Phylogenetic Diversity and Ecological Pattern of Ammonia-oxidizing Archaea in the Surface Sediments of the Western Pacific

Microbial Ecology

Volumn 62, Issue 4, 2011, Pages 813-823

  Cao, Huiluo ^a   Hong, Yiguo ^a,b   Li, Meng ^a   Gu, Ji Dong ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEA;

EID: 80255133161     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-011-9901-0     Document Type: Article

References (69)

1. Auguet JC, Barberan A, Casamayor EO (2010) Global ecological patterns in uncultured archaea. ISME J 4: 182-190.
2. Bartossek R, Nicol GW, Lanzen A, Klenk HP, Schleper C (2010) Homologues of nitrite reductases in ammonia-oxidizing archaea: diversity and genomic context. Environ Microbiol 12: 1075-1088.
3. Bayer K, Schmitt S, Hentschel U (2008) Physiology, phylogeny and in situ evidence for bacterial and archaeal nitrifiers in the marine sponge Aplysina aerophoba. Environ Microbiol 10: 2942-2955.
4. Beman JM, Francis CA (2006) Diversity of ammonia-oxidizing archaea and bacteria in the sediments of a hypernutrified subtropical estuary: Bahia del Tobari, Mexico. Appl Environ Microbiol 72: 7767-7777.
5. Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P (2008) Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol 6: 245-252.
6. 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.
7. Cao H, Hong Y, Li M, Gu J-D (2011) Lower abundance of ammonia-oxidizing archaea than ammonia-oxidizing bacteria detected in the subsurface sediments of the Northern South China Sea. Geomicrobiol J (in press).
8. Cao H, Hong Y, Li M, Gu J-D (2011) Diversity and abundance of ammonia-oxidizing prokaryotes in sediments from the coastal margin to the South China Sea. Antonie van Leeuwenhoek. doi: 10. 1007/s10482-011-9610-1.
9. Cao H, Li M, Dang H, Gu JD (2011) Responses of aerobic and anaerobic ammonia/ammonium oxidizing microorganisms to anthropogenic pollution in coastal marine environments. In: Klotz MG, Stein LY (eds) Methods in enzymology, part B: research on nitrification and related processes, vol 496. Academic Press, San Diego, California, pp 35-62.
10. Cao H, Li M, Hong Y, Gu J-D (2011) Diversity and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in polluted mangrove sediment. Syst Appl Microbiol. doi: 10. 1016/j. syapm. 2010. 11. 023.
11. Church MJ, Wai B, Karl DM, DeLong EF (2010) Abundance of crenarchaeal amoA genes and transcripts in the Pacific Ocean. Environ Microbiol 12: 679-688.
12. Coolen MJ, Abbas B, van Bleijswijk J, Hopmans EC, Kuypers MM, 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.
13. 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.
14. Dang H, Zhang X, Sun J, Li T, Zhang Z, Yang G (2008) Diversity and spatial distribution of sediment ammonia-oxidizing Crenarchaeota in response to estuarine and environmental gradients in the Changjiang Estuary and East China Sea. Microbiology 154: 2084-2095.
15. Dang H, Luan XW, Chen R, Zhang X, Guo L, Klotz MG (2010) Diversity, abundance and distribution of amoA-encoding archaea in deep-sea methane seep sediments of the Okhotsk Sea. FEMS Microbiol Ecol 72: 370-385.
16. De'Ath G (2002) Multivariate regression trees: a new technique for modeling species-environment relationships. Ecology 83: 1105-1117.
17. de la Torre JR, Walker CB, Ingalls AE, Könneke M, Stahl DA (2008) Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ Microbiol 10: 810-818.
18. Faith DP (1992) Conservation evaluation and phylogenetic diversity. Biol Conserv 61: 1-10.
19. 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. Proc Natl Acad Sci USA 102: 14683-14688.
20. Ginsburg GD, Soloviev VA, Cranston RE, Lorenson TD, Kvenvolden KA (1993) Gas hydrates from the continental slope, offshore Sakhalin Island, Okhotsk Sea. Geo-Mar Lett 13: 41-48.
21. Gubry-Rangin C, Nicol GW, Prosser JI (2010) Archaea rather than bacteria control nitrification in two agricultural acidic soils. FEMS Microbiol Ecol 74: 566-574.
22. Hallam SJ, Konstantinidis KT, Putnam N, Schleper C, Watanabe Y, Sugahara J, Preston C, de la Torre J, Richardson PM, DeLong EF (2006) Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc Natl Acad Sci USA 103: 18296-18301.
23. 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: e95.
24. 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 USA 105: 2134-21349.
25. Helmus MR, Bland TJ, Williams CK, Ives AR (2007) Phylogenetic measures of biodiversity. Am Nat 169: 68-83.
26. Herrmann M, Saunders AM, Schramm A (2009) Effect of lake trophic status and rooted macrophytes on community composition and abundance of ammonia-oxidizing prokaryotes in freshwater sediments. Appl Environ Microbiol 75: 3127-3136.
27. Hubert C, Loy A, Nickel M, Arnosti C, Baranyi C, Brüchert V, Ferdelman T, Finster K, Christensen FM, Rezende JR, Vandieken V, Jørgensen BB (2009) A constant flux of diverse thermophilic bacteria into the cold Arctic seabed. Science 325: 1541-1544.
28. Inagaki F, Takai K, Komatsu T, Kanamatsu T, Fujioka K, Horikoshi K (2001) Archaeology of Archaea: geomicrobiological record of Pleistocene thermal events concealed in a deep-sea subseafloor environment. Extremophiles 5: 385-392.
29. Jackson CR, Weeks AQ (2008) Influence of particle size on bacterial community structure in aquatic sediments as revealed by 16S rRNA gene sequence analysis. Appl Environ Microb 74: 5237-5240.
30. Jia Z, Conrad R (2009) Bacteria rather than archaea dominate microbial ammonia oxidation in an agricultural soil. Environ Microbiol 11: 1658-1671.
31. Jiang H, Huang Q, Dong H, Wang P, Wang F, Li W, Zhang C (2010) RNA-based investigation of ammonia-oxidizing archaea in hot springs of Yunnan Province, China. Appl Environ Microbiol 76: 4538-4541.
32. Kato S, Kobayashi C, Kakegawa T, Yamagishi A (2009) Microbial communities in iron-silica-rich microbial mats at deep-sea hydrothermal fields of the Southern Mariana Trough. Environ Microbiol 11: 2094-2111.
33. Kembel S, Ackerly D, Blomberg S, Cowan P, Helmus M, Webb C (2008) Picante: tools for integrating phylogenies and ecology. Version 0. 4. 0. Available at http://picante.r-forge.r-project.org/.
34. Lam P, Jensen MM, Lavik G, McGinnis DF, Muller B, Schubert CJ, Amann R, Thamdrup B, Kuypers MM (2007) Linking crenarchaeal and bacterial nitrification to anammox in the Black Sea. Proc Natl Acad Sci USA 104: 7104-7109.
35. Lee OO, Wang Y, Yang J, Lafi FF, Al-Suwailem A, Qian PY (2011) Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea. ISME J 5: 650-664.
36. Li M, Cao H, Hong Y, Gu J-D (2011) Spatial distribution and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in mangrove sediments. Appl Microbiol Biotechnol 89: 1243-1254.
37. Liu Z, Huang S, Sun G, Xu Z, Xu M (2011) Diversity and abundance of ammonia-oxidizing archaea in the Dongjiang River, China. Microbiol Res. doi: 10. 1016/j. micres. 2010. 08. 002.
38. López-Legentil S, Erwin PM, Pawlik JR, Song B (2010) Effects of sponge bleaching on ammonia-oxidizing archaea: distribution and relative expression of ammonia monooxygenase genes associated with the barrel sponge Xestospongia muta. Microb Ecol 60: 561-571.
39. Lozupone C, Hamady M, Knight R (2006) UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinforma 7: 371.
40. Martens-Habbena W, Berube PM, Urakawa H, de la Torre JR, Stahl DA (2009) Ammonia oxidation kinetics determine niche separation of nitrifying archaea and bacteria. Nature 461: 976-979.
41. McArdle B (2001) Fitting multivariate models to community data: a comment on distance-based redundancy analysis. Ecology 82: 290-297.
42. Molina V, Belmar L, Ulloa O (2010) High diversity of ammonia-oxidizing archaea in permanent and seasonal oxygen-deficient waters of the eastern South Pacific. Environ Microbiol 12: 2450-2465.
43. Mosier AC, Francis CA (2008) Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary. Environ Microbiol 10: 3002-3016.
44. Nakagawa T, Mori K, Kato C, Takahashi R, Tokuyama T (2007) Distribution of cold-adapted ammonia-oxidizing microorganisms in the deep-ocean of the northeastern Japan Sea. Microbes Environ 22: 365-372.
45. Nicol GW, Leininger S, Schleper C, Prosser JI (2008) The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ Microbiol 10: 2966-2978.
46. Nunoura T, Oida H, Nakaseama M, Kosaka A, Ohkubo SB, Kikuchi T, Kazama H, Hosoi-Tanabe S, Nakamura K, Kinoshita M, Hirayama H, Inagaki F, Tsunogai U, Ishibashi J, Takai K (2010) Archaeal diversity and distribution along thermal and geochemical gradients in hydrothermal sediments at the Yonaguni Knoll IV hydrothermal field in the Southern Okinawa trough. Appl Environ Microbiol 76: 1198-11211.
47. Oksanen J, Kindt R, Legendre P, O'hara B, Simpson GL, Stevens MHH (2008) Vegan: community ecology package. Version 1. 11. 14. Available at http://vegan.r-forge.r-project.org.
48. Offre P, Nicol GW, Prosser JI (2011) Community profiling and quantification of putative autotrophic thaumarchaeal communities in environmental samples. Environ Microbiol Reports. doi: 10. 1111/j. 1758-2229. 2010. 00217.
49. Prosser JI, Nicol GW (2008) Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environ Microbiol 10: 2931-2941.
50. Rogers DR, Casciotti KL (2010) Abundance and diversity of archaeal ammonia oxidizers in a coastal groundwater system. Appl Environ Microbiol 76: 7938-7948.
51. Sahan E, Muyzer G (2008) Diversity and spatio-temporal distribution of ammonia-oxidizing archaea and bacteria in sediments of the Westerschelde estuary. FEMS Microbiol Ecol 64: 175-186.
52. 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.
53. Santoro AE, Casciotti KL, Francis CA (2010) Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current. Environ Microbiol 12: 1989-2006.
54. Schauss K, Focks A, Leininger S, Kotzerke A, Heuer H, Thiele-Bruhn S, Sharma S, Wilke BM, Matthies M, Smalla K, Munch JC, Amelung W, Kaupenjohann M, Schloter M, Schleper C (2009) Dynamics and functional relevance of ammonia-oxidizing archaea in two agricultural soils. Environ Microbiol 11: 446-456.
55. Schleper C, Jurgens G, Jonuscheit M (2005) Genomic studies of uncultivated archaea. Nat Rev Microbiol 3: 479-488.
56. Schleper C, Nicol GW (2010) Ammonia-oxidising archaea-physiology, ecology and evolution. Adv Microb Physiol 57: 1-41.
57. Schloss PD, 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.
58. Sonthiphand P, Limpiyakorn T (2011) Change in ammonia-oxidizing microorganisms in enriched nitrifying activated sludge. Appl Microbiol Biotechnol 89: 843-853.
59. Spang A, Hatzenpichler R, Brochler-Armanet C, Rattei T, Tischler P, Spieck E, Streit W, Stahl DA, Wagner M, Schleper C (2010) Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol 18: 331-340.
60. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using likelihood, distance, and parsimony methods. Mol Biol Evol. doi: 10. 1093/molbev/msr113.
61. ter Braak CJF, Smilauer P (2002) CANOCO reference manual and CanoDraw for Windows User's Guide: Software for Canonical Community Ordination (Version 4. 5). Microcomputer Power, Ithaca.
62. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, 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.
63. Wang S, Xiao X, Jiang L, Peng X, Zhou H, Meng J, Wang F (2009) Diversity and abundance of ammonia-oxidizing archaea in hydrothermal vent chimneys, Juan de Fuca Ridge. Appl Environ Microbiol 75: 4216-4220.
64. Walker CB, de la Torre JR, Klotz MG, Urakawa H, Pinel N, Arp DJ, Brochier-Armanet C, Chain PS, Chan PP, Gollabgir A, Hemp J, Hügler M, Karr EA, Könneke M, Shin M, Lawton TJ, Lowe T, Martens-Habbena W, Sayavedra-Soto LA, Lang D, Sievert SM, Rosenzweig AC, Manning G, Stahl DA (2010) Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine Crenarchaea. Proc Natl Acad Sci USA 107: 8818-8823.
65. Wankel SD, Mosier AC, Hansel CM, Paytan A, Francis CA (2011) Spatial variability in nitrification rates and ammonia-oxidizing microbial communities in the agriculturally-impacted Elkhorn Slough Estuary. Appl Environ Microbiol 77: 269-280.
66. Weidler GW, Gerbl FW, Stan-Lotter H (2008) Crenarchaeota and their role in the nitrogen cycle in a subsurface radioactive thermal spring in the Austrian Central Alps. Appl Environ Microbiol 74: 5934-5942.
67. Wu Y, Xiang Y, Wang J, Zhong J, He J, Wu Q (2010) Heterogeneity of archaeal and bacterial ammonia-oxidizing communities in Lake Taihu, China. Environ Microbiol Reports 2: 569-576.
68. Zhang CL, Ye Q, Huang Z, Li W, Chen J, Song Z, Zhao W, Bagwell C, Inskeep WP, Ross C, Gao L, Wiegel J, Romanek CS, Shock EL, Hedlund BP (2008) Global occurrence of archaeal amoA genes in terrestrial hot springs. Appl Environ Microbiol 74: 6417-6426.
69. Zhang LM, Offre PR, He JZ, Verhamme DT, Nicol GW, Prosser JI (2010) Autotrophic ammonia oxidation by soil thaumarchaea. Proc Natl Acad Sci USA 107: 17240-17245.