Archaea in Biogeochemical Cycles

Offre, Pierre; Spang, Anja; Schleper, Christa

doi:10.1146/annurev-micro-092412-155614

Cited by 397 publications

(325 citation statements)

References 144 publications

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“…We were not able to resolve the branching position of SAGMEG within the Euryarchaeota solely on the basis of rRNA phylogenies. The placement of the group is also inconsistent in the literature 4,9 . Therefore, to investigate the phylogenetic position of SAGMEG within the Archaea in more detail, we constructed phylogenetic trees based on concatenated ribosomal proteins ( Supplementary Fig.…”

mentioning

confidence: 99%

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

Baker¹,

et al. 2016

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The subsurface biosphere is largely unexplored and contains a broad diversity of uncultured microbes1. Despite being one of the few prokaryotic lineages that is cosmopolitan in both the terrestrial and marine subsurface2–4, the physiological and ecological roles of SAGMEG (South-African Gold Mine Miscellaneous Euryarchaeal Group) Archaea are unknown. Here, we report the metabolic capabilities of this enigmatic group as inferred from genomic reconstructions. Four high-quality (63–90% complete) genomes were obtained from White Oak River estuary and Yellowstone National Park hot spring sediment metagenomes. Phylogenomic analyses place SAGMEG Archaea as a deeply rooting sister clade of the Thermococci, leading us to propose the name Hadesarchaea for this new Archaeal class. With an estimated genome size of around 1.5 Mbp, the genomes of Hadesarchaea are distinctly streamlined, yet metabolically versatile. They share several physiological mechanisms with strict anaerobic Euryarchaeota. Several metabolic characteristics make them successful in the subsurface, including genes involved in CO and H2 oxidation (or H2 production), with potential coupling to nitrite reduction to ammonia (DNRA). This first glimpse into the metabolic capabilities of these cosmopolitan Archaea suggests they are mediating key geochemical processes and are specialized for survival in the subsurface biosphere.

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confidence: 99%

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

Baker¹,

et al. 2016

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“…The binning of nitrogenase transcripts from the LI were to Archaea, including methanogens and ANME. Methanogens are considered to be among the nitrogen-fixing free-living anaerobes (Madigan et al, 2008), and recently it was demonstrated that deep-sea ANME from ammoniumreplete sediments fix N 2 and share the products of nitrogen fixation with sulfate-reducing bacterial partners (Dekas et al, 2009;Offre et al, 2013). We do not have an explanation for why methanogens/ ANME compensate for the energetic burden of diazotrophy in an ammonium-rich environment.…”

Section: Metabolism Of Nitrogen Compoundsmentioning

confidence: 75%

Unveiling microbial activities along the halocline of Thetis, a deep-sea hypersaline anoxic basin

et al. 2014

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Deep-sea hypersaline anoxic basins (DHABs) in the Eastern Mediterranean Sea are considered some of the most hostile environments on Earth. Little is known about the biochemical adaptations of microorganisms living in these habitats. This first metatranscriptome analysis of DHAB samples provides significant insights into shifts in metabolic activities of microorganisms as physicochemical conditions change from deep Mediterranean sea water to brine. The analysis of Thetis DHAB interface indicates that sulfate reduction occurs in both the upper (7.0-16.3% salinity) and lower (21.4-27.6%) halocline, but that expression of dissimilatory sulfate reductase is reduced in the more hypersaline lower halocline. High dark-carbon assimilation rates in the upper interface coincided with high abundance of transcripts for ribulose 1,5-bisphosphate carboxylase affiliated to sulfuroxidizing bacteria. In the lower interface, increased expression of genes associated with methane metabolism and osmoregulation is noted. In addition, in this layer, nitrogenase transcripts affiliated to uncultivated putative methanotrophic archaea were detected, implying nitrogen fixation in this anoxic habitat, and providing evidence of linked carbon, nitrogen and sulfur cycles.

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“…Abundances of soil Crenarchaeota also are positively correlated with soil N content (36). Conversely, several reports have shown the potential for members of the Euryarchaeota, which are predominately methanogens, to fix atmospheric N 2 (38,39). This characteristic could place them at a competitive disadvantage under conditions of elevated N availability and explain their strong proportional decrease with N fertilization.…”

Section: Resultsmentioning

confidence: 98%

“…For example, nutrient-induced shifts in copiotrophic vs. oligotrophic traits could have important implications for soil C cycling (52) if their traits elicit effects rather than solely reflect responses (53). Likewise, decreases in mycorrhizae and methanogens could have important impacts on ecosystem-level processes (39,54). This work moves us toward a more mechanistic understanding of how shifts in microbial community composition mediate and reflect the effects of anthropogenically elevated nutrient inputs on terrestrial ecosystems.…”

Section: Discussionmentioning

confidence: 99%

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe

Leff

Jones

Prober

et al. 2015

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

1,095

702

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Soil microorganisms are critical to ecosystem functioning and the maintenance of soil fertility. However, despite global increases in the inputs of nitrogen (N) and phosphorus (P) to ecosystems due to human activities, we lack a predictive understanding of how microbial communities respond to elevated nutrient inputs across environmental gradients. Here we used high-throughput sequencing of marker genes to elucidate the responses of soil fungal, archaeal, and bacterial communities using an N and P addition experiment replicated at 25 globally distributed grassland sites. We also sequenced metagenomes from a subset of the sites to determine how the functional attributes of bacterial communities change in response to elevated nutrients. Despite strong compositional differences across sites, microbial communities shifted in a consistent manner with N or P additions, and the magnitude of these shifts was related to the magnitude of plant community responses to nutrient inputs. Mycorrhizal fungi and methanogenic archaea decreased in relative abundance with nutrient additions, as did the relative abundances of oligotrophic bacterial taxa. The metagenomic data provided additional evidence for this shift in bacterial life history strategies because nutrient additions decreased the average genome sizes of the bacterial community members and elicited changes in the relative abundances of representative functional genes. Our results suggest that elevated N and P inputs lead to predictable shifts in the taxonomic and functional traits of soil microbial communities, including increases in the relative abundances of fastergrowing, copiotrophic bacterial taxa, with these shifts likely to impact belowground ecosystems worldwide.soil bacteria | soil fungi | shotgun metagenomics | soil ecology | fertilization

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Archaea in Biogeochemical Cycles

Cited by 397 publications

References 144 publications

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

Unveiling microbial activities along the halocline of Thetis, a deep-sea hypersaline anoxic basin

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe

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