Molecular Detection of Novel Anammox Bacterial Clusters in the Sediments of the Shallow Freshwater Lake Taihu

Geomicrobiology Journal

Volumn 29, Issue 9, 2012, Pages 852-859

  Wu, Yucheng ^a,b   Xiang, Yan ^a,c   Wang, Jianjun ^a   Wu, Qinglong L ^a  

^a NANJING INSTITUTE OF GEOGRAPHY AND LIMNOLOGY   (China)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^c Guizhou Institute of Fisheries   (China)

Author keywords

16S ribosomal RNA; anaerobic ammonium oxidation; in situ detection; lake sediment; niche separation

Indexed keywords

AMMONIUM; BACTERIUM; COMMUNITY COMPOSITION; LACUSTRINE DEPOSIT; MICROBIAL COMMUNITY; MOLECULAR ANALYSIS; NICHE PARTITIONING; NITRITE; RNA;

CHINA; TAIHU LAKE;

BACTERIA (MICROORGANISMS);

EID: 84865816370     PISSN: 01490451     EISSN: 15210529     Source Type: Journal    
DOI: 10.1080/01490451.2011.635760     Document Type: Article

References (42)

1. Amano, T, Yoshinaga, I, Okada, K, Yamagishi, T, Ueda, S, Obuchi, A, Sako, Y and Suwa, Y. 2007. Detection of anammox activity and diversity of anammox bacteria-related 16S rRNA genes in coastal marine sediment in Japan. Microbes Environ, 22: 232-242.
2. Dale, O R, Tobias, C R and Song, B. 2009. Biogeographical distribution of diverse anaerobic ammonium oxidizing (anammox) bacteria in Cape Fear River Estuary. Environ Microbiol, 11: 1194-1207.
3. 2 production by the anammox reaction in the anoxic water column of Golfo Dulce, Costa Rica. Nature, 422: 606-608.
4. 2 production in coastal marine sediments. Geochim Cosmochim Acta, 69: 2057-2065.
5. Guo, L. 2007. Doing battle with the green monster of Taihu Lake. Science, 317: 1166
6. Hong, Y G, Li, M, Cao, H and Gu, J D. 2010. Residence of habitat-specific anammox bacteria in the deep-sea subsurface sediments of the South China Sea: Analyses of marker gene abundance with physical chemical parameters. Microb Ecol, 62: 36-47.
7. Horner-Devine, M C and Martiny, A C. 2008. News about nitrogen. Science, 320: 757-758.
8. Huber, T, Faulkner, G and Hugenholtz, P. 2004. Bellerophon: A program to detect chimeric sequences in multiple sequence alignments. Bioinformatics, 20: 2317-2319.
9. Humbert, S, Tarnawski, S, Fromin, N, Mallet, M-P, Aragno, M and Zopfi, J. 2010. Molecular detection of anammox bacteria in terrestrial ecosystems: Distribution and diversity. ISME J, 4: 450-454.
10. Jetten, M SM, van Niftrik, L, Strous, M, Kartal, B, Keltjens, J T and op den Camp, H JM. 2009. Biochemistry and molecular biology of anammox bacteria. Crit Rev Biochem Mol Biol, 44: 65-84.
11. Kartal, B, Koleva, M, Arsov, R, van de Star, W, Jetten, M SM and Strous, M. 2006. Adaptation of a freshwater anammox population to high salinity wastewater. J Biotechnol, 126: 546-553.
12. Kartal, B, Rattray, J, van Niftrik, L A, van de Vossenberg, J, Schmid, M C, Webb, R, Schouten, S, Fuerst, J A, Damsté, J SS, Jetten, M SM and Strous, M. 2007. Anammoxoglobus propionicus "a new propionate oxidizing species of anaerobic ammonium oxidizing bacteria". Syst Appl Microbiol. Candidatus, 30: 39-49.
13. Kartal, B, van Niftrik, L, Rattray, J, van de Vossenberg, JLCM, Schmid, M C, Damst, J S, Jetten, M SM and Strous, M. 2008. Candidatus "Brocadia fulgida": An autofluorescent anaerobic ammonium oxidizing bacterium. FEMS Microbiol Ecol, 63: 46-55.
14. Klotz, M G, Schmid, M C, Strous, M, op den Camp, H JM, Jetten, M SM and Hooper, A B. 2008. Evolution of an octahaem cytochrome c protein family that is key to aerobic and anaerobic ammonia oxidation by bacteria. Environ Microbiol, 10: 3150-3163.
15. Kuenen, JG. 2008. Anammox bacteria: From discovery to application. Nat Rev Microbiol, 6: 320-326.
16. Kuypers, M MM, Lavik, G, Woebken, D, Schmid, M, Fuchs, B M, Amann, R, Jorgensen, B B and Jetten, M SM. 2005. Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation. Proc Nat Acad Sci, 102: 6478-6483.
17. Kuypers, M MM, Sliekers, A O, Lavik, G, Schmid, M, Jorgensen, B B, Kuenen, J G, Sinninghe Damste, J S, Strous, M and Jetten, M SM. 2003. Anaerobic ammonium oxidation by anammox bacteria in the Black Sea. Nature, 422: 608-611.
18. Li, H, Chen, S, Mu, B Z and Gu, J D. 2010a. Molecular detection of anaerobic ammonium-oxidizing (anammox) bacteria in high-temperature petroleum reservoirs. Microb Ecol, 60: 771-783.
19. Li, M, Ford, T, Li, X and Gu, J D. 2011. Cytochrome cd1-containing nitrite reductase encoding gene nirS as a new functional biomarker for detection of anaerobic ammonium oxidizing (anammox) bacteria. Environ Sci Technol, 45: 3547-3553.
20. Li, M and Gu, J D. 2011. Advances in methods for detection of anaerobic ammonium oxidizing (anammox) bacteria. Appl Microbiol Biotechnol, 90: 1241-1252.
21. Li, M, Hong, Y, Klotz, M G and Gu, J D. 2010b. A comparison of primer sets for detecting 16S rRNA and hydrazine oxidoreductase genes of anaerobic ammonium-oxidizing bacteria in marine sediments. Appl Microbiol Biotechnol, 86: 781-790.
22. Mulder, A, van de Graaf, A A, Robertson, L A and Kuenen, J G. 1995. Anaerobic ammonium oxidation discovered in a denitrifying fluidized bed reactor. FEMS Microbiol Ecol, 16: 177-183.
23. Penton, C R, Devol, A H and Tiedje, J M. 2006. Molecular evidence for the broad distribution of anaerobic ammonium-oxidizing bacteria in freshwater and marine sediments. Appl Environ Microbiol, 72: 6829-6832.
24. Purkhold, U, Pommerening-Roser, A, Juretschko, S, Schmid, M C, Koops, H-P and Wagner, M. 2000. Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: Implications for molecular diversity surveys. Appl Environ Microbiol, 66: 5368-5382.
25. Qin, BQ. 2008. Lake Taihu, China: Dynamics and environmental change. Dordrecht: Springer.
26. Ramette, A. 2007. Multivariate analyses in microbial ecology. FEMS Microbiol Ecol, 62: 142-140.
27. Rich, J J, Dale, O R, Song, B and Ward, B B. 2008. Anaerobic ammonium oxidation (anammox) in Chesapeake Bay sediments. Microb Ecol, 55: 311-320.
28. Risgaard-Petersen, N and Jensen, K. 1997. Nitrification and denitrification in the rhizosphere of the aquatic macrophyte Lobelia dortmanna L. Limnol Oceanogr, 42: 529-537.
29. Schloss, P D and Handelsman, J. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol, 71: 1501-1506.
30. Schloss, P D and Handelsman, J. 2006. Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures. Appl Environ Microbiol, 72: 6773-6779.
31. Schloss, P D, Larget, B R and Handelsman, J. 2004. Integration of microbial ecology and statistics: A test to compare gene libraries. Appl Environ Microbiol, 70: 5485-5492.
32. Schmid, M C, Hooper, A B, Klotz, M G, Woebken, D, Lam, P, Kuypers, M MM, Pommerening-Roeser, A, od Camp, H JM and Jetten, M SM. 2008. Environmental detection of octahaem cytochrome c hydroxylamine/hydrazine oxidoreductase genes of aerobic and anaerobic ammonium-oxidizing bacteria. Environ Microbiol, 10: 3140-3149.
33. Schubert, C J, Durisch-Kaiser, E, Wehrli, B, Thamdrup, B, Lam, P and Kuypers, M MM. 2006. Anaerobic ammonium oxidation in a tropical freshwater system (Lake Tanganyika). Environ Microbiol, 8: 1857-1863.
34. Strous, M, Pelletier, E, Mangenot, S, Rattei, T, Lehner, A, Taylor, M W, Horn, M, Daims, H, Bartol-Mavel, D, Wincker, P, Barbe, V, Fonknechten, N, Vallenet, D, Segurens, B, Schenowitz-Truong, C, Medigue, C, Collingro, A, Snel, B, Dutilh, B E, Op den Camp, H JM, van der Drift, C, Cirpus, I, van de Pas-Schoonen, K T, Harhangi, H R, van Niftrik, L, Schmid, M, Keltjens, J, van de Vossenberg, J, Kartal, B, Meier, H, Frishman, D, Huynen, M A, Mewes, H W, Weissenbach, J, Jetten, M SM, Wagner, M and Le Paslier, D. 2006. Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature, 440: 790-794.
35. Trimmer, M, Nicholls, J C, Morley, N, Davies, C A and Aldridge, J. 2005. Biphasic behavior of anammox regulated by nitrite and nitrate in an estuarine sediment. Appl Environ Microbiol, 71: 1923-1930.
36. Woebken, D, Lam, P, Kuypers, M, Naqul, S WA, Kartal, B, Strous, M, Jetten, M SM, Fuchs, B M and Amann, R. 2008. A microdiversity study of anammox bacteria reveals a novel Candidatus Scalindua phylotype in marine oxygen minimum zones. Environ Microbiol, 10: 3106-3119.
37. Wu, Q L, Zwart, G, Wu, J, Agterveld, MPK-V, Liu, S and Hahn, M W. 2007. Submersed macrophytes play a key role in structuring bacterioplankton community composition in the large, shallow, subtropical Taihu Lake, China. Environ Microbiol, 9: 2765-2774.
38. Wu, Y, Xiang, Y, Wang, J, Zhong, J, He, J and Wu, Q L. 2010. Heterogeneity of archaeal and bacterial ammonia-oxidizing communities in Lake Taihu, China. Environ Microbiol Rep, 2: 569-576.
39. Xing, P and Kong, F. 2007. Intra-habitat heterogeneity of environmental factors regulating bacterioplankton community composition in Lake Taihu, China. Aquat Microb Ecol, 48: 113-122.
40. Xu, H, Zhang, L, Shang, J, Dai, J and Fan, C. 2009. Denitrification and anammox on the sediment-water interface in the Meiliang Bay of Lake Taihu. J Lake Sci, 21: 775-781.
41. Zhang, Y, Ruan, X-H, Op den Camp, H JM, Smits, T JM, Jetten, M SM and Schmid, M C. 2007. Diversity and abundance of aerobic and anaerobic ammonium-oxidizing bacteria in freshwater sediments of the Xinyi River (China). Environ Microbiol, 9: 2375-2382.
42. Zhou, J, Bruns, M A and Tiedje, J M. 1996. DNA recovery from soils of diverse composition. Appl Environ Microbiol, 62: 316-322.