Archaeal Diversity and the Prevalence of
            <i>Crenarchaeota</i>
            in Salt Marsh Sediments

Nelson, Katelyn A.; Moin, Nicole S.; Bernhard, Anne E.

doi:10.1128/aem.00201-09

Cited by 35 publications

(28 citation statements)

References 19 publications

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“…The high abundance of ammonia-oxidizing archaea (∼50%) within the archaea in this soil, as visualized by fluorescence microscopy, also was confirmed by qPCR of amoA and 16S rRNA genes. Because ammonia-oxidizing archaea such as Nitrosopumilus maritimus are thought to harbor only one copy of the 16S rRNA gene and only one copy of the amoA gene, the gene copy numbers derived by qPCR should be equivalent to cell numbers (34,35). We also analyzed the archaeal 16S rRNA transcripts from light and heavy fractions of RNA-SIP and observed a close relation to Nitrososphaera gargensis.…”

Section: Discussionmentioning

confidence: 94%

Ammonia oxidation coupled to CO ₂ fixation by archaea and bacteria in an agricultural soil

Pratscher

Dumont

Conrad

2011

Proc. Natl. Acad. Sci. U.S.A.

212

132

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Ammonia oxidation is an essential part of the global nitrogen cycling and was long thought to be driven only by bacteria. Recent findings expanded this pathway also to the archaea. However, most questions concerning the metabolism of ammonia-oxidizing archaea, such as ammonia oxidation and potential CO 2 fixation, remain open, especially for terrestrial environments. Here, we investigated the activity of ammonia-oxidizing archaea and bacteria in an agricultural soil by comparison of RNA-and DNA-stable isotope probing (SIP). RNA-SIP demonstrated a highly dynamic and diverse community involved in CO 2 fixation and carbon assimilation coupled to ammonia oxidation. DNA-SIP showed growth of the ammonia-oxidizing bacteria but not of archaea. Furthermore, the analysis of labeled RNA found transcripts of the archaeal acetyl-CoA/propionyl-CoA carboxylase (accA/pccB) to be expressed and labeled. These findings strongly suggest that ammoniaoxidizing archaeal groups in soil autotrophically fix CO 2 using the 3-hydroxypropionate-4-hydroxybutyrate cycle, one of the two pathways recently identified for CO 2 fixation in Crenarchaeota. Catalyzed reporter deposition (CARD)-FISH targeting the gene encoding subunit A of ammonia monooxygenase (amoA) mRNA and 16S rRNA of archaea also revealed ammonia-oxidizing archaea to be numerically relevant among the archaea in this soil. Our results demonstrate a diverse and dynamic contribution of ammonia-oxidizing archaea in soil to nitrification and CO 2 assimilation and that their importance to the overall archaeal community might be larger than previously thought.

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Section: Discussionmentioning

confidence: 94%

Ammonia oxidation coupled to CO ₂ fixation by archaea and bacteria in an agricultural soil

Pratscher

Dumont

Conrad

2011

Proc. Natl. Acad. Sci. U.S.A.

212

132

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“…In contrast, Mosier and Francis, (2008) found that copies of b-proteobacterial amoA were two orders of magnitude higher than archaeal amoA in high-salinity estuarine sediments. In salt marshes specifically, a report from southeastern Connecticut found a high abundance of 16S rRNA genes related to the ammonia-oxidizing 'Candidatus Nitrosopumilus maritimus' isolate (Nelson et al, 2009). Thus, although the study here focuses solely on AOB, further study on AOA is needed to expand the picture of the salt marsh nitrifying community.…”

Section: Introductionmentioning

confidence: 90%

Nitrogen and phosphorus enrichment alter the composition of ammonia-oxidizing bacteria in salt marsh sediments

et al. 2010

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Ammonia oxidation is a central process in the nitrogen cycle. Particularly in marine and estuarine environments, few experiments have been conducted to tease apart the factors influencing their abundance and composition. To investigate the effect of nitrogen and phosphorus availability on ammonia-oxidizing bacteria (AOB), we conducted a nutrient enrichment experiment in a Maine salt marsh and sampled sediment communities in three seasons over 2 years. We assessed community composition using terminal restriction fragment length polymorphism analysis and sequencing of cloned fragments of the ammonia monooxygenase (amoA) gene. Almost all of the amoA sequences fell within the marine and estuarine-specific Nitrosospira-like clade. Applied separately, nitrogen and phosphorus significantly altered AOB composition; however, together the nutrients had an interactive effect, and composition did not change. In contrast, nutrient enrichment did not alter AOB abundance. Furthermore, the response of AOB composition to nutrient enrichment varied over time. We conclude that closely related taxa within the marine/estuarine-specific Nitrosospira-like clade vary in their preference for nutrient concentrations, and this preference may depend on other temporally variable abiotic factors. Finally, AOB composition was highly variable within and across years even in untreated plots. Further studies are needed to test how these different aspects of compositional variability in AOB communities influence nitrogen cycling.

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“…Overall, these results provide strong evidence for niche partitioning among the AOA in the water column and brine pools of the Red Sea. Moreover, a large number of environmental sequences that cluster with the Nitrosopumilus cluster were retrieved from habitats with a broad salinity range (5-33% (w/v)), or replete with ammonium (0.1-2 mM) and sulfate (0.1-701 mM; Yakimov et al, 2007;Nelson et al, 2009;Swan et al, 2010;Park et al, 2010;La Cono et al, 2011), which implies a broader halotolerance and greater tolerance for ammonium in some species of this genus.…”

Section: G I 1 a -A S S O C Ia T E D M G I 1 B E U R Y A R C H A mentioning

confidence: 99%

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

et al. 2014

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The bottom of the Red Sea harbors over 25 deep hypersaline anoxic basins that are geochemically distinct and characterized by vertical gradients of extreme physicochemical conditions. Because of strong changes in density, particulate and microbial debris get entrapped in the brine-seawater interface (BSI), resulting in increased dissolved organic carbon, reduced dissolved oxygen toward the brines and enhanced microbial activities in the BSI. These features coupled with the deep-sea prevalence of ammonia-oxidizing archaea (AOA) in the global ocean make the BSI a suitable environment for studying the osmotic adaptations and ecology of these important players in the marine nitrogen cycle. Using phylogenomic-based approaches, we show that the local archaeal community of five different BSI habitats (with up to 18.2% salinity) is composed mostly of a single, highly abundant Nitrosopumilus-like phylotype that is phylogenetically distinct from the bathypelagic thaumarchaea; ammonia-oxidizing bacteria were absent. The composite genome of this novel Nitrosopumilus-like subpopulation (RSA3) co-assembled from multiple single-cell amplified genomes (SAGs) from one such BSI habitat further revealed that it shares B54% of its predicted genomic inventory with sequenced Nitrosopumilus species. RSA3 also carries several, albeit variable gene sets that further illuminate the phylogenetic diversity and metabolic plasticity of this genus. Specifically, it encodes for a putative proline-glutamate 'switch' with a potential role in osmotolerance and indirect impact on carbon and energy flows. Metagenomic fragment recruitment analyses against the composite RSA3 genome, Nitrosopumilus maritimus, and SAGs of mesopelagic thaumarchaea also reiterate the divergence of the BSI genotypes from other AOA.

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Archaeal Diversity and the Prevalence of Crenarchaeota in Salt Marsh Sediments

Cited by 35 publications

References 19 publications

Ammonia oxidation coupled to CO ₂ fixation by archaea and bacteria in an agricultural soil

Ammonia oxidation coupled to CO ₂ fixation by archaea and bacteria in an agricultural soil

Nitrogen and phosphorus enrichment alter the composition of ammonia-oxidizing bacteria in salt marsh sediments

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

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Archaeal Diversity and the Prevalence of Crenarchaeota in Salt Marsh Sediments

Cited by 35 publications

References 19 publications

Ammonia oxidation coupled to CO 2 fixation by archaea and bacteria in an agricultural soil

Ammonia oxidation coupled to CO 2 fixation by archaea and bacteria in an agricultural soil

Nitrogen and phosphorus enrichment alter the composition of ammonia-oxidizing bacteria in salt marsh sediments

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

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Ammonia oxidation coupled to CO ₂ fixation by archaea and bacteria in an agricultural soil

Ammonia oxidation coupled to CO ₂ fixation by archaea and bacteria in an agricultural soil