Depth-related changes of sediment ammonia-oxidizing microorganisms in a high-altitude freshwater wetland

Applied Microbiology and Biotechnology

Volumn 98, Issue 12, 2014, Pages 5697-5707

  Liu, Yong ^a   Zhang, Jingxu ^a   Zhang, Xiaoling ^a   Xie, Shuguang ^a  

^a PEKING UNIVERSITY   (China)

Author keywords

Ammonia oxidizing archaea (AOA); Ammonia oxidizing bacteria (AOB); Freshwater; Nitrification; Sediment; Wetland

Indexed keywords

AMMONIA; BACTERIA; CORRELATION METHODS; ECOSYSTEMS; MICROBIOLOGY; NITRIFICATION; SOCIAL SCIENCES; WATER; WETLANDS;

AMMONIA OXIDIZING BACTERIA; AMMONIA-OXIDIZING ARCHAEA; AVAILABLE PHOSPHORUS; COMMUNITY STRUCTURES; CORRELATION ANALYSIS; FRESHWATER; FRESHWATER WETLANDS; RELATIVE CONTRIBUTION;

SEDIMENTS;

BACTERIAL RNA; FRESH WATER; RNA 16S; AMMONIA; AMMONIA MONOOXYGENASE; ARCHAEAL DNA; ARCHAEAL RNA; BACTERIAL DNA; OXIDOREDUCTASE; RIBOSOME DNA;

ALTITUDE; BACTERIUM; BIOGEOCHEMISTRY; COMMUNITY STRUCTURE; FRESHWATER ENVIRONMENT; MICROORGANISM; NITRIFICATION; OXIDATION; PHOSPHORUS; RELATIVE ABUNDANCE; SEDIMENT CHEMISTRY; WETLAND;

ALTITUDE; AMMONIA OXIDIZING ARCHAEON; AMMONIA OXIDIZING BACTERIUM; ARCHAEAL GENE; ARTICLE; BACTERIAL GENE; CHINA; COMMUNITY STRUCTURE; GENE SEQUENCE; MICROBIAL DIVERSITY; NITRIFICATION; NITROSOSPIRA; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; SEDIMENT; WETLAND; ARCHAEON; BACTERIUM; BIODIVERSITY; BIOTA; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; GENETICS; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; OXIDATION REDUCTION REACTION; PHYLOGENY; RNA GENE; SEQUENCE HOMOLOGY;

NITROSOMONADALES; NITROSOSPIRA;

ALTITUDE; AMMONIA; ARCHAEA; BACTERIA; BIODIVERSITY; BIOTA; CHINA; CLUSTER ANALYSIS; DNA, ARCHAEAL; DNA, BACTERIAL; DNA, RIBOSOMAL; FRESH WATER; GENES, RRNA; GEOLOGIC SEDIMENTS; MOLECULAR SEQUENCE DATA; OXIDATION-REDUCTION; OXIDOREDUCTASES; PHYLOGENY; RNA, ARCHAEAL; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; WETLANDS;

EID: 84903815177     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-014-5651-5     Document Type: Article

References (45)

1. Caffrey JM, Bano N, Kalanetra K, Hollibaugh JT (2007) Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia. ISME J 1:660-662 (Pubitemid 350076523)
2. Cao HL, Hong YG, Li M, Gu JD (2011a) Diversity and abundance of ammonia-oxidizing prokaryotes in sediments from the coastal Pearl River estuary to the South China Sea. Antonie Van Leeuwenhoek 100:545-556
3. Cao HL, Li M, Hong YG, Gu JD (2011b) Diversity and abundance of ammonia-oxidizing archaea and bacteria in polluted mangrove sediment. Syst Appl Microbiol 34:513-523
4. Cao HL, Hong YG, Li M, Gu JD (2012) Lower abundance of ammonia oxidizing archaea than ammonia-oxidizing bacteria detected in the subsurface sediments of the Northern South China Sea. Geomicrobiol J 29:332-339
5. Chen X, Zhang LM, Shen JP, Xu ZH, He JZ (2010) Soil type determines the abundance and community structure of ammonia-oxidizing bacteria and archaea in flooded paddy soils. J Soils Sediments 10:1510-1516
6. Cheng W, Zhang JX, Wang Z, Wang M, Xie SG (2014) Bacterial communities in sediments of a drinking water reservoir. Ann Microbiol. doi:10.1007/s13213-013- 0712-z
7. Dang H, Li J, Zhang X, Li T, Tian F, Jin W (2009) Diversity and spatial distribution of amoA-encoding archaea in the deep-sea sediments of the tropical West Pacific Continental Margin. J Appl Microbiol 106:1482-1493
8. Di HJ, Cameron KC, Shen JP,Winefield CS, O'Callaghan M, Bowatte S, He JZ (2009) Nitrification driven by bacteria and not archaea in nitrogen-rich grassland soils. Nat Geosci 2:621-624
9. Erguder TH, Boon N, Wittebolle L, Marzorati M, Verstraete W (2009) Environmental actors shaping the ecological niches of ammonia oxidizing archaea. FEMS Microbiol Rev 33:855-869
10. Feng S, Zhang XJ, Wang QF, Wan R, Chen C, Xie SG (2012) Heterogeneity of ammonia-oxidizing community structures in a pilot-scale drinking water biofilter. Int Biodeterior Biodegrad 70:148-152
11. Hatzenpichler R, Lebedeva EV, Spieck E, Stoecker K, Richter A, Daims H, Wagner M (2008) A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc Natl Acad Sci U S A 105:2134-2139 (Pubitemid 351439477)
12. He J, Shen J, Zhang L, Zhu Y, Zheng Y, Xu M, Di HJ (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 (Pubitemid 47222127)
13. Hou J, Song CL, Cao XY, Zhou YY (2013) Shifts between ammonia-oxidizing bacteria and archaea in relation to nitrification potential across trophic gradients in two large Chinese lakes (Lake Taihu and Lake Chaohu). Water Res 47:2285-2296
14. Hu BL, Liu SA, Shen LD, Zheng P, Xu XY, Lou LP (2012) Effect of different ammonia concentrations on community succession of ammonia-oxidizing microorganisms in a simulated paddy soil column. PLOS One. doi:10.1371/ journalpone0044122
15. Im J, Lee SW, Bodrossy L, Barcelona MJ, Semrau JD (2011) Field application of nitrogen and phenylacetylene to mitigate greenhouse gas emissions from landfill cover soils: effects on microbial community structure. Appl Microbiol Biotechnol 89:189-200
16. Jung J, Yeom J, Kim J, Han J, Lim HS, Park H, Hyun S, Park W (2011) Change in gene abundance in the nitrogen biogeochemical cycle with temperature and nitrogen addition in Antarctic soils. Res Microbiol 162:1018-1026
17. Kim JG, Jung MY, Park SJ, Rijpstra WIC, Damste JSS, Madsen EL,Min D, Kim JS, Kim GJ, Rhee SK (2012) Cultivation of a highly enriched ammonia-oxidizing archaeon of thaumarchaeotal group I1b from an agricultural soil. Environ Microbiol 14:1528-1543
18. 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 (Pubitemid 41613550)
19. Li M, Cao HL, Hong YG, Gu JD (2011) Spatial distribution and abundances of ammonia-oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) in mangrove sediments. Appl Microbiol Biotechnol 89:1243-1254
20. Li XR, Xiao YP, Ren WW, Liu ZF, Shi JH, Quan ZX (2012) Abundance and composition of ammonia-oxidizing bacteria and archaea in different types of soil in the Yangtze River estuary. J Zhejiang Univ-SCI B 13:769-782
21. Liu L, Peng Y, Zheng XH, Xiao L, Yang LY (2010) Vertical structure of bacterial and archaeal communities within the sediment of a eutrophic lake as revealed by culture-independent methods. J Freshw Ecol 25:565-573
22. Liu S, Shen L, Lou L, Tian G, Zheng P, Hu B (2013) Spatial distribution and factors shaping the niche segregation of ammonia-oxidizing microorganisms in the Qiantang River, China. Appl Environ Microbiol 9:4065-4071
23. 2. Soil Biol Biochem 46:163-171
24. Moin NS, Nelson KA, Bush A, Bernhard AE (2009) Distribution and diversity of archaeal and bacterial ammonia oxidizers in salt marsh sediments. Appl Environ Microbiol 75:7461-7468
25. 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 inmarine sediments. Extremophiles 12:605-615
26. Purkhold U, Wagner M, Timmermann G, Pommerening-Roser A, Koops HP (2003) 16S rRNA and amoA-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates: extension of the dataset and proposal of a new lineage within the nitrosomonads. Int J Syst Evol Microbiol 53:1485-1494 (Pubitemid 37184980)
27. Sakami T (2012) Distribution of ammonia-oxidizing archaea and bacteria in the surface sediments of Matsushima Bay in relation to environmental variables. Microbes Environ 27:61-66
28. Santoro AE, Francis CA, de Sieyes NR, Boehm AB (2008) Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary. Environ Microbiol 10:1068-1079 (Pubitemid 351406104)
29. Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71:1501-1506 (Pubitemid 40396689)
30. Shivaji S, Kumari K, Kishore KH, Pindi PK, Rao PS, Srinivas TNR, Asthana R, Ravindra R (2011) Vertical distribution of bacteria in a lake sediment from Antarctica by culture-independent and culturedependent approaches. Res Microbiol 162:191-203
31. Sims A, Horton J, Gajaraj S, McIntosh S, Miles RJ, Mueller R, Reed R, Hu ZQ (2012) Temporal and spatial distributions of ammonia-oxidizing archaea and bacteria and their ratio as an indicator of oligotrophic conditions in natural wetlands. Water Res 46:4121-4129
32. Suwa Y, Sumino T, Noto K (1997) Phylogenetic relationships of activated sludge isolates of ammonia oxidizers with different sensitivities to ammonium sulfate. J Gen Appl Microbiol 43:373-379 (Pubitemid 28174782)
33. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4, molecular evolutionary genetics analysis, MEGA software version 4.0. Mol Biol Evol 24:1596-1599 (Pubitemid 47236692)
34. Tourna M, Stieglmeier M, Spang A, Konneke M, Schintlmeister A, Urich T, Engel M, Schloter M, Wagner M, Richter A, Schleper C (2011) Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proc Natl Acad Sci U S A 108:8420-8425
35. van der Wielen PWJJ, Voost S, van der Kooij D (2009) Ammonia-oxidizing bacteria and archaea in groundwater treatment and drinking water distribution systems. Appl Environ Microbiol 75:4687-4695
36. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu DY, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74 (Pubitemid 38451457)
37. Verhamme DT, Prosser JI, Nicol GW (2011) Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms. ISME J 5:1067-1071
38. Wang YF, Gu JD (2013) Higher diversity of ammonia/ammonium-oxidizing prokaryotes in constructed freshwater wetland than natural coastal marine wetland. Appl Microbiol Biotechnol 97:7015-7033
39. Wang YF, Feng YY, Ma XJ, Gu JD (2013) Seasonal dynamics of ammonia/ammonium-oxidizing prokaryotes in oxic and anoxic wetland sediments of subtropical coastal mangrove. Appl Microbiol Biotechnol 97:7919-7934
40. Wang XY, Wang C, Bao LL, Xie SG (2014) Abundance and community structure of ammonia-oxidizing microorganisms in reservoir sediment and adjacent soils. Appl Microbiol Biotechnol 98:1883-1892
41. Wu YC, Xiang Y, Wang JJ, Zhong JC, He JZ, Wu QLL (2010) Heterogeneity of archaeal and bacterial ammonia oxidizing communities in Lake Taihu, China. Environ Microbiol Rep 2:569-576
42. Zhang JX, Zhang XL, Liu Y, Xie SG, Liu YG (2013) Bacterioplankton communities in a high-altitude freshwater wetland. Ann Microbiol. doi:10.1007/s13213-013-0785-8
43. Zhao XQ, Yang LY, Yu ZY, Peng NY, Xiao L, Yin DQ, Qin BQ (2008) Characterization of depth-related microbial communities in lake sediment by denaturing gradient gel electrophoresis of amplified 16S rRNA fragments. J Environ Sci 20:224-230
44. Zhao DY, Zeng J, Wan WH, Liang HD, Huang R, Wu QLL (2013) Vertical distribution of ammonia-oxidizing archaea and bacteria in sediments of a eutrophic lake. Curr Microbiol 67:327-332
45. Zheng YL, Hou LJ, Liu M, Lu M, Zhao H, Yin GY, Zhou JL (2013) Diversity, abundance, and activity of ammonia-oxidizing bacteria and archaea in Chongming eastern intertidal sediments. Appl Microbiol Biotechnol 97:8351-8363