The vertical distribution of bacterial and archaeal communities in the water and sediment of Lake Taihu

FEMS Microbiology Ecology

Volumn 70, Issue 2, 2009, Pages 263-276

  Ye, Wenjin ^a   Liu, Xianglong ^a   Lin, Shengqin ^a   Tan, Jing ^a   Pan, Jianliang ^a   Li, Daotang ^a   Yang, Hong ^a  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

Author keywords

Clone library; Denaturing gradient gel electrophoresis; Lake Taihu; Microbial diversity; Real time PCR; Sediment

Indexed keywords

RNA 16S; UNSPECIFIC MONOOXYGENASE; WATER;

ABUNDANCE; BACTERIUM; LACUSTRINE DEPOSIT; LAKE WATER; MICROBIAL COMMUNITY; POLYMERASE CHAIN REACTION; POPULATION STRUCTURE; VERTICAL DISTRIBUTION;

ACTINOBACTERIA; ALPHAPROTEOBACTERIA; ARCHAEBACTERIUM; ARTICLE; BACTERIAL GENE; BACTEROIDETES; BETAPROTEOBACTERIA; CHLOROBI; CONTROLLED STUDY; CRENARCHAEOTA; DELTAPROTEOBACTERIA; DENATURING GRADIENT GEL ELECTROPHORESIS; EUTROPHICATION; FIRMICUTES; GAMMAPROTEOBACTERIA; GENE AMPLIFICATION; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; LAKE; METHANOGENIC ARCHAEON; MICROBIAL COMMUNITY; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; SEDIMENT; UNINDEXED SEQUENCE;

ASIA; CHINA; EURASIA; FAR EAST; TAIHU LAKE;

ACIDOBACTERIA; ACTINOBACTERIA; ARCHAEA; BACTERIA (MICROORGANISMS); BACTEROIDETES; CHLOROBI; CRENARCHAEOTA; DELTAPROTEOBACTERIA; EURYARCHAEOTA; FIRMICUTES; GEMMATIMONADETES; NITROSOMONADALES; NITROSPIRA; VERRUCOMICROBIA;

EID: 70349852874     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2009.00761.x     Document Type: Article

References (82)

1. Adair KL Schwartz E (2007) Evidence that ammonia-oxidizing Archaea are more abundant than ammonia-oxidizing Bacteria in semiarid soils of Northern Arizona, USA. Microb Ecol 56 : 1 7.
2. Alm EW Stahl DA (2000) Critical factors influencing the recovery and integrity of rRNA extracted from environmental samples: use of an optimized protocol to measure depth-related biomass distribution in freshwater sediments. J Microbiol Meth 40 : 153 162.
3. Altschul SF, Gish W, Miller W, Myers EW Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215 : 403 410.
4. Ambrosetti W, Barbanti L Sala N (2003) Residence time and physical processes in lakes. J Limnol 62 : 1 15.
5. Arp DJ Stein LY (2003) Metabolism of inorganic N Compounds by ammonia-oxidizing bacteria. Crit Rev Biochem Mol 38 : 471 495.
6. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA Struhl K (2002) Short Protocols in Molecular Biology. Wiley, New York.
7. Banning N, Brock F, Fry JC, Parkes RJ, Hornibrook ERC Weightman AJ (2005) Investigation of the methanogen population structure and activity in a brackish lake sediment. Environ Microbiol 7 : 947 960.
8. Bernasconi SM, Barbieri A Simona M (1998) Carbon and nitrogen isotope variations in sedimenting organic matter in Lake Lugano. Limnol Oceanogr 42 : 1755 1765.
9. Briée C, Moreira D López-García P (2007) Archaeal and bacterial community composition of sediment and plankton from a suboxic freshwater pond. Res Microbiol 158 : 213 227.
10. Burrell PC, Keller J Blackall LL (1998) Microbiology of a nitrite-oxidizing bioreactor. Appl Environ Microb 64 : 1878 1883.
11. Cadillo-Quiroz H, Yashiro E, Yavitt JB Zinder SH (2008) Characterization of the archaeal community in a minerotrophic fen and terminal restriction fragment length polymorphism-directed isolation of a novel hydrogenotrophic methanogen. Appl Environ Microb 74 : 2059 2068.
12. Chachkhiani M, Dabert P, Abzianidze T, Partskhaladze G, Tsiklauri L, Dudauri T Godon JJ (2004) 16S rDNA characterisation of bacterial and archaeal communities during start-up of anaerobic thermophilic digestion of cattle manure. Bioresource Technol 93 : 227 232.
13. Coolen MJL, Abbas B, Van Bleijswijk J, Hopmans EC, Kuypers MMM, Wakeham SG Sinninghe Damste JS (2007) Putative ammonia-oxidizing Crenarchaeota in suboxic waters of the Black Sea: a basin-wide ecological study using 16S ribosomal and functional genes and membrane lipids. Environ Microbiol 9 : 1001 1016.
14. Daims H, Nielsen JL, Nielsen PH, Schleifer KH Wagner M (2001) In situ characterization of nitrospira-like nitrite-oxidizing bacteria active in wastewater treatment plants. Appl Environ Microb 67 : 5273 5284.
15. Dionisi HM, Harms G, Layton AC, Gregory IR, Parker J, Hawkins SA, Robinson KG Sayler GS (2003) Power analysis for real-time PCR quantification of genes in activated sludge and analysis of the variability introduced by DNA extraction. Appl Environ Microb 69 : 6597 6604.
16. Edlund A, Soule T, Sjöling S Jansson JK (2006) Microbial community structure in polluted Baltic Sea sediments. Environ Microbiol 8 : 223 232.
17. Ekholm P, Malve O Kirkkala T (1997) Internal and external loading as regulators of nutrient concentrations in the agriculturally loaded Lake Pyhajarvi (southwest Finland). Hydrobiologia 345 : 3 14.
18. Francis CA, Roberts KJ, Beman JM, Santoro AE Oakley BB (2005) Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. P Natl Acad Sci USA 102 : 14683 14688.
19. Galand PE, Lovejoy C Vincent WF (2006) Remarkably diverse and contrasting archaeal communities in a large arctic river and the coastal Arctic Ocean. Aquat Microb Ecol 44 : 115 126.
20. Glissmann K, Chin KJ, Casper P Conrad R (2004) Methanogenic pathway and archaeal community structure in the sediment of eutrophic Lake Dagow: effect of temperature. Microb Ecol 48 : 389 399.
21. Griffiths RI, Whiteley AS, O'Donnell AG Bailey MJ (2000) Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl Environ Microb 66 : 5488 5491.
22. Großkopf R, Janssen PH Liesack W (1998a) Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl Environ Microb 64 : 960 969.
23. Großkopf R, Stubner S Liesack W (1998b) Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms. Appl Environ Microb 64 : 4983 4989.
24. Hallam SJ, Mincer TJ, Schleper C, Preston CM, Roberts K, Richardson PM DeLong EF (2006) Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol 4 : 520 536.
25. Hansel CM, Fendorf S, Jardine PM Francis CA (2008) Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile. Appl Environ Microb 74 : 1620 1633.
26. Harms G, Layton AC, Dionisi HM, Gregory IR, Garrett VM, Hawkins SA, Robinson KG Sayler GS (2003) Real-time quantification of nitrifying bacteria in a municipal wastewater treatment plant. Environ Sci Technol 37 : 343 351.
27. He JZ, Shen JP, Zhang LM, Zhu YG, Zheng YM, Xu MG Di H (2007) Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environ Microbiol 9 : 2364 2374.
28. Hideyuki T, Yuji S, Satoshi H Kazunori N (2005) Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques. Appl Environ Microb 71 : 2162 2169.
29. Høj L, Olsen RA Torsvik VL (2008) Effects of temperature on the diversity and community structure of known methanogenic groups and other archaea in high Arctic peat. ISME J 2 : 37 48.
30. Ingalls AE, Shah SR, Hansman RL, Aluwihare LI, Santos GM, Druffel ERM Pearson A (2006) Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon. P Natl Acad Sci USA 103 : 6442 6447.
31. Jeppesen E, Jensen JP, Søndergaard M Lauridsen T (1999) Trophic dynamics in turbid and clearwater lakes with special emphasis on the role of zooplankton for water clarity. Hydrobiologia 408-409 : 217 231.
32. Jinglu W, Gagan MK, Xuezhong J, Weilan X Sumin W (2004) Sedimentary geochemical evidence for recent eutrophication of Lake Chenghai, Yunnan, China. J Paleolimn 32 : 85 94.
33. Jinglu W, Chengmin H, Haiao Z, Schleser G Battarbee R (2007) Sedimentary evidence for recent eutrophication in the northern basin of Lake Taihu, China: human impacts on a large shallow lake. J Paleolimn 38 : 13 23.
34. Jørgensen BB Marais DJD (1990) The Diffusive boundary layer of sediments: oxygen microgradients over a microbial mat. Limnol Oceanogr 35 : 1343 1355.
35. Junier P, Witzel KP Hadas O (2007) Genetic diversity of cyanobacterial communities in Lake Kinneret (Israel) using 16S rRNA gene, psbA and ntcA sequence analyses. Aquat Microb Ecol 49 : 233 241.
36. Jurgens G, Göckner FO, Amann R, Saano A, Montonen L, Likolammi M Münster U (2000) Identification of novel Archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization. FEMS Microbiol Ecol 34 : 45 56.
37. Koizumi Y, Takii S, Nishino M Nakajima T (2003) Vertical distributions of sulfate-reducing bacteria and methane-producing archaea quantified by oligonucleotide probe hybridization in the profundal sediment of a mesotrophic lake. FEMS Microbiol Ecol 44 : 101 108.
38. Koizumi Y, Kojima H Fukui M (2004) Dominant microbial composition and its vertical distribution in saline meromictic Lake Kaiike (Japan) as revealed by quantitative oligonucleotide probe membrane hybridization. Appl Environ Microb 70 : 4930 4940.
39. Kondo R Butani J (2007) Comparison of the diversity of sulfate-reducing bacterial communities in the water column and the surface sediments of a Japanese meromictic lake. Limnology 8 : 131 141.
40. Könneke M, Bernhard AE, De La Torre JR, Walker CB, Waterbury JB Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437 : 543 546.
41. Koops HP Pommerening-Röser A (2001) Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species. FEMS Microbiol Ecol 37 : 1 9.
42. Kowalchuk GA Stephen JR (2001) Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annu Rev Microbiol 55 : 485 529.
43. Kumar S, Tamura K, Jakobsen IB Nei M (2002) MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 70 : 1244 1245.
44. Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC Schleper C (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442 : 806 809.
45. 2 affects soil microbial diversity associated with trembling aspen. Environ Microbiol 10 : 926 941.
46. Li S, Xiao X, Yin X Wang F (2006) Bacterial community along a historic lake sediment core of Ardley Island, west Antarctica. Extremophiles 10 : 461 467.
47. Liang JB, Chen YQ, Lan CY, Tam NFY, Zan QJ Huang LN (2007) Recovery of novel bacterial diversity from mangrove sediment. Mar Biol 150 : 739 747.
48. Lin LH, Hall J, Onstott TC, Gihring T, Lollar BS, Boice E, Pratt L, Lippmann-Pipke J Bellamy RES (2006) Planktonic microbial communities associated with fracture-derived groundwater in a deep gold mine of South Africa. Geomicrobiol J 23 : 475 497.
49. Liu B, Zhang F, Feng X, Liu Y, Yan X, Zhang X, Wang L Zhao L (2006) Thauera and Azoarcus as functionally important genera in a denitrifying quinoline-removal bioreactor as revealed by microbial community structure comparison. FEMS Microbiol Ecol 55 : 274 286.
50. Meyers PA (2003) Applications of organic geochemistry to paleolimnological reconstructions: a summary of examples from the Laurentian Great Lakes. Org Geochem 34 : 261 289.
51. Moss B (1998) Ecology of Fresh Waters: Man and Medium, Past to Future. Blackwell Science, Oxford.
52. Muyzer G Stams AJM (2008) The ecology and biotechnology of sulphate-reducing bacteria. Nat Rev Microbiol 6 : 441 454.
53. Muyzer G, De Waal EC Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microb 59 : 695 700.
54. Nam Y-D, Sung Y, Chang H-W, Roh S, Kim K-H, Rhee S-K, Kim J-C, Kim J-Y, Yoon J-H Bae J-W (2008) Characterization of the depth-related changes in the microbial communities in Lake Hovsgol sediment by 16S rRNA gene-based approaches. J Microbiol 46 : 125 136.
55. Nealson KH (1997) Sediment bacteria: who's there, what are they doing, and what's new? Annu Rev Earth Pl Sc 25 : 403 434.
56. Nelson DM, Ohene-Adjei S, Hu FS, Cann IKO Mackie RI (2007) Bacterial diversity and distribution in the holocene sediments of a northern temperate lake. Microb Ecol 54 : 252 263.
57. Orphan VJ, Hinrichs KU, Ussler W III., Paull CK, Taylor LT, Sylva SP, Hayes JM Delong EF (2001) Comparative analysis of methane-oxidizing Archaea and sulfate-reducing Bacteria in anoxic marine sediments. Appl Environ Microb 67 : 1922 1934.
58. Oude Elferink SJWH (1999) Desulfobacca acetoxidans gen. nov., sp. nov., a novel acetate-degrading sulfate reducer isolated from sulfidogenic granular sludge. Int J Syst Bacteriol 49 : 345 350.
59. Oude Elferink SJWH, Maas RN, Harmsen HJM Stams AJM (1995) Desulforhabdus amnigenus gen. nov. sp. nov., a sulfate reducer isolated from anaerobic granular sludge. Arch Microbiol 164 : 119 124.
60. Park SJ, Park BJ Rhee SK (2008) Comparative analysis of archaeal 16S rRNA and amoA genes to estimate the abundance and diversity of ammonia-oxidizing archaea in marine sediments. Extremophiles 12 : 605 615.
61. Parkes RJ, Webster G, Cragg BA, Weightman AJ, Newberry CJ, Ferdelman TG, Kallmeyer J, Jorgensen BB, Aiello IW Fry JC (2005) Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436 : 390 394.
62. Qin YY, Li DT Yang H (2007) Investigation of total bacterial and ammonia-oxidizing bacterial community composition in a full-scale aerated submerged biofilm reactor for drinking water pretreatment in China. FEMS Microbiol Lett 268 : 126 134.
63. Rippey B Jewson DH (1982) The rates of sediment-water exchange of oxygen and sediment bioturbation in Lough Neagh, Northern Ireland. Hydrobiologia 91-92 : 377 382.
64. Rölleke S, Witte A, Wanner G Lubitz W (1998) Medieval wall paintings - A habitat for archaea: identification of archaea by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified gene fragments coding for 16S rRNA in a medieval wall painting. Int Biodeter Biodegr 41 : 85 92.
65. Rotthauwe JH, Witzel KP Liesack W (1997) The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl Environ Microb 63 : 4704 4712.
66. Routh J, Meyers PA, Gustafsson Ö, Baskaran M, Hallberg R Schöldström A (2004) Sedimentary geochemical record of human-induced environmental changes in the Lake Brunnsviken watershed, Sweden. Limnol Oceanogr 49 : 1560 1569.
67. Rudolph C, Moissl C, Henneberger R Huber R (2004) Ecology and microbial structures of archaeal/bacterial strings-of-pearls communities and archaeal relatives thriving in cold sulfidic springs. FEMS Microbiol Ecol 50 : 1 11.
68. Ryan J, Estefan G Rashid A (2001) Soil and Plant Analysis Laboratory Manual. International Center for Agricultural Research in the Dry Area (ICARDA) and the National Agricultural Research Center (NARC), Aleppo, Syria, and Islamabad, Pakistan.
69. Sawayama S, Tsukahara K Yagishita T (2006) Phylogenetic description of immobilized methanogenic community using real-time PCR in a fixed-bed anaerobic digester. Bioresource Technol 97 : 69 76.
70. Schwarz JIK, Eckert W Conrad R (2007) Community structure of Archaea and Bacteria in a profundal lake sediment Lake Kinneret (Israel). Syst Appl Microbiol 30 : 239 254.
71. Shaw AK, Halpern AL, Beeson K, Tran B, Venter JC Martiny JBH (2008) It's all relative: ranking the diversity of aquatic bacterial communities. Environ Microbiol 10 : 2200 2210.
72. Šlapeta J, Moreira D López-García P (2005) The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes. P Roy Soc B-Biol Sci 272 : 2073 2081.
73. Speksnijder AGCL, Kowalchuk GA, Roest K Laanbroek HJ (1998) Recovery of a Nitrosomonas-like 16S rDNA sequence group from freshwater habitats. Syst Appl Microbiol 21 : 321 330.
74. Stein LY, La Duc MT, Grund TJ Nealson KH (2001) Bacterial and archaeal populations associated with freshwater ferromanganous micronodules and sediments. Environ Microbiol 3 : 10 18.
75. Takai K Horikoshi K (2000) Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes. Appl Environ Microb 66 : 5066 5072.
76. Teske A, Hinrichs KU, Edgcomb V, De Vera Gomez A, Kysela D, Sylva SP, Sogin ML Jannasch HW (2002) Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities. Appl Environ Microb 68 : 1994 2007.
77. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F Higgins DG (1997) The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25 : 4876 4882.
78. 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 1364.
79. Venter JC, Remington K, Heidelberg JF et al 2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304 : 66 74.
80. Wobus A, Bleul C, Maassen S, Scheerer C, Schuppler M, Jacobs E Röske I (2003) Microbial diversity and functional characterization of sediments from reservoirs of different trophic state. FEMS Microbiol Ecol 46 : 331 347. (Pubitemid 37494874)
81. Wu X, Xi W, Ye W Yang H (2007) Bacterial community composition of a shallow hypertrophic freshwater lake in China, revealed by 16S rRNA gene sequences. FEMS Microbiol Ecol 61 : 85 96.
82. Zeng J, Yang L, Li J, Liang Y, Xiao L, Jiang L Zhao D (2009) Vertical distribution of bacterial community structure in the sediments of two eutrophic lakes revealed by denaturing gradient gel electrophoresis (DGGE) and multivariate analysis techniques. World J Microb Biot 25 : 225 233.