89.
14. Kato T, Tang YH, Gu S, Hirota M, Du MY, Li YN, Zhao XQ. Temperature and biomass influences on interannual changes in CO2 exchange in an alpine meadow on the Qinghai-Tibetan Plateau. Global Change Biol 2006, 12(7):1285-1298.
15. Qiu J. China: the third pole. Nature 2008, 454(7203):393-396.
16. Liu Y, Yao T, Jiao N, Kang S, Xu B, Zeng Y, Huang S, Liu X. Bacterial diversity in the snow over Tibetan Plateau Glaciers. Extremophiles 2009, 13(3):411-423.
17. Jiang H, Dong H, Yu B, Liu X, Li Y, Ji S, Zhang CL. Microbial response to salinity change in Lake Chaka, a hypersaline lake on Tibetan plateau. Environ Microbiol 2007, 9(10):2603-2621.
18. Wong FK, Lacap DC, Lau MC, Aitchison JC, Cowan DA, Pointing SB. Hypolithic microbial community of quartz pavement in the high-altitude tundra of central Tibet. Microb Ecol 2010, 60(4):730-739.
19. Wong FK, Lau MC, Lacap DC, Aitchison JC, Cowan DA, Pointing SB. Endolithic microbial colonization of limestone in a high-altitude arid environment. Microb Ecol 2010, 59(4):689-699.
20. Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, Lauber CL, Owens S, Gilbert JA, Wall DH, Caporaso JG. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci U S A 2012, 109(52):21390-21395.
21. Mackelprang R, Waldrop MP, DeAngelis KM, David MM, Chavarria KL, Blazewicz SJ, Rubin EM, Jansson JK. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 2011, 480(7377):368-371.
22. Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, et al. Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc Natl Acad Sci U S A 2009, 106(5):1374-1379.
23. Cao GM, Tang YH, Mo WH, Wang YA, Li YN, Zhao XQ. Grazing intensity alters soil respiration in an alpine meadow on the Tibetan plateau. Soil Biol Biochem 2004, 36(2):237-243.
24. Wang GX, Qian J, Cheng GD, Lai YM. Soil organic carbon pool of grassland soils on the Qinghai-Tibetan Plateau and its global implication. Sci Total Environ 2002, 291(1-3):207-217.
25. Zheng D, Zhang Q. Mountain Geoecology and Sustainable Development of the TibetanPlateau 2000, Dordrecht, The Netherlands: Kluwer Academic Publishers.
26. Fan JW, Zhong HP, Harris W, Yu GR, Wang SQ, Hu ZM, Yue YZ. Carbon storage in the grasslands of China based on field measurements of above- and below-ground biomass. Clim Change 2008, 86(3-4):375-396.
27. Genxu W, Ju Q, Guodong C, Yuanmin L. Soil organic carbon pool of grassland soils on the Qinghai-Tibetan Plateau and its global implication. Sci Total Environ 2002, 291(1-3):207-217.
28. Pan ZF, Deng GB, Zhai XG, Wu F, Yu MQ. Genetic diversity of Acid-PAGE monomeric prolamins in cultivated hulless barley (Hordeum vulgare L.) from Qinghai-Tibet plateau in China. Genet Resour Crop Ev 2007, 54(8):1691-1699.
29. Xu JQ, Yu SM, Liu JS, Haginoya S, Ishigooka Y, Kuwagata T, Hara M, Yasunari T. The implication of heat and water balance changes in a lake basin on the tibetan plateau. Hydrol Res Lett 2009, 3:1-5.
30. Wu YH, Zhu LP, Q H Y, L B W. The response of lake-glacier area change to climate variations in Namco Basin, Central Tibetan Plateau, during the last three decades. Acta Geograph Sin 2007, 3:301-311.
31. Hallin S, Jones CM, Schloter M, Philippot L. Relationship between N-cycling communities and ecosystem functioning in a 50-year-old fertilization experiment. Isme J 2009, 3(5):597-605.
32. Bowers RM, McLetchie S, Knight R, Fierer N. Spatial variability in airborne bacterial communities across land-use types and their relationship to the bacterial communities of potential source environments. Isme J 2011, 5(4):601-612.
33. Eilers KG, Debenport S, Anderson S, Fierer N. Digging deeper to find unique microbial communities: the strong effect of depth on the structure of bacterial and archaeal communities in soil. Soil Biol Biochem 2012, 50:58-65.
34. Islam KR, Weil RR. A rapid microwave digestion method for colorimetric measurement of soil organic carbon. Commun Soil Sci Plant Anal 1998, 29:2269-2284.
35. Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC. Integrative analysis of environmental sequences using MEGAN4. Genome Res 2011, 21(9):1552-1560.
36. Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, et al. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinforma 2008, 9:386.
37. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y. SOAPdenovo2: An Empirically Improved Memory-Efficient Short-Read De Novo Assembler 2012,
38. Zhao F, Zhao F, Li T, Bryant DA. A new pheromone trail-based genetic algorithm for comparative genome assembly. Nucleic Acids Res 2008, 36(10):3455-3462.
39. Zhu W, Lomsadze A, Borodovsky M. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res 2010, 38(12):e132.
40. Wang J, Qi J, Zhao H, He S, Zhang Y, Wei S, Zhao F. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci Rep 2013, 3:1843.
41. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res 2008, 36:D480-D484.
42. Liu J, Wang H, Yang H, Zhang Y, Wang J, Zhao F, Qi J. Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms. Nucleic Acids Res 2013, 41(1):e3.
43. Li H, Durbin R. Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics 2009, 25(14):1754-1760.
44. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. Genome project data P: the sequence alignment/map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079.
45. Qi J, Zhao F, Buboltz A, Schuster SC. inGAP: an integrated next-generation genome analysis pipeline. Bioinformatics 2010, 26(1):127-129.
46. Qi J, Zhao F. inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data. Nucleic Acids Res 2011, 39:W567-W575.
47. Wang J, Shen J, Wu Y, Tu C, Soininen J, Stegen JC, He J, Liu X, Zhang L, Zhang E. Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes. Isme J 2013, 7:1310-1321.
48. Grapov D, Newman JW. imDEV: a graphical user interface to R multivariate analysis tools in microsoft excel. Bioinformatics 2012, 28(17):2288-2290.
49. Parton WJ, Stewart JWB, Cole CV. Dynamics of C, N, P and S in grassland soils: a model. Biogeochemistry 1988, 5:109-131.
50. Liu Y, Yao T, Jiao N, Kang S, Zeng Y, Huang S. Microbial community structure in moraine lakes and glacial meltwaters, Mount Everest. FEMS Microbiol Lett 2006, 265(1):98-105.
51. Rousk J, Baath E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, Knight R, Fierer N. Soil bacterial and fungal communities across a pH gradient in an arable soil. Isme J 2010, 4(10):1340-1351.
52. Campbell BJ, Polson SW, Hanson TE, Mack MC, Schuur EA. The effect of nutrient deposition on bacterial communities in Arctic tundra soil. Environ Microbiol 2010, 12(7):1842-1854.
53. Zhang H, Sekiguchi Y, Hanada S, Hugenholtz P, Kim H, Kamagata Y, Nakamura K. Gemmatimonas aurantiaca gen. nov., sp. nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. Int J Syst Evol Microbiol 2003, 53(4):1155-1163.
54. Beller HR, Chain PS, Letain TE, Chakicherla A, Larimer FW, Richardson PM, Coleman MA, Wood AP, Kelly DP. The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans. J Bacteriol 2006, 188(4):1473-1488.
55. Off S, Alawi M, Spieck E. Enrichment and physiological characterization of a novel Nitrospira-like bacterium obtained from a marine sponge. Appl Environ Microbiol 2010, 76(14):4640-4646.
56. Kant R, van Passel MW, Palva A, Lucas S, Lapidus A, Glavina del Rio T, Dalin E, Tice H, Bruce D, Goodwin L, et al. Genome sequence of Chthoniobacter flavus Ellin428, an aerobic heterotrophic soil bacterium. J Bacteriol 2011, 193(11):2902-2903.
57. Sanford RA, Cole JR, Tiedje JM. Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiring facultative anaerobic myxobacterium. Appl Environ Microbiol 2002, 68(2):893-900.
58. Chin KJ, Janssen PH. Propionate formation by Opitutus terrae in pure culture and in mixed culture with a hydrogenotrophic methanogen and implications for carbon fluxes in anoxic rice paddy soil. Appl Environ Microbiol 2002, 68(4):2089-2092.
59. Rodrigues JL, Pellizari VH, Mueller R, Baek K, Jesus Eda C, Paula FS, Mirza B, Hamaoui GS, Tsai SM, Feigl B, et al. Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities. Proc Natl Acad Sci U S A 2013, 110(3):988-993.
60. MacDougall AS, McCann KS, Gellner G, Turkington R. Diversity loss with persistent human disturbance increases vulnerability to ecosystem collapse. Nature 2013, 494(7435):86-89.
61. Galloway JN, Townsend AR, Erisman JW, Bekunda M, Cai Z, Freney JR, Martinelli LA, Seitzinger SP, Sutton MA. Transformation of the nitrogen cycle: recent trends, questions, and potential solutions. Science 2008, 320(5878):889-892.
62. Zhang YQ, Li YZ, Wang B, Wu ZH, Zhang CY, Gong X, Qiu ZJ, Zhang Y. Characteristics and living patterns of marine myxobacterial isolates. Appl Environ Microbiol 2005, 71(6):3331-3336.
63. Martinez-Romero E. Coevolution in Rhizobium-legume symbiosis?. DNA Cell Biol 2009, 28(8):361-370.
64. Zhang YM, Li Y, Chen WF, Wang ET, Tian CF, Li QQ, Zhang YZ, Sui XH, Chen WX. Biodiversity and biogeography of rhizobia associated with soybean plants grown in the North China Plain. Appl Environ Microbiol 2011, 77(18):6331-6342.
65. Saros JE, Rose KC, Clow DW, Stephens VC, Nurse AB, Arnett HA, Stone JR, Williamson CE, Wolfe AP. Melting Alpine glaciers enrich high-elevation lakes with reactive nitrogen. Environ Sci Technol 2010, 44(13):4891-4896.
66. Klimmek O. The biological cycle of sulfur. Met Ions Biol Syst 2005, 43:105-130.
67. Beller HR. Anaerobic, nitrate-dependent oxidation of U(IV) oxide minerals by the chemolithoautotrophic bacterium Thiobacillus denitrificans. Appl Environ Microbiol 2005, 71(4):2170-2174.
68. Straub KL, Benz M, Schink B, Widdel F. Anaerobic, nitrate-dependent microbial oxidation of ferrous iron. Appl Environ Microbiol 1996, 62(4):1458-1460.
69. Hoppe U, Bergemann J, Diembeck W, Ennen J, Gohla S, Harris I, Jacob J, Kielholz J, Mei W, Pollet D, et al. Coenzyme Q10, a cutaneous antioxidant and energizer. Biofactors 1999, 9(2-4):371-378.
70. Dunlap WC, Fujisawa A, Yamamoto Y. UV radiation increases the reduced coenzyme Q ratio in marine bacteria. Redox Rep 2002, 7(5):320-323.