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Article: Dominance of Candidatus Scalindua species in anammox community revealed in soils with different duration of rice paddy cultivation in Northeast China
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TitleDominance of Candidatus Scalindua species in anammox community revealed in soils with different duration of rice paddy cultivation in Northeast China
 
AuthorsWang, J1
Gu, JD1
 
Keywords16S rRNA gene
Anammox bacteria
Hydrazine oxidoreductase gene
Rice paddy soil
 
Issue Date2013
 
PublisherSpringer. The Journal's web site is located at http://link.springer.de/link/service/journals/00253/index.htm
 
CitationApplied Microbiology And Biotechnology, 2013, v. 97 n. 4, p. 1785-1798 [How to Cite?]
DOI: http://dx.doi.org/10.1007/s00253-012-4036-x
 
AbstractThe anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the oxygen-limited zone for nitrogen cycling, but their roles in agricultural ecosystems are still poorly understood. In this study, soil samples were taken from the rhizosphere and non-rhizosphere and from surface (0-5 cm) and subsurface (20-25 cm) layers with 1, 4, and 9 years of rice cultivation history on the typical albic soil of Northeast China to examine the diversity and distribution of anammox bacteria based on 16S rRNA gene and hydrazine oxidoreductase encoding gene (hzo). By comparing these soil samples, no obvious difference was observed in community composition between the rhizosphere and non-rhizosphere or the surface and subsurface layers. Surprisingly, anammox bacterial communities of these rice paddy soils were consisted of mainly Candidatus Scalindua species, which are best known to be dominant in marine and pristine environments. The highest diversity was revealed in the 4-year paddy soil based on clone library analysis. Phylogenetic analysis of 16S rRNA gene and deduced HZO from the corresponding encoding gene showed that most of the obtained clones are grouped together with Candidatus Scalindua sorokinii, Candidatus Scalindua brodae, and Candidatus Scalindua spp. of seawater. The obtained clone sequences from all samples are distributed in two subclusters that contain sequences from environmental samples only. Tentative new species were also discovered in this paddy soil. This study provides the first evidence on the existence of anammox bacteria with limited diversity in agricultural ecosystems in Northern China. © 2012 The Author(s).
 
ISSN0175-7598
2012 Impact Factor: 3.689
2012 SCImago Journal Rankings: 1.307
 
DOIhttp://dx.doi.org/10.1007/s00253-012-4036-x
 
ReferencesAmano T, Yoshinaga I, Okada K, Yamagishi T, Ueda S, Obuchi A, Sakoand Y, Suwa Y (2007) Detection of anammox activity and diversity of anammox bacteria-related 16S rRNA genes in coastal marine sediment in Japan. Microbes Environ 22:232–242. doi: 10.1264/jsme2.22.232

Bothe H, Jost G, Schloter M, Ward B, Witzel KP (2000) Molecular analysis of ammonia oxidation and denitrification in natural environments. FEMS Microbiol Ecol 24:673–690

Cao H, Hong Y, Li M, Gu J-D (2011a) Diversity and abundance of ammonia-oxidizing prokaryotes in sediments from the coastal Pearl River Estuary to the South China Sea. Anton Leeuw Int J G 100:545–556. doi: 10.1007/s10482-011-9610-1

Cao H, Hong Y, Li M, Gu J-D (2011b) Phylogenetic diversity and ecological pattern of ammonia-oxidizing archaea in the surface sediments of the Western Pacific. Microb Ecol 62:813–823. doi: 10.1007/s00248-011-9901-0

Cao H, Li M, Dang H, Gu J-D (2011c) Responses of aerobic and anaerobic ammonia/ammonium-oxidizing microorganisms to anthropogenic pollution in coastal marine environments. Method Enzymol 496:35–62. doi: 10.1016/B978-0-12-386489-5.00002-6

Cao H, Li M, Hong Y, Gu J-D (2011d) Diversity and abundance of ammonia-oxidizing archaea and bacteria in polluted mangrove sediment. Syst Appl Microbiol 34:513–523. doi: 10.1016/j.syapm.2010.11.023


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Jetten MSM, Sliekers O, Kuypers M, Dalsgaard T, van Niftrik L, Cirpus I, van de Pas-Schoonen K, Lavik G, Thamdrup B, Le Paslier D, Op den Camp HJM, Hulth S, Nielsen LP, Abma W, Third K, Engström P, Kuenen JG, Jorgensen BB, Canfield DE, Damsté JSS, Revsbech NP, Fuerst J, Weissenbach J, Wagner M, Schmidt I, Schmid M, Strous M (2003) Anaerobic ammonium oxidation by marine and freshwater planctomycete-like bacteria. Appl Microbiol Biotechnol 63:107–114. doi: 10.1007/s00253-003-1422-4

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Konneke 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. doi: 10.1038/nature03911

Koop-Jakobsen K, Giblin A (2009) Anammox in tidal marsh sediments: The role of salinity, nitrogen loading, and marsh vegetation. Estuar Coasts 32:238–245. doi: 10.1007/s12237-008-9131-y

Kumar S, Dudley J, Nei M, Tamura K (2008) MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9:299–306. doi: 10.1093/bib/bbn017


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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. doi: 10.1073/pnas.0611081104

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Li H, Chen S, Mu BZ, Gu J-D (2010a) Molecular detection of anaerobic ammonium-oxidizing (anammox) bacteria in high-temperature petroleum reservoirs. Microb Ecol 60:771–783. doi: 10.1007/s00248-010-9733-3

Li M, Hong Y, Klotz MG, Gu J-D (2010b) A comparison of primer sets for detecting 16S rRNA and hydrazine oxidoreductase genes of anaerobic ammonium-oxidizing bacteria in marine sediments. Appl Microbiol Biotechnol 86:781–790. doi: 10.1007/s00253-009-2361-5

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Li M, Cao H, Hong Y, Gu J-D (2011d) Spatial distribution and abundances of ammonia-oxidizing archaea (AOA) and ammonia–oxidizing bacteria (AOB) in mangrove sediments. Appl Microbiol Biotechnol 89:1243–1254. doi: 10.1007/s00253-010-2929-0

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DC FieldValue
dc.contributor.authorWang, J
 
dc.contributor.authorGu, JD
 
dc.date.accessioned2012-05-28T08:19:23Z
 
dc.date.available2012-05-28T08:19:23Z
 
dc.date.issued2013
 
dc.description.abstractThe anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the oxygen-limited zone for nitrogen cycling, but their roles in agricultural ecosystems are still poorly understood. In this study, soil samples were taken from the rhizosphere and non-rhizosphere and from surface (0-5 cm) and subsurface (20-25 cm) layers with 1, 4, and 9 years of rice cultivation history on the typical albic soil of Northeast China to examine the diversity and distribution of anammox bacteria based on 16S rRNA gene and hydrazine oxidoreductase encoding gene (hzo). By comparing these soil samples, no obvious difference was observed in community composition between the rhizosphere and non-rhizosphere or the surface and subsurface layers. Surprisingly, anammox bacterial communities of these rice paddy soils were consisted of mainly Candidatus Scalindua species, which are best known to be dominant in marine and pristine environments. The highest diversity was revealed in the 4-year paddy soil based on clone library analysis. Phylogenetic analysis of 16S rRNA gene and deduced HZO from the corresponding encoding gene showed that most of the obtained clones are grouped together with Candidatus Scalindua sorokinii, Candidatus Scalindua brodae, and Candidatus Scalindua spp. of seawater. The obtained clone sequences from all samples are distributed in two subclusters that contain sequences from environmental samples only. Tentative new species were also discovered in this paddy soil. This study provides the first evidence on the existence of anammox bacteria with limited diversity in agricultural ecosystems in Northern China. © 2012 The Author(s).
 
dc.description.naturepublished_or_final_version
 
dc.description.otherSpringer Open Choice, 28 May 2012
 
dc.identifier.citationApplied Microbiology And Biotechnology, 2013, v. 97 n. 4, p. 1785-1798 [How to Cite?]
DOI: http://dx.doi.org/10.1007/s00253-012-4036-x
 
dc.identifier.citeulike10639525
 
dc.identifier.doihttp://dx.doi.org/10.1007/s00253-012-4036-x
 
dc.identifier.eissn1432-0614
 
dc.identifier.epage1798
 
dc.identifier.hkuros224973
 
dc.identifier.issn0175-7598
2012 Impact Factor: 3.689
2012 SCImago Journal Rankings: 1.307
 
dc.identifier.openurl
 
dc.identifier.scopuseid_2-s2.0-84874354885
 
dc.identifier.spage1785
 
dc.identifier.urihttp://hdl.handle.net/10722/147125
 
dc.languageEng
 
dc.publisherSpringer. The Journal's web site is located at http://link.springer.de/link/service/journals/00253/index.htm
 
dc.publisher.placeGermany
 
dc.relation.ispartofApplied Microbiology and Biotechnology
 
dc.relation.referencesAmano T, Yoshinaga I, Okada K, Yamagishi T, Ueda S, Obuchi A, Sakoand Y, Suwa Y (2007) Detection of anammox activity and diversity of anammox bacteria-related 16S rRNA genes in coastal marine sediment in Japan. Microbes Environ 22:232–242. doi: 10.1264/jsme2.22.232
 
dc.relation.referencesBothe H, Jost G, Schloter M, Ward B, Witzel KP (2000) Molecular analysis of ammonia oxidation and denitrification in natural environments. FEMS Microbiol Ecol 24:673–690
 
dc.relation.referencesCao H, Hong Y, Li M, Gu J-D (2011a) Diversity and abundance of ammonia-oxidizing prokaryotes in sediments from the coastal Pearl River Estuary to the South China Sea. Anton Leeuw Int J G 100:545–556. doi: 10.1007/s10482-011-9610-1
 
dc.relation.referencesCao H, Hong Y, Li M, Gu J-D (2011b) Phylogenetic diversity and ecological pattern of ammonia-oxidizing archaea in the surface sediments of the Western Pacific. Microb Ecol 62:813–823. doi: 10.1007/s00248-011-9901-0
 
dc.relation.referencesCao H, Li M, Dang H, Gu J-D (2011c) Responses of aerobic and anaerobic ammonia/ammonium-oxidizing microorganisms to anthropogenic pollution in coastal marine environments. Method Enzymol 496:35–62. doi: 10.1016/B978-0-12-386489-5.00002-6
 
dc.relation.referencesCao H, Li M, Hong Y, Gu J-D (2011d) Diversity and abundance of ammonia-oxidizing archaea and bacteria in polluted mangrove sediment. Syst Appl Microbiol 34:513–523. doi: 10.1016/j.syapm.2010.11.023
 
dc.relation.referencesJetten MSM (2008) The microbial nitrogen cycle. Environ Microbiol 10:2903–2909. doi: 10.1111/j.1462-2920.2008.01786.x
 
dc.relation.referencesJetten MSM, de Bruijn P, Kuenen JG (1997) Hydroxylamine metabolism in Pseudomonas PB16: involvement of a novel hydroxylamine oxidoreductase. Antonie Van Leeuwenhoek 71:69–74. doi: 10.1023/A:1000145617904
 
dc.relation.referencesJetten MSM, Sliekers O, Kuypers M, Dalsgaard T, van Niftrik L, Cirpus I, van de Pas-Schoonen K, Lavik G, Thamdrup B, Le Paslier D, Op den Camp HJM, Hulth S, Nielsen LP, Abma W, Third K, Engström P, Kuenen JG, Jorgensen BB, Canfield DE, Damsté JSS, Revsbech NP, Fuerst J, Weissenbach J, Wagner M, Schmidt I, Schmid M, Strous M (2003) Anaerobic ammonium oxidation by marine and freshwater planctomycete-like bacteria. Appl Microbiol Biotechnol 63:107–114. doi: 10.1007/s00253-003-1422-4
 
dc.relation.referencesJetten MSM, van Niftrik L, Strous M, Kartal B, Keltjens JT, Op den Camp HJ (2009) Biochemistry and molecular biology of anammox bacteria. Crit Rev Biochem Mol Biol 44:65–84
 
dc.relation.referencesKartal B, Geerts W, Jetten MS (2011) Cultivation, detection, and ecophysiology of anaerobic ammonium-oxidizing bacteria. Methods Enzymol 486:89–108. doi: 10.1016/B978-0-12-381294-0.00004-3
 
dc.relation.referencesLi M, Gu J-D (2011) Advances in methods for detection of anaerobic ammonium oxidizing (anammox) bacteria. Appl Microbiol Biotechnol 90:1241–1252
 
dc.relation.referencesKlotz MG, Stein LY (2008) Nitrifier genomics and evolution of the nitrogen cycle. FEMS Microbiol Lett 278:146–156. doi: 10.1111/j.1574-6968.2007.00970.x
 
dc.relation.referencesKlotz MG, Schmid MC, Strous M, Op den Camp HJ, Jetten MS, Hooper AB (2008) Evolution of an octahaem cytochrome c protein family that is key to aerobic and anaerobic ammonia oxidation by bacteria. Environ Microbiol 10:3150–3163. doi: 10.1111/j.1462-2920.2008.01733.x
 
dc.relation.referencesKonneke 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. doi: 10.1038/nature03911
 
dc.relation.referencesKoop-Jakobsen K, Giblin A (2009) Anammox in tidal marsh sediments: The role of salinity, nitrogen loading, and marsh vegetation. Estuar Coasts 32:238–245. doi: 10.1007/s12237-008-9131-y
 
dc.relation.referencesKumar S, Dudley J, Nei M, Tamura K (2008) MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9:299–306. doi: 10.1093/bib/bbn017
 
dc.relation.referencesKuypers MM, Lavik G, Woebken D, Schmid M, Fuchs BM, Amann R, Jorgensen BB, Jetten MS (2005) Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation. Proc Natl Acad Sci USA 102:6478–6483. doi: 10.1073/pnas.0502088102
 
dc.relation.referencesLam 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. doi: 10.1073/pnas.0611081104
 
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dc.rightsThe Author(s)
 
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License
 
dc.subject16S rRNA gene
 
dc.subjectAnammox bacteria
 
dc.subjectHydrazine oxidoreductase gene
 
dc.subjectRice paddy soil
 
dc.titleDominance of Candidatus Scalindua species in anammox community revealed in soils with different duration of rice paddy cultivation in Northeast China
 
dc.typeArticle
 
<?xml encoding="utf-8" version="1.0"?>
<item><contributor.author>Wang, J</contributor.author>
<contributor.author>Gu, JD</contributor.author>
<date.accessioned>2012-05-28T08:19:23Z</date.accessioned>
<date.available>2012-05-28T08:19:23Z</date.available>
<date.issued>2013</date.issued>
<identifier.citation>Applied Microbiology And Biotechnology, 2013, v. 97 n. 4, p. 1785-1798</identifier.citation>
<identifier.issn>0175-7598</identifier.issn>
<identifier.uri>http://hdl.handle.net/10722/147125</identifier.uri>
<description.abstract>The anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the oxygen-limited zone for nitrogen cycling, but their roles in agricultural ecosystems are still poorly understood. In this study, soil samples were taken from the rhizosphere and non-rhizosphere and from surface (0-5&#160;cm) and subsurface (20-25&#160;cm) layers with 1, 4, and 9&#160;years of rice cultivation history on the typical albic soil of Northeast China to examine the diversity and distribution of anammox bacteria based on 16S rRNA gene and hydrazine oxidoreductase encoding gene (hzo). By comparing these soil samples, no obvious difference was observed in community composition between the rhizosphere and non-rhizosphere or the surface and subsurface layers. Surprisingly, anammox bacterial communities of these rice paddy soils were consisted of mainly Candidatus Scalindua species, which are best known to be dominant in marine and pristine environments. The highest diversity was revealed in the 4-year paddy soil based on clone library analysis. Phylogenetic analysis of 16S rRNA gene and deduced HZO from the corresponding encoding gene showed that most of the obtained clones are grouped together with Candidatus Scalindua sorokinii, Candidatus Scalindua brodae, and Candidatus Scalindua spp. of seawater. The obtained clone sequences from all samples are distributed in two subclusters that contain sequences from environmental samples only. Tentative new species were also discovered in this paddy soil. This study provides the first evidence on the existence of anammox bacteria with limited diversity in agricultural ecosystems in Northern China. &#169; 2012 The Author(s).</description.abstract>
<language>Eng</language>
<publisher>Springer. The Journal&apos;s web site is located at http://link.springer.de/link/service/journals/00253/index.htm</publisher>
<relation.ispartof>Applied Microbiology and Biotechnology</relation.ispartof>
<rights>The Author(s)</rights>
<rights>Creative Commons: Attribution 3.0 Hong Kong License</rights>
<subject>16S rRNA gene</subject>
<subject>Anammox bacteria</subject>
<subject>Hydrazine oxidoreductase gene</subject>
<subject>Rice paddy soil</subject>
<title>Dominance of Candidatus Scalindua species in anammox community revealed in soils with different duration of rice paddy cultivation in Northeast China</title>
<type>Article</type>
<identifier.openurl>http://www.springerlink.com/link-out/?id=2104&amp;code=P0897G11P8L691V5&amp;MUD=MP</identifier.openurl>
<description.nature>published_or_final_version</description.nature>
<identifier.doi>10.1007/s00253-012-4036-x</identifier.doi>
<identifier.scopus>eid_2-s2.0-84874354885</identifier.scopus>
<identifier.hkuros>224973</identifier.hkuros>
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<identifier.spage>1785</identifier.spage>
<identifier.epage>1798</identifier.epage>
<identifier.eissn>1432-0614</identifier.eissn>
<publisher.place>Germany</publisher.place>
<description.other>Springer Open Choice, 28 May 2012</description.other>
<identifier.citeulike>10639525</identifier.citeulike>
<bitstream.url>http://hub.hku.hk/bitstream/10722/147125/1/fulltext.pdf</bitstream.url>
</item>
Author Affiliations
  1. The University of Hong Kong