publication . Article . 2012

Diversity and abundance of ammonia oxidizing archaea in tropical compost systems

David H. Dyer; Vidya de Gannes; William J. Hickey; Gaius Eudoxie;
Open Access
  • Published: 01 Jul 2012 Journal: Frontiers in Microbiology, volume 3 (eissn: 1664-302X, Copyright policy)
  • Publisher: Frontiers Media SA
Abstract
None: Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA) has changed the paradigm of nitrification being initiated solely by ammonia oxidizing bacteria. In the present study, AOA abundance and diversity was examined in composts produced from...
Subjects
free text keywords: Microbiology (medical), Microbiology, Original Research Article, ammonia oxidizing archaea, diversity, molecular ecology, QR1-502, Compost, engineering.material, engineering, Ecology, Agronomy, Agriculture, business.industry, business, Archaea, biology.organism_classification, biology, Tropics, Nitrification, Tropical agriculture, Mesophile, Bagasse
Communities
Agricultural and Food Sciences
Rural Digital Europe
65 references, page 1 of 5

Adair K. L. Schwartz E. (2008). Evidence that ammonia-oxidizing archaea are more abundant than ammonia-oxidizing bacteria in semiarid soils of northern Arizona, USA. Microb. Ecol. 56, 420–426. 10.1007/s00248-007-9360-9 18204798 [OpenAIRE] [PubMed] [DOI]

Anastasi A. Varese G. C. Marchisio V. F. (2005). Isolation and identification of fungal communities in compost and vermicompost. Mycologia 97, 33–44. 10.3852/mycologia.97.1.33 16389954 [PubMed] [DOI]

Arezi B. Xing W. Sorge J. A. Hogrefe H. H. (2003). Amplification efficiency of thermostable DNA polymerases. Anal. Biochem. 321, 226–235. 10.1016/S0003-2697(03)00465-2 14511688 [OpenAIRE] [PubMed] [DOI]

Barrington S. Choiniere D. Trigui M. Knight W. (2002). Effect of carbon source on compost nitrogen and carbon losses. Bioresour. Technol. 83, 189–194. 12094792 [OpenAIRE] [PubMed]

Bates S. T. Berg-Lyons D. Caporaso J. G. Walters W. A. Knight R. Fierer N. (2010). Examining the global distribution of dominant archaeal populations in soil. ISME J. 5, 908–917. 10.1038/ismej.2010.171 21085198 [OpenAIRE] [PubMed] [DOI]

Beman J. M. Popp B. N. Francis C. A. (2008). Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California. ISME J. 2, 429–441. 10.1038/ismej.2007.118 18200070 [OpenAIRE] [PubMed] [DOI]

Bernal M. P. Alburquerque J. A. Moral R. (2009). Composting of animal manures and chemical criteria for compost maturity assessment. A review. Bioresour. Technol. 100, 5444–5453. 10.1016/j.biortech.2008.11.027 19119002 [OpenAIRE] [PubMed] [DOI]

Blainey P. C. Mosier A. C. Potanina A. Francis C. A. Quake S. R. (2011). Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. PLoS ONE 6:e16626. 10.1371/journal.pone.0016626 21364937 [OpenAIRE] [PubMed] [DOI]

Caffrey J. M. Bano N. Kalanetra K. Hollibaugh J. T. (2007). Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia. ISME J. 1, 660–662. 10.1038/ismej.2007.79 18043673 [OpenAIRE] [PubMed] [DOI]

Charest M. H. Antoun H. Beuchamp C. J. (2004). Dynamics of water-soluble carbon substances and microbial populations during the composting of de-inking paper sludge. Bioresour. Technol. 91, 53–67. 10.1016/S0960-8524(03)00155-X 14585622 [OpenAIRE] [PubMed] [DOI]

Chen X. Zhu Y. Xia Y. Shen J. He J. (2008). Ammonia-oxidising archaea:important players in paddy rhizosphere soil? Environ. Microbiol. 10, 1978–1987. 10.1111/j.1462-2920.2008.01613.x 18430011 [OpenAIRE] [PubMed] [DOI]

De La Torre J. R. Walker C. B. Ingalls A. E. Konneke M. Stahl D. A. (2008). Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ. Microbiol. 10, 810–818. 10.1111/j.1462-2920.2007.01506.x 18205821 [OpenAIRE] [PubMed] [DOI]

Di H. J. Cameron K. C. Shen J. P. Winefield C. S. O'Callaghan M. Bowatte S. He J. Z. (2010). Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions. FEMS Microbiol. Ecol. 72, 386–394. 10.1111/j.1574-6941.2010.00861.x 20370827 [OpenAIRE] [PubMed] [DOI]

Erguder T. H. 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. 10.1111/j.1574-6976.2009.00179.x 19453522 [OpenAIRE] [PubMed] [DOI]

Francis C. A. Roberts K. J. Beman J. M. Santoro A. E. Oakley B. B. (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. 10.1073/pnas.0506625102 16186488 [OpenAIRE] [PubMed] [DOI]

65 references, page 1 of 5
Abstract
None: Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA) has changed the paradigm of nitrification being initiated solely by ammonia oxidizing bacteria. In the present study, AOA abundance and diversity was examined in composts produced from...
Subjects
free text keywords: Microbiology (medical), Microbiology, Original Research Article, ammonia oxidizing archaea, diversity, molecular ecology, QR1-502, Compost, engineering.material, engineering, Ecology, Agronomy, Agriculture, business.industry, business, Archaea, biology.organism_classification, biology, Tropics, Nitrification, Tropical agriculture, Mesophile, Bagasse
Communities
Agricultural and Food Sciences
Rural Digital Europe
65 references, page 1 of 5

Adair K. L. Schwartz E. (2008). Evidence that ammonia-oxidizing archaea are more abundant than ammonia-oxidizing bacteria in semiarid soils of northern Arizona, USA. Microb. Ecol. 56, 420–426. 10.1007/s00248-007-9360-9 18204798 [OpenAIRE] [PubMed] [DOI]

Anastasi A. Varese G. C. Marchisio V. F. (2005). Isolation and identification of fungal communities in compost and vermicompost. Mycologia 97, 33–44. 10.3852/mycologia.97.1.33 16389954 [PubMed] [DOI]

Arezi B. Xing W. Sorge J. A. Hogrefe H. H. (2003). Amplification efficiency of thermostable DNA polymerases. Anal. Biochem. 321, 226–235. 10.1016/S0003-2697(03)00465-2 14511688 [OpenAIRE] [PubMed] [DOI]

Barrington S. Choiniere D. Trigui M. Knight W. (2002). Effect of carbon source on compost nitrogen and carbon losses. Bioresour. Technol. 83, 189–194. 12094792 [OpenAIRE] [PubMed]

Bates S. T. Berg-Lyons D. Caporaso J. G. Walters W. A. Knight R. Fierer N. (2010). Examining the global distribution of dominant archaeal populations in soil. ISME J. 5, 908–917. 10.1038/ismej.2010.171 21085198 [OpenAIRE] [PubMed] [DOI]

Beman J. M. Popp B. N. Francis C. A. (2008). Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California. ISME J. 2, 429–441. 10.1038/ismej.2007.118 18200070 [OpenAIRE] [PubMed] [DOI]

Bernal M. P. Alburquerque J. A. Moral R. (2009). Composting of animal manures and chemical criteria for compost maturity assessment. A review. Bioresour. Technol. 100, 5444–5453. 10.1016/j.biortech.2008.11.027 19119002 [OpenAIRE] [PubMed] [DOI]

Blainey P. C. Mosier A. C. Potanina A. Francis C. A. Quake S. R. (2011). Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. PLoS ONE 6:e16626. 10.1371/journal.pone.0016626 21364937 [OpenAIRE] [PubMed] [DOI]

Caffrey J. M. Bano N. Kalanetra K. Hollibaugh J. T. (2007). Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia. ISME J. 1, 660–662. 10.1038/ismej.2007.79 18043673 [OpenAIRE] [PubMed] [DOI]

Charest M. H. Antoun H. Beuchamp C. J. (2004). Dynamics of water-soluble carbon substances and microbial populations during the composting of de-inking paper sludge. Bioresour. Technol. 91, 53–67. 10.1016/S0960-8524(03)00155-X 14585622 [OpenAIRE] [PubMed] [DOI]

Chen X. Zhu Y. Xia Y. Shen J. He J. (2008). Ammonia-oxidising archaea:important players in paddy rhizosphere soil? Environ. Microbiol. 10, 1978–1987. 10.1111/j.1462-2920.2008.01613.x 18430011 [OpenAIRE] [PubMed] [DOI]

De La Torre J. R. Walker C. B. Ingalls A. E. Konneke M. Stahl D. A. (2008). Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ. Microbiol. 10, 810–818. 10.1111/j.1462-2920.2007.01506.x 18205821 [OpenAIRE] [PubMed] [DOI]

Di H. J. Cameron K. C. Shen J. P. Winefield C. S. O'Callaghan M. Bowatte S. He J. Z. (2010). Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions. FEMS Microbiol. Ecol. 72, 386–394. 10.1111/j.1574-6941.2010.00861.x 20370827 [OpenAIRE] [PubMed] [DOI]

Erguder T. H. 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. 10.1111/j.1574-6976.2009.00179.x 19453522 [OpenAIRE] [PubMed] [DOI]

Francis C. A. Roberts K. J. Beman J. M. Santoro A. E. Oakley B. B. (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. 10.1073/pnas.0506625102 16186488 [OpenAIRE] [PubMed] [DOI]

65 references, page 1 of 5
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