Ammonia‐oxidizing archaea and nitrite‐oxidizing nitrospiras in the biofilter of a shrimp recirculating aquaculture system

This study analysed the nitrifier community in the biofilter of a zero discharge, recirculating aquaculture system ( RAS ) for the production of marine shrimp in a low density (low ammonium production) system. The ammonia‐oxidizing populations were examined by targeting 16 S rRNA and amoA genes of a...

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Published in:FEMS Microbiology Ecology
Main Authors: Brown, Monisha N., Briones, Aurelio, Diana, James, Raskin, Lutgarde
Format: Article in Journal/Newspaper
Language:unknown
Published: Elsevier 2013
Subjects:
Shrimp Aquaculture
Recirculating Aquaculture System
Ammonia Oxidation
Nitrite Oxidation
N Itrospira
N Itrosopumilus Maritimus
Microbiology and Immunology
Ecology and Evolutionary Biology
Science
Health Sciences
Arctic
Online Access:http://hdl.handle.net/2027.42/95109
https://doi.org/10.1111/j.1574-6941.2012.01448.x
id ftumdeepblue:oai:deepblue.lib.umich.edu:2027.42/95109
record_format openpolar
institution Open Polar
collection University of Michigan: Deep Blue
op_collection_id ftumdeepblue
language unknown
topic Shrimp Aquaculture
Recirculating Aquaculture System
Ammonia Oxidation
Nitrite Oxidation
N Itrospira
N Itrosopumilus Maritimus
Microbiology and Immunology
Ecology and Evolutionary Biology
Science
Health Sciences
spellingShingle Shrimp Aquaculture
Recirculating Aquaculture System
Ammonia Oxidation
Nitrite Oxidation
N Itrospira
N Itrosopumilus Maritimus
Microbiology and Immunology
Ecology and Evolutionary Biology
Science
Health Sciences
Brown, Monisha N.
Briones, Aurelio
Diana, James
Raskin, Lutgarde
Ammonia‐oxidizing archaea and nitrite‐oxidizing nitrospiras in the biofilter of a shrimp recirculating aquaculture system
topic_facet Shrimp Aquaculture
Recirculating Aquaculture System
Ammonia Oxidation
Nitrite Oxidation
N Itrospira
N Itrosopumilus Maritimus
Microbiology and Immunology
Ecology and Evolutionary Biology
Science
Health Sciences
description This study analysed the nitrifier community in the biofilter of a zero discharge, recirculating aquaculture system ( RAS ) for the production of marine shrimp in a low density (low ammonium production) system. The ammonia‐oxidizing populations were examined by targeting 16 S rRNA and amoA genes of ammonia‐oxidizing bacteria ( AOB ) and archaea ( AOA ). The nitrite‐oxidizing bacteria ( NOB ) were investigated by targeting the 16 S rRNA gene. Archaeal amoA genes were more abundant in all compartments of the RAS than bacterial amoA genes. Analysis of bacterial and archaeal amoA gene sequences revealed that most ammonia oxidizers were related to N itrosomonas marina and N itrosopumilus maritimus . The NOB detected were related to N itrospira marina and N itrospira moscoviensis, and Nitrospira marina ‐type NOB were more abundant than N . moscoviensis ‐type NOB . Water quality and biofilm attachment media played a role in the competitiveness of AOA over AOB and Nitrospira marina‐ over N . moscoviensis‐ type NOB . Peer Reviewed http://deepblue.lib.umich.edu/bitstream/2027.42/95109/1/fem1448.pdf
format Article in Journal/Newspaper
author Brown, Monisha N.
Briones, Aurelio
Diana, James
Raskin, Lutgarde
author_facet Brown, Monisha N.
Briones, Aurelio
Diana, James
Raskin, Lutgarde
author_sort Brown, Monisha N.
title Ammonia‐oxidizing archaea and nitrite‐oxidizing nitrospiras in the biofilter of a shrimp recirculating aquaculture system
title_short Ammonia‐oxidizing archaea and nitrite‐oxidizing nitrospiras in the biofilter of a shrimp recirculating aquaculture system
title_full Ammonia‐oxidizing archaea and nitrite‐oxidizing nitrospiras in the biofilter of a shrimp recirculating aquaculture system
title_fullStr Ammonia‐oxidizing archaea and nitrite‐oxidizing nitrospiras in the biofilter of a shrimp recirculating aquaculture system
title_full_unstemmed Ammonia‐oxidizing archaea and nitrite‐oxidizing nitrospiras in the biofilter of a shrimp recirculating aquaculture system
title_sort ammonia‐oxidizing archaea and nitrite‐oxidizing nitrospiras in the biofilter of a shrimp recirculating aquaculture system
publisher Elsevier
publishDate 2013
url http://hdl.handle.net/2027.42/95109
https://doi.org/10.1111/j.1574-6941.2012.01448.x
genre Arctic
genre_facet Arctic
op_relation Brown, Monisha N.; Briones, Aurelio; Diana, James; Raskin, Lutgarde (2013). "Ammonia‐oxidizing archaea and nitrite‐oxidizing nitrospiras in the biofilter of a shrimp recirculating aquaculture system." FEMS Microbiology Ecology 83(1): 17-25. <http://hdl.handle.net/2027.42/95109>
0168-6496
1574-6941
http://hdl.handle.net/2027.42/95109
22775980
doi:10.1111/j.1574-6941.2012.01448.x
FEMS Microbiology Ecology
Off S, Alawi M & Spieck E ( 2010 ) Enrichment and physiological characterization of a novel nitrospira‐like bacterium obtained from a marine sponge. Appl Environ Microbiol 76: 4640 – 4646.
Joye SB & Hollibaugh JT ( 1995 ) Influence of sulfide inhibition of nitrification on nitrogen regeneration in sediments. Science 270: 623 – 625.
Juretschko S, Timmermann G, Schmid M, Schleifer KH, Pommerening‐Roser A, Koops HP & Wagner M ( 1998 ) Combined molecular and conventional analyses of nitrifying bacterium diversity in activated sludge: Nitrosococcus mobilis and Nitrospira ‐like bacteria as dominant populations. Appl Environ Microbiol 64: 3042 – 3051.
Keuter S, Kruse M, Lipski A & Spieck E ( 2011 ) Relevance of Nitrospira for nitrite oxidation in a marine recirculation aquaculture system and physiological features of a Nitrospira marina‐like isolate. Environ Microbiol 13: 2536 – 2547.
Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB & Stahl DA ( 2005 ) Isolation of an autotrophic ammonia‐oxidizing marine archaeon. Nature 437: 543 – 546.
Koops HP & Pommerening‐Roser A ( 2001 ) Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species. FEMS Microbiol Ecol 37: 1 – 9.
Lane DJ ( 1991 ) 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics ( Stackebrandt E & Goodfellow M, eds), pp. 115 – 175. John Wiley & Sons, Chichester, UK.
Lebedeva EV, Off S, Zumbrägel S, Kruse M, Shagzhina A, Lücker S et al. ( 2011 ) Isolation and characterization of a moderately thermophilic nitrite‐oxidizing bacterium from a geothermal spring. FEMS Microbiol Ecol 75: 195 – 204.
Lin YC & Chen JC ( 2001 ) Acute toxicity of ammonia on Litopenaeus vannamei Boone juveniles at different salinity levels. J Exp Mar Biol Ecol 259: 109 – 119.
Lin YC & Chen JC ( 2003 ) Acute toxicity of nitrite on Litopenaeus vannamei (Boone) juveniles at different salinity levels. Aquaculture 224: 193 – 201.
Ling J & Chen SL ( 2005 ) Impact of organic carbon on nitrification performance of different biofilters. Aquacult Eng 33: 150 – 162.
Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, Hiom SJ & Wade WG ( 1998 ) Design and evaluation of useful bacterium‐specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64: 795 – 799.
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.
Masser MP, Rakocy J & Losordo TM ( 1999 ) Recirculating Aquaculture Tank Production Systems – Management Of Recirculating Systems. Southern Regional Aquaculture Center, Stoneville, MS.
Prosser JI & Nicol GW ( 2008 ) Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environ Microbiol 10: 2931 – 2941.
Purkhold U, Pommerening‐Roser A, Juretschko S, Schmid MC, Koops HP & 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.
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.
Rozen S & Skaletsky H ( 2000 ) Primer3 on the WWW for general users and for biologist programmers. Methods in Molecular Biology, Vol. 132 ( Misener S & Krawetz SA, eds), pp. 365 – 386. Humana Press Inc., Totowa, NJ.
Ruijter JM, Ramakers C, Hoogaars WMH, Karlen Y, Bakker O, van den Hoff MJB & Moorman AFM ( 2009 ) Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Res 37: 12.
Saitou N & Nei M ( 1987 ) The neighbor‐joining method – a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406 – 425.
Schramm A, de Beer D, van den Heuvel JC, Ottengraf S & Amann R ( 1999 ) Microscale distribution of populations and activities of Nitrosospira and Nitrospira spp. along a macroscale gradient in a nitrifying bioreactor: quantification by in situ hybridization and the use of microsensors. Appl Environ Microbiol 65: 3690 – 3696.
Tamura K, Nei M & Kumar S ( 2004 ) Prospects for inferring very large phylogenies by using the neighbor‐joining method. P Natl Acad Sci USA 101: 11030 – 11035.
Tamura K, Dudley J, Nei M & Kumar S ( 2007 ) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596 – 1599.
Watson SW, Bock E, Valois FW, Waterbury JB & Schlosser U ( 1986 ) Nitrospira marina gen. nov. sp. nov.: a chemolithotrophic nitrite‐oxidizing bacterium. Arch Microbiol 144: 1 – 7.
Whang LM, Chien IC, Yuan SL & Wu YJ ( 2009 ) Nitrifying community structures and nitrification performance of full‐scale municipal and swine wastewater treatment plants. Chemosphere 75: 234 – 242.
You J, Das A, Dolan EM & Hu ZQ ( 2009 ) Ammonia‐oxidizing archaea involved in nitrogen removal. Water Res 43: 1801 – 1809.
Alawi M, Lipski A, Sanders T, Eva Maria P & Spieck E ( 2007 ) Cultivation of a novel cold‐adapted nitrite oxidizing betaproteobacterium from the Siberian Arctic. ISME J 1: 256 – 264.
Bartosch S, Wolgast I, Spieck E & Bock E ( 1999 ) Identification of nitrite‐oxidizing bacteria with monoclonal antibodies recognizing the nitrite oxidoreductase. Appl Environ Microbiol 65: 4126 – 4133.
Bartosch S, Hartwig C, Spieck E & Bock E ( 2002 ) Immunological detection of Nitrospira ‐like bacteria in various soils. Microb Ecol 43: 26 – 33.
Brankatschk R, Bodenhausen N, Zeyer J & Buergmann H ( 2012 ) Simple absolute quantification method correcting for quantitative PCR efficiency variations for microbial community samples. Appl Environ Microbiol 78: 4481 – 4489.
Briones AM, Daugherty BJ, Angenent LT, Rausch KD, Tumbleson ME & Raskin L ( 2007 ) Microbial diversity and dynamics in multi‐ and single‐compartment anaerobic bioreactors processing sulfate‐rich waste streams. Environ Microbiol 9: 93 – 106.
Burrell P, Keller J & Blackall LL ( 1999 ) Characterisation of the bacterial consortium involved in nitrite oxidation in activated sludge. Water Sci Technol 39: 45 – 52.
Coolen MJL, Abbas B, van Bleijswijk J, Hopmans EC, Kuypers MMM, Wakeham SG & Damste JSS ( 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.
Daims H, Nielsen JL, Nielsen PH, Schleifer KH & Wagner M ( 2001 ) In situ characterization of Nitrospira ‐like nitrite oxidizing bacteria active in wastewater treatment plants. Appl Environ Microbiol 67: 5273 – 5284.
Daims H, Taylor MW & Wagner M ( 2006 ) Wastewater treatment: a model system for microbial ecology. Trends Biotechnol 24: 483 – 489.
DeSantis TZ, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R & Andersen GL ( 2006a ) NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34: W394 – W399.
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P & Andersen GL ( 2006b ) Greengenes, a chimera‐checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069 – 5072.
Ebeling JM ( 2000 ) Engineering aspects of recirculating aquaculture systems. Mar Technol Soc J 34: 68 – 78.
Ehrich S, Behrens D, Lebedeva E, Ludwig W & Bock E ( 1995 ) A new obligately chemolithoautotrophic, nitrite‐oxidizing bacterium, Nitrospira ‐moscoviensis sp‐nov and its phylogenetic relationship. Arch Microbiol 164: 16 – 23.
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.
Fast AW ( 1991 ) Marine shrimp pond growout conditions and strategies – a review and prognosis. Rev Aquat Sci 3: 357 – 399.
Fast AW & Lester LJ ( 1992 ) Marine Shrimp Culture: Principles and Practices. Elsevier, Amsterdam.
Felsenstein J ( 1985 ) Confidence‐limits on phylogenies – an approach using the bootstrap. Evolution 39: 783 – 791.
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spelling ftumdeepblue:oai:deepblue.lib.umich.edu:2027.42/95109 2023-08-20T04:03:12+02:00 Ammonia‐oxidizing archaea and nitrite‐oxidizing nitrospiras in the biofilter of a shrimp recirculating aquaculture system Brown, Monisha N. Briones, Aurelio Diana, James Raskin, Lutgarde 2013-01 application/pdf http://hdl.handle.net/2027.42/95109 https://doi.org/10.1111/j.1574-6941.2012.01448.x unknown Elsevier Wiley Periodicals, Inc. Brown, Monisha N.; Briones, Aurelio; Diana, James; Raskin, Lutgarde (2013). "Ammonia‐oxidizing archaea and nitrite‐oxidizing nitrospiras in the biofilter of a shrimp recirculating aquaculture system." FEMS Microbiology Ecology 83(1): 17-25. <http://hdl.handle.net/2027.42/95109> 0168-6496 1574-6941 http://hdl.handle.net/2027.42/95109 22775980 doi:10.1111/j.1574-6941.2012.01448.x FEMS Microbiology Ecology Off S, Alawi M & Spieck E ( 2010 ) Enrichment and physiological characterization of a novel nitrospira‐like bacterium obtained from a marine sponge. Appl Environ Microbiol 76: 4640 – 4646. Joye SB & Hollibaugh JT ( 1995 ) Influence of sulfide inhibition of nitrification on nitrogen regeneration in sediments. Science 270: 623 – 625. Juretschko S, Timmermann G, Schmid M, Schleifer KH, Pommerening‐Roser A, Koops HP & Wagner M ( 1998 ) Combined molecular and conventional analyses of nitrifying bacterium diversity in activated sludge: Nitrosococcus mobilis and Nitrospira ‐like bacteria as dominant populations. Appl Environ Microbiol 64: 3042 – 3051. Keuter S, Kruse M, Lipski A & Spieck E ( 2011 ) Relevance of Nitrospira for nitrite oxidation in a marine recirculation aquaculture system and physiological features of a Nitrospira marina‐like isolate. Environ Microbiol 13: 2536 – 2547. Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB & Stahl DA ( 2005 ) Isolation of an autotrophic ammonia‐oxidizing marine archaeon. Nature 437: 543 – 546. Koops HP & Pommerening‐Roser A ( 2001 ) Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species. FEMS Microbiol Ecol 37: 1 – 9. Lane DJ ( 1991 ) 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics ( Stackebrandt E & Goodfellow M, eds), pp. 115 – 175. John Wiley & Sons, Chichester, UK. Lebedeva EV, Off S, Zumbrägel S, Kruse M, Shagzhina A, Lücker S et al. ( 2011 ) Isolation and characterization of a moderately thermophilic nitrite‐oxidizing bacterium from a geothermal spring. FEMS Microbiol Ecol 75: 195 – 204. Lin YC & Chen JC ( 2001 ) Acute toxicity of ammonia on Litopenaeus vannamei Boone juveniles at different salinity levels. J Exp Mar Biol Ecol 259: 109 – 119. Lin YC & Chen JC ( 2003 ) Acute toxicity of nitrite on Litopenaeus vannamei (Boone) juveniles at different salinity levels. Aquaculture 224: 193 – 201. Ling J & Chen SL ( 2005 ) Impact of organic carbon on nitrification performance of different biofilters. Aquacult Eng 33: 150 – 162. Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, Hiom SJ & Wade WG ( 1998 ) Design and evaluation of useful bacterium‐specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64: 795 – 799. 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. Masser MP, Rakocy J & Losordo TM ( 1999 ) Recirculating Aquaculture Tank Production Systems – Management Of Recirculating Systems. Southern Regional Aquaculture Center, Stoneville, MS. Prosser JI & Nicol GW ( 2008 ) Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environ Microbiol 10: 2931 – 2941. Purkhold U, Pommerening‐Roser A, Juretschko S, Schmid MC, Koops HP & 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. 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. Rozen S & Skaletsky H ( 2000 ) Primer3 on the WWW for general users and for biologist programmers. Methods in Molecular Biology, Vol. 132 ( Misener S & Krawetz SA, eds), pp. 365 – 386. Humana Press Inc., Totowa, NJ. Ruijter JM, Ramakers C, Hoogaars WMH, Karlen Y, Bakker O, van den Hoff MJB & Moorman AFM ( 2009 ) Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Res 37: 12. Saitou N & Nei M ( 1987 ) The neighbor‐joining method – a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406 – 425. Schramm A, de Beer D, van den Heuvel JC, Ottengraf S & Amann R ( 1999 ) Microscale distribution of populations and activities of Nitrosospira and Nitrospira spp. along a macroscale gradient in a nitrifying bioreactor: quantification by in situ hybridization and the use of microsensors. Appl Environ Microbiol 65: 3690 – 3696. Tamura K, Nei M & Kumar S ( 2004 ) Prospects for inferring very large phylogenies by using the neighbor‐joining method. P Natl Acad Sci USA 101: 11030 – 11035. Tamura K, Dudley J, Nei M & Kumar S ( 2007 ) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596 – 1599. Watson SW, Bock E, Valois FW, Waterbury JB & Schlosser U ( 1986 ) Nitrospira marina gen. nov. sp. nov.: a chemolithotrophic nitrite‐oxidizing bacterium. Arch Microbiol 144: 1 – 7. Whang LM, Chien IC, Yuan SL & Wu YJ ( 2009 ) Nitrifying community structures and nitrification performance of full‐scale municipal and swine wastewater treatment plants. Chemosphere 75: 234 – 242. You J, Das A, Dolan EM & Hu ZQ ( 2009 ) Ammonia‐oxidizing archaea involved in nitrogen removal. Water Res 43: 1801 – 1809. Alawi M, Lipski A, Sanders T, Eva Maria P & Spieck E ( 2007 ) Cultivation of a novel cold‐adapted nitrite oxidizing betaproteobacterium from the Siberian Arctic. ISME J 1: 256 – 264. Bartosch S, Wolgast I, Spieck E & Bock E ( 1999 ) Identification of nitrite‐oxidizing bacteria with monoclonal antibodies recognizing the nitrite oxidoreductase. Appl Environ Microbiol 65: 4126 – 4133. Bartosch S, Hartwig C, Spieck E & Bock E ( 2002 ) Immunological detection of Nitrospira ‐like bacteria in various soils. Microb Ecol 43: 26 – 33. Brankatschk R, Bodenhausen N, Zeyer J & Buergmann H ( 2012 ) Simple absolute quantification method correcting for quantitative PCR efficiency variations for microbial community samples. Appl Environ Microbiol 78: 4481 – 4489. Briones AM, Daugherty BJ, Angenent LT, Rausch KD, Tumbleson ME & Raskin L ( 2007 ) Microbial diversity and dynamics in multi‐ and single‐compartment anaerobic bioreactors processing sulfate‐rich waste streams. Environ Microbiol 9: 93 – 106. Burrell P, Keller J & Blackall LL ( 1999 ) Characterisation of the bacterial consortium involved in nitrite oxidation in activated sludge. Water Sci Technol 39: 45 – 52. Coolen MJL, Abbas B, van Bleijswijk J, Hopmans EC, Kuypers MMM, Wakeham SG & Damste JSS ( 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. Daims H, Nielsen JL, Nielsen PH, Schleifer KH & Wagner M ( 2001 ) In situ characterization of Nitrospira ‐like nitrite oxidizing bacteria active in wastewater treatment plants. Appl Environ Microbiol 67: 5273 – 5284. Daims H, Taylor MW & Wagner M ( 2006 ) Wastewater treatment: a model system for microbial ecology. Trends Biotechnol 24: 483 – 489. DeSantis TZ, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R & Andersen GL ( 2006a ) NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34: W394 – W399. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P & Andersen GL ( 2006b ) Greengenes, a chimera‐checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069 – 5072. Ebeling JM ( 2000 ) Engineering aspects of recirculating aquaculture systems. Mar Technol Soc J 34: 68 – 78. Ehrich S, Behrens D, Lebedeva E, Ludwig W & Bock E ( 1995 ) A new obligately chemolithoautotrophic, nitrite‐oxidizing bacterium, Nitrospira ‐moscoviensis sp‐nov and its phylogenetic relationship. Arch Microbiol 164: 16 – 23. 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. Fast AW ( 1991 ) Marine shrimp pond growout conditions and strategies – a review and prognosis. Rev Aquat Sci 3: 357 – 399. Fast AW & Lester LJ ( 1992 ) Marine Shrimp Culture: Principles and Practices. Elsevier, Amsterdam. Felsenstein J ( 1985 ) Confidence‐limits on phylogenies – an approach using the bootstrap. Evolution 39: 783 – 791. IndexNoFollow Shrimp Aquaculture Recirculating Aquaculture System Ammonia Oxidation Nitrite Oxidation N Itrospira N Itrosopumilus Maritimus Microbiology and Immunology Ecology and Evolutionary Biology Science Health Sciences Article 2013 ftumdeepblue https://doi.org/10.1111/j.1574-6941.2012.01448.x 2023-07-31T20:31:13Z This study analysed the nitrifier community in the biofilter of a zero discharge, recirculating aquaculture system ( RAS ) for the production of marine shrimp in a low density (low ammonium production) system. The ammonia‐oxidizing populations were examined by targeting 16 S rRNA and amoA genes of ammonia‐oxidizing bacteria ( AOB ) and archaea ( AOA ). The nitrite‐oxidizing bacteria ( NOB ) were investigated by targeting the 16 S rRNA gene. Archaeal amoA genes were more abundant in all compartments of the RAS than bacterial amoA genes. Analysis of bacterial and archaeal amoA gene sequences revealed that most ammonia oxidizers were related to N itrosomonas marina and N itrosopumilus maritimus . The NOB detected were related to N itrospira marina and N itrospira moscoviensis, and Nitrospira marina ‐type NOB were more abundant than N . moscoviensis ‐type NOB . Water quality and biofilm attachment media played a role in the competitiveness of AOA over AOB and Nitrospira marina‐ over N . moscoviensis‐ type NOB . Peer Reviewed http://deepblue.lib.umich.edu/bitstream/2027.42/95109/1/fem1448.pdf Article in Journal/Newspaper Arctic University of Michigan: Deep Blue FEMS Microbiology Ecology 83 1 17 25

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