Comparative Analysis of 16S rRNA andamoAGenes from Archaea Selected with Organic and Inorganic Amendments in Enrichment Culture

Abstract

<jats:title>ABSTRACT</jats:title><jats:p>We took advantage of a plant-root enrichment culture system to characterize mesophilic soil archaea selected through the use of organic and inorganic amendments. Comparative analysis of 16S rRNA and<jats:italic>amoA</jats:italic>genes indicated that specific archaeal clades were selected under different conditions. Three<jats:italic>amoA</jats:italic>sequence clades were identified, while for a fourth group, identified by 16S rRNA gene analysis alone and referred to as the “root” clade, we detected no corresponding<jats:italic>amoA</jats:italic>gene. The<jats:italic>amoA-</jats:italic>containing archaea were present in media with either organic or inorganic amendments, whereas archaea representing the root clade were present only when organic amendment was used. Analysis of<jats:italic>amoA</jats:italic>gene abundance and expression, together with nitrification-coupled growth assays, indicated potential growth by autotrophic ammonia oxidation for members of two group 1.1b clades. Increased abundance of one of these clades, however, also occurred upon the addition of organic amendment. Finally, although<jats:italic>amoA</jats:italic>-containing group 1.1a archaea were present in enrichments, we detected neither expression of<jats:italic>amoA</jats:italic>genes nor evidence for nitrification-coupled growth of these organisms. These data support a model of a diverse metabolic community in mesophilic soil archaea that is just beginning to be characterized.</jats:p>

Diversity, Physiology, and Niche Differentiation of Ammonia-Oxidizing Archaea

“…Very recently, SIP experiments demonstrated the incorporation of 13 C from labeled rice callus into the DNA of both AOA and AOB (142). While potential cross-feeding-via respiration of labeled substrates by other microbes and subsequent fixation of exhaled 13 CO 2 -cannot be ruled out completely, the results of this study correspond to those of other reports of root-colonizing group I.1b thaumarchaeotes (121,122,146).…”

Ecophysiological Characterization of Ammonia-Oxidizing Archaea and Bacteria from Freshwater

“…In nature, however, conditions are often less defined with respect to energy-generating processes. It has been suggested that not all Thaumarchaeota are chemolithoautotrophic ammonia oxidizers; some carry the amoA gene but are not actively oxidizing NH 4 ϩ , and others utilize mixotrophic or heterotrophic lifestyles in pure and enrichment cultures (39,56,65). On the basis of these observations and our data, one could speculate that AOA in natural samples utilize a mixotrophic and/or heterotrophic lifestyle rather than a completely autotrophic lifestyle, which could explain their success in nature compared to that in the laboratory.…”

Filogenia molecular e cultivo de Archaea de solos de Cerrado sensu strictoc

“…Desta forma, a identificação de muitas sequências posicionadas neste grupo poderia estar relacionada ao pH mais ácido encontrado nos solos de Cerrado (Haridasan, 1994;Moreira, 2000;Araújo et al, 2012) O grupo I.1b de Thaumarchaetota foi identificado como sendo o grupo dominante de archaeas em diversos tipos de solos (Brintim et al, 1997;Auguet et al, 2010;Bates et al, 2011). Até o momento, são poucos os relatos que descrevem o cultivo de enriquecimento de organismos deste grupo (Simon et al, 2005;Kim et al, 2012, Xu et al, 2012) e a espécie Nitrososphaera viennensis, isolada de amostras de solo de um jardim em Viena, é a única a ter sido obtida na forma de culturas puras (Stieglmeier et al, 2014). Outra archaea deste grupo, a qual encontra-se melhor descrita, é Candidatus Nitrososphaera gargensis que, apesar de ainda não ter sido obtida na forma de cultura pura, já teve seu genoma completamente sequenciado após uma cultura de enriquecimento obtida a partir de amostras de uma fonte termal terrestre (Hatzenpichler et al, 2008).…”

“…Do ponto de vista ecológico, o filo Thaumarchaeota inclui organismos conhecidos por apresentarem o metabolismo nitrificante, podendo ter importante papel no ciclo do nitrogênio em diversos ambientes Kim et al, 2012;Xu et al, 2012). Dados obtidos após o sequenciamento do genoma completo de Candidatus Nitrososphaera gargensis e Candidatus Nitrososphaera evergladensis (Zhalnina et al, 2014) e a obtenção e caracterização de Nitrososphaera viennensis em cultura pura (Tourna et al, 2011;Stieglmeier et al, 2014), permitiram elucidar alguns aspectos do metabolismo de oxidação de amônia nos organismos do grupo I.1b, revelando que estes organismos provavelmente apresentam importante papel ecológico no ciclo do nitrogênio em solos.…”

“…Tal fato mostra-se bastante curioso, tendo em vista que dentre as poucas archaeas mesófilas de solo não anaeróbias cultivadas até o momento, todas foram cultivadas com sucesso em meios líquidos (Simon et al, 2005;Kim et al, 2012;Xu et al, 2012;Stieglmeier et al, 2014;Zhalnina et al, 2014 …”