Geographic Specific Coral-Associated Ammonia-Oxidizing Archaea in the Northern Gulf of Eilat (Red Sea)

Microbial Ecology

Volumn 64, Issue 1, 2012, Pages 18-24

  Siboni, Nachshon ^a,d   Ben Dov, Eitan ^a,b   Sivan, Alex ^a   Kushmaro, Ariel ^a,c  

^a BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

^b ACHVA ACADEMIC COLLEGE   (Israel)

^c NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^d AUSTRALIAN INSTITUTE OF MARINE SCIENCE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA; AMMONIA MONOOXYGENASE; ARCHAEAL PROTEIN; OXIDOREDUCTASE;

ANIMAL; ANTHOZOA; ARCHAEON; ARTICLE; BIODIVERSITY; CLASSIFICATION; GENETICS; GEOGRAPHY; INDIAN OCEAN; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OXIDATION REDUCTION REACTION; PHYLOGENY;

AMMONIA; ANIMALS; ANTHOZOA; ARCHAEA; ARCHAEAL PROTEINS; BIODIVERSITY; GEOGRAPHY; INDIAN OCEAN; MOLECULAR SEQUENCE DATA; OXIDATION-REDUCTION; OXIDOREDUCTASES; PHYLOGENY;

ACANTHASTREA; ANTHOZOA; ARCHAEA; FAVIA; FUNGIA GRANULOSA;

EID: 84862503992     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-011-0006-6     Document Type: Article

References (41)

1. Beman JM, Roberts KJ, Wegley L, Rohwer F, Francis CA (2007) Distribution and diversity of archaeal ammonia monooxygenase genes associated with corals. Appl Environ Microbiol 73: 5642-5647.
2. Beman JM, Sachdeva R, Fuhrman JA (2010) Population ecology of nitrifying Archaea and Bacteria in the Southern California Bight. Environ Microbiol 12: 1282-1292.
3. Beman JM, Steele JA, Fuhrman JA (2011) Co-occurrence patterns for abundant marine archaeal and bacterial lineages in the deep chlorophyll maximum of coastal California. ISME J 5: 1077-1085.
4. Bernhard AB, Landry ZC, Blevins A, de la Torre JR, Giblin AE, Stahl DA (2010) Abundance of ammonia-oxidizing archaea and bacteria along an estuarine salinity gradient in relationship to potential nitrification rates. Appl Environ Microbiol 76: 1285-1289.
5. Brown BE, Bythell JC (2005) Perspectives on mucus secretion in reef corals. Mar Ecol Prog Ser 296: 291-309.
6. Church MJ, Wai B, Karl DM, DeLong EF (2010) Abundances of crenarchaeal amoA genes and transcripts in the Pacific Ocean. Environ Microbiol 12: 679-688.
7. Coolen MJL, Abbas B, van Bleijswijk J, Hopmans EC, Kuypers MMM, Wakeham SG, Sinninghe Damsté 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.
8. De Corte D, Yokokawa T, Varela MM, Agogué H, Herndl GJ (2009) Spatial distribution of Bacteria and Archaea and amoA gene copy numbers throughout the water column of the Eastern Mediterranean Sea. ISME J 3: 147-158.
9. Erguder TH, Boon N, Wittebolle L, Marzorati M, Verstraete W (2009) Environmental factors shaping the ecological niches of ammonia-oxidizing archaea. FEMS Microbiol Rev 33: 855-869.
10. Felsenstein J (1985) Confidence limits of phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
11. Francis CA, Beman JM, Kuyper MMM (2007) New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. ISME J 1: 19-27.
12. 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 U S A 102: 14683-14688.
13. Genin A, Shaked Y, Ayalon I, Drey M, Rivlin T, Segev N, Chernihovsky M (2008) Scientific report of the Israel National Monitoring Program at the Gulf of Eilat.
14. Gubry-Rangin C, Nicol GW, Prosser JI (2010) Archaea rather than bacteria control nitrification in two agricultural acidic soils. FEMS Microb Ecol 74: 566-574.
15. Huber T, Faulkner G, Hugenholtz P (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20: 2317-2319.
16. Jetten MSM (2008) The microbial nitrogen cycle. Environ Microbiol 10: 2903-2909.
17. Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30: 3059-3066.
18. Lam P, Jensen MM, Lavik G, McGinnis DF, Müller B, Schubert CJ, Amann R, Thamdrup B, Kuypers MMM (2007) Linking crenarchaeal and bacterial nitrification to anammox in the Black Sea. Proc Natl Acad Sci U S A 104: 7104-7109.
19. Limpiyakorn T, Sonthiphand P, Rongsayamanont C, Polprasert C (2011) Abundance of amoA genes of ammonia-oxidizing archaea and bacteria in activated sludge of full-scale wastewater treatment plants. Bioresour Technol 102: 3694-3701.
20. Lücker S, Wagner M, Maixner F, Pelletier E, Koch H, Vacherie B, Rattei T, Damste JSS, Spieck E, Paslier DL, Daims H (2010) A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc Natl Acad Sci U S A 107: 13479-13484.
21. Martens-Habbena W, Berube PM, Urakawa H, de la Torre JR, Stahl DL (2009) Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 461: 976-979.
22. Martínez-García M, Stief P, Díaz-Valdés M, Wanner G, Ramos-Esplá A, Dubilier N, Antón J (2008) Ammonia-oxidizing Crenarchaeota and nitrification inside the tissue of a colonial ascidian. Environ Microbiol 10: 2991-3001.
23. Merom D, Atias E, Lasur Kruh L, Elifantz H, Minz D, Fine M, Banin E (2011) The impact of reduced pH on the microbial community of the coral Acropora eurystoma. ISME J 5: 51-60.
24. Nicol GW, Schleper C (2006) Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle. Trends Microbiol 14: 207-212.
25. Norton JM, Alzerreca JJ, Suwa Y, Klotz MG (2002) Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria. Arch Microbiol 177: 139-149.
26. Prosser JI, Nicol GW (2008) Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environ Microbiol 10: 2931-2941.
27. Rosenberg E, Koren O, Reshef L, Efrony R, Zilber-Rosenberg I (2007) The role of microorganisms in coral health, disease and evolution. Nat Rev Microbiol 5: 355-362.
28. Rosenfeld M, Bresler V, Abelson A (1999) Sediment as a possible source of food for corals. Ecol Lett 2: 345-348.
29. Rotthauwe JH, Boer W, Liesack W (1997) The ammonia monooxygenase structural gene amoA as a functional marker, molecular fine scale analysis of natural ammonia oxidizing populations. Appl Environ Microbiol 63: 4704-4712.
30. 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.
31. 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.
32. Shashar N, Cohen Y, Loya Y (1993) Extreme diel fluctuations of oxygen in diffusive boundary layers surrounding stony corals. Bio Bull 185: 455-461.
33. Shen JP, Zhang LM, Zhu YG, Zhang JB, He JZ (2008) Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam. Environ Microbiol 10: 1601-1611.
34. Siboni N, Ben-Dov E, Sivan A, Kushmaro A (2008) Global distribution and diversity of coral-associated archaea and their possible role in the coral holobiont nitrogen cycle. Environ Microbiol 10: 979-2990.
35. Steger D, Ettinger-Epstein P, Whalan S, Hentschel U, de Nys R, Wagner M, Taylor MW (2008) Diversity and mode of transmission of ammonia-oxidizing archaea in marine sponges. Environ Microbiol 10: 1087-1094.
36. Szmant AM, Ferrer LM, FitzGerald LM (1990) Nitrogen excretion and O: N ratios in reef corals: evidence for conservation of nitrogen. Mar Bio 104: 119-127.
37. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Bio Evol 10: 512-526.
38. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
39. Vega-Thurber R, Willner-Hall D, Rodriguez-Mueller B, Desnues C, Edwards RA, Angly F, Dlnsbale E, Kelly L, Rohwer F (2009) Metagenomic analysis of stressed coral holobionts. Environ Microbiol 11: 2148-2163.
40. Wiled C, Woyt H, Huettei M (2005) Influence of coral mucus on nutrient fluxes in carbonate sands. Mar Ecol Prog Ser 287: 87-98.
41. Wuchter C, Abbas B, Coolen MJL, Herfort L, van Bleijswijk J, Timmers P, Strous E, Teira E, Herndl GJ, Middelburg JJ, Schouten S, Sinninghe Damste JS (2006) Archaeal nitrification in the ocean. Proc Natl Acad Sci U S A 103: 12317-12322.