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Phylogenetically Diverse Denitrifying and Ammonia-Oxidizing Bacteria in Corals Alcyonium gracillimum and Tubastraea coccinea

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Abstract

To date, the association of coral–bacteria and the ecological roles of bacterial symbionts in corals remain largely unknown. In particular, little is known about the community components of bacterial symbionts of corals involved in the process of denitrification and ammonia oxidation. In this study, the nitrite reductase (nirS and nirK) and ammonia monooxygenase subunit A (amoA) genes were used as functional markers. Diverse bacteria with the potential to be active as denitrifiers and ammonia-oxidizing bacteria (AOB) were found in two East China Sea corals: stony coral Alcyonium gracillimum and soft coral Tubastraea coccinea. The 16S rRNA gene library analysis demonstrated different communities of bacterial symbionts in these two corals of the same location. Nitrite reductase nirK gene was found only in T. coccinea, while both nirK and nirS genes were detected in A. gracillimum, which might be the result of the presence of different bacterial symbionts in these two corals. AOB rather than ammonia-oxidizing archaea were detected in both corals, suggesting that AOB might play an important role in the ammonia oxidation process of the corals. This study indicates that the coral bacterial symbionts with the potential for nitrite reduction and ammonia oxidation might have multiple ecological roles in the coral holobiont, which promotes our understanding of bacteria-mediated nitrogen cycling in corals. To our knowledge, this study is the first assessment of the community structure and phylogenetic diversity of denitrifying bacteria and AOB in corals based on nirK, nirS, and amoA gene library analysis.

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References

  • Ainsworth TD, Thurber RV, Gates RD (2010) The future of coral reefs: a microbial perspective. Trends Ecol Evol 25:233–240

    Article  PubMed  Google Scholar 

  • Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Mol Biol R 59:143–169

    CAS  Google Scholar 

  • Baker AC (2004) Symbiont diversity on coral reefs and its relationship to bleaching resistance and resilience. In: Rosenberg E, Loya Y (eds) Coral heath and disease. Springer, Berlin, pp 177–194

    Chapter  Google Scholar 

  • Beman JM, Popp BN, Francis CA (2008) Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California. ISME J 2:429–441

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Bourne DG, Munn CB (2005) Diversity of bacteria associated with the coral Pocillopora damicornis from the Great Barrier Reef. Environ Microbiol 7:1162–1174

    Article  PubMed  CAS  Google Scholar 

  • Braker G, Fesefeldt A, Witzel KP (1998) Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples. Appl Environ Microbiol 64:3769–3775

    PubMed  CAS  Google Scholar 

  • Braker G, Zhou J, Wu L, Devol AH, Tiedje JM (2000) Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in Pacific Northwest marine sediment communities. Appl Environ Microbiol 66:2096–2104

    Article  PubMed  CAS  Google Scholar 

  • Capone D, Dunham S, Horrigan S, Duguay L (1992) Microbial nitrogen transformations in unconsolidated coral reef sediments. Mar Ecol - Prog Ser 80:75–88

    Article  CAS  Google Scholar 

  • Curtis TP, Sloan WT, Scannell JW (2002) Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci USA 99:10494–10499

    Article  PubMed  CAS  Google Scholar 

  • Delong EF (1992) Archaea in coastal marine environment. Proc Natl Acad Sci USA 89:5685–5689

    Article  PubMed  CAS  Google Scholar 

  • DiSalvo L, Gundersen K (1971) Regenerative functions and microbial ecology of coral reefs. I. Assays for microbial population. Can J Microbiol 17:1081–1089

    Article  PubMed  CAS  Google Scholar 

  • Fiore CL, Jarett JK, Olson ND, Lesser MP (2010) Nitrogen fixation and nitrogen transformations in marine symbioses. Trends Microbiol 18:455–463

    Article  PubMed  CAS  Google Scholar 

  • Heylen K, Gevers D, Vanparys B, Wittebolle L, Geets J, Boon N, De Vos P (2006) The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers. Environ Microbiol 8:2012–21

    Article  PubMed  CAS  Google Scholar 

  • Hoffmann F, Radax R, Woebken D, Holtappels M, Lavik G et al (2009) Complex nitrogen cycling in the sponge Geodia barretti. Environ Microbiol 11:2228–2243

    Article  PubMed  CAS  Google Scholar 

  • Huber T (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:2317–2319

    Article  PubMed  CAS  Google Scholar 

  • Jayakumar DA, Francis CA, Naqvi SWA, Ward BB (2004) Diversity of nitrite reductase genes (nirS) in the denitrifying water column of the coastal Arabian Sea. Aquat Microb Ecol 34:69–78

    Article  Google Scholar 

  • Jones CM, Stres B, Rosenquist M, Hallin S (2008) Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification. Mol Biol Evol 25:1955–1966

    Article  PubMed  CAS  Google Scholar 

  • Kellogg CA (2004) Tropical archaea: diversity associated with the surface microlayer of corals. Mar Ecol-Prog Ser 273:81–88

    Article  CAS  Google Scholar 

  • Kimes NE, Van Nostrand JD, Weil E, Zhou J, Morris PJ (2010) Microbial functional structure of Montastraea faveolata, an important Caribbean reef-building coral, differs between healthy and yellow-band diseased colonies. Environ Microbiol 12:541–556

    Article  PubMed  CAS  Google Scholar 

  • Knowlton N, Rohwer F (2003) Multispecies microbial mutualisms on coral reefs: the host as a habitat. The American Naturalist 162:S51–S62

    Article  PubMed  Google Scholar 

  • Kooperman N, Ben-Dov E, Kramarsky-Winter E, Barak Z, Kushmaro A (2007) Coral mucus-associated bacterial communities from natural and aquarium environments. FEMS Microbiol Lett 276:106–113

    Article  PubMed  CAS  Google Scholar 

  • Koren O, Rosenberg E (2006) Bacteria associated with mucus and tissues of the coral Oculina patagonica in summer and winter. Appl Environ Microbiol 72:5254–5259

    Article  PubMed  CAS  Google Scholar 

  • Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115–175

    Google Scholar 

  • Lesser MP, Mazel CH, Gorbunov MY, Falkowski PG (2004) Discovery of symbiotic nitrogen-fixing cyanobacteria in corals. Science 305:997–1000

    Article  PubMed  CAS  Google Scholar 

  • Lins-de-Barros MM, Vieira RP, Cardoso AM, Monteiro VA, Turque AS et al (2010) Archaea, bacteria, and algal plastid associated with the reef-building corals Siderastrea stellata and Mussismilia hispida from Buzios, South Atlantic Ocean, Brazil. Microb Ecol 59:523–532

    Article  PubMed  CAS  Google Scholar 

  • Markell DA, Trench RK (1993) Macromolecules exuded bysymbiotic dinoflagellates in culture: amino acid and sugar composition. J Phycol 29:64–68

    Article  CAS  Google Scholar 

  • Mohamed NM, Colman AS, Tal Y, Hill RT (2008) Diversity and expression of nitrogen fixation genes in bacterial symbionts of marine sponges. Environ Microbiol 10:2910–2921

    Article  PubMed  CAS  Google Scholar 

  • Mouchka ME, Hewson I, Harvell CD (2010) Coral-associated bacterial assemblages: current knowledge and the potential for climate-driven impacts. Integr Comp Biol 50:662–674

    Article  PubMed  Google Scholar 

  • Neulinger SC, Gartner A, Jarnegren J, Ludvigsen M, Lochte K et al (2009) Tissue-associated “Candidatus Mycoplasma corallicola” and filamentous bacteria on the cold-water coral Lophelia pertusa (Scleractinia). Appl Environ Microbiol 75:1437–1444

    Article  PubMed  CAS  Google Scholar 

  • Oakley BB, Francis CA, Roberts KJ, Fuchsman CA, Srinivasan S et al (2007) Analysis of nitrite reductase (nirK and nirS) genes and cultivation reveal depauperate community of denitrifying bacteria in the Black Sea suboxic zone. Environ Microbiol 9:118–130

    Article  PubMed  CAS  Google Scholar 

  • Olson ND, Ainsworth TD, Gates RD, Takabayashi M (2009) Diazotrophic bacteria associated with Hawaiian Montipora corals: diversity and abundance in correlation with symbiotic dinoflagellates. J Exp Mar Biol Ecol 371:140–146

    Article  CAS  Google Scholar 

  • Ritchie KB (2006) Regulation of microbial populations by coral surface mucus and mucus-associated bacteria. Mar Ecol-Prog Ser 322:1–14

    Article  CAS  Google Scholar 

  • Rohwer F, Seguritan V, Azam F, Knowlton N (2002) Diversity and distribution of coral-associated bacteria. Mar Ecol-Prog Ser 243:1–10

    Article  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Rotthauwe J, Boer W, Liesack W (1995) Comparative analysis of gene sequences encoding ammonia monooxygenase of Nitrosospira sp. AHB1 and Nitrosolobus multiformis C–71. FEMS Microbiol Lett 133:131–135

    Article  PubMed  CAS  Google Scholar 

  • 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 Microbiol 63:4704–4712

    PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Shnit-Orland M, Kushmaro A (2009) Coral mucus-associated bacteria: a possible first line of defense. FEMS Microbiol Ecol 67:371–380

    Article  PubMed  CAS  Google Scholar 

  • 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 10:2979–2990

    Article  PubMed  CAS  Google Scholar 

  • Sorokin YI (1973) Trophical role of bacteria in the ecosystem of the coral reef. Nature 242:415–417

    Article  Google Scholar 

  • Spain AM, Peacock AD, Istok JD, Elshahed MS, Najar FZ et al (2007) Identification and isolation of a Castellaniella species important during biostimulation of an acidic nitrate- and uranium-contaminated aquifer. Appl Environ Microbiol 73:4892–4904

    Article  PubMed  CAS  Google Scholar 

  • Steger D, Ettinger-Epstein P, Whalan S, Hentschel U, De Nys R et al (2008) Diversity and mode of transmission of ammonia-oxidizing archaea in marine sponges. Environ Microbiol 10:1087–1094

    Article  PubMed  CAS  Google Scholar 

  • Wegley L, Edwards R, Rodriguez-Brito B, Liu H, Rohwer F (2007) Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environ Microbiol 9:2707–2719

    Article  PubMed  CAS  Google Scholar 

  • Williams WM (1987) Nitrogen fixation (acetylene reduction) associated with the living coral Acropora variabili. Mar Biol 94:531–535

    Article  Google Scholar 

  • Yan T, Fields MW, Wu L, Zu Y, Tiedje JM, Zhou J (2003) Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate– and uranium–contaminated groundwater. Environ Microbiol 5:13–24

    Article  PubMed  CAS  Google Scholar 

  • Yellowlees D, Rees TAV, Fitt WK (1994) Effect of ammonium-supplemented seawater on glutamine synthetase and glutamate dehydrogenase activities in host tissue and zooxanthellae of Pocillopora damicornis and on ammonium uptake rates of the zooxanthellae. Pac Sci 48:291–295

    CAS  Google Scholar 

  • Yokouchi H, Fukuoka Y, Mukoyama D, Calugay R, Takeyama H, Matsunaga T (2006) Whole-metagenome amplification of a microbial community associated with scleractinian coral by multiple displacement amplification using ϕ29 polymerase. Environ Microbiol 8:1155–1163

    Article  PubMed  CAS  Google Scholar 

  • Yonge C (1929) Progress of the Great Barrier Reef expedition. Nature 123:89–99

    Article  Google Scholar 

  • Zehr JP, Kudela RM (2011) Nitrogen cycle of the open ocean: from genes to ecosystems. Annu Rev Mar Sci 3:197–225

    Article  Google Scholar 

  • Zumft WG (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol R 61:533–616

    CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by the National Major Scientific Research Program of China (2013CB956103). The authors are grateful to Prof. Wen Zhang at the Second Military Medical University (China) for the assistance in collecting the coral samples.

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Authors and Affiliations

  1. Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, People’s Republic of China

    Shan Yang, Wei Sun, Fengli Zhang & Zhiyong Li

  2. School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People’s Republic of China

    Shan Yang, Wei Sun, Fengli Zhang & Zhiyong Li

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  1. Shan Yang
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Correspondence to Zhiyong Li.

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Yang, S., Sun, W., Zhang, F. et al. Phylogenetically Diverse Denitrifying and Ammonia-Oxidizing Bacteria in Corals Alcyonium gracillimum and Tubastraea coccinea . Mar Biotechnol 15, 540–551 (2013). https://doi.org/10.1007/s10126-013-9503-6

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