Diversity, ecology and evolution of Archaea

Baker, Brett J.; Anda, Valerie De; Seitz, Kiley W.; Dombrowski, Nina; Santoro, Alyson E.; Lloyd, Karen G.

doi:10.1038/s41564-020-0715-z

Cited by 326 publications

(271 citation statements)

References 190 publications

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“…The presence of this energy-dependent efflux process related detoxification proteins, could also indicate that Brockarchaeota in hot springs genomes could use arsenate as terminal electron acceptor, as seen in bacteria 42,43 The discovery of Brockarchaeota genomes from sediments around the world, overlooked by conventional rRNA gene diversity approaches, highlights the need for further exploration of subsurface microbial communities. The addition of these genomes to public databases, like other recently described novel archaeal lineages [44][45][46] , will enhance their detection in future environmental studies. A lack of recognition of their existence prior to this, limited our ability to fully describe sediment community structure and function.…”

Section: Discussionmentioning

confidence: 99%

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Brockarchaeota, a novel archaeal lineage capable of methylotrophy

Anda¹,

Chen²,

Dombrowski³

et al. 2020

Preprint

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Single carbon (C1) compounds such as methanol, methylamines and formaldehyde are ubiquitous in nature and they are large components of the carbon cycle. In anoxic environments C1-utilizing microbes (methylotrophs) play an important role in controlling global carbon degradation. Currently described anaerobic methylotrophs are limited to methanogenic archaea, acetogenic bacteria, and sulfate-reducing bacteria. Here, we report the first archaeal lineage outside of methanogenic taxa that are capable of anaerobic methylotrophy. Phylogenetic analyses suggest these archaea form a new phylum within the TACK superphylum, which we propose be named Brockarchaeota. A survey revealed Brockarchaeota are globally distributed in geothermal springs. Metabolic inference from 15 metagenome-assembled genomes from hot springs and deep-sea sediments indicates that Brockarchaeota are strict anaerobes. They contain a variety C1 metabolisms including the methanol and trimethylamine methyltransferases system, the ribulose bisphosphate pathway coupled with the non-oxidative pentoses phosphate pathway, and reductive glycine pathway. Brockarchaeota have an incomplete methyl-branch of the Wood-Ljungdahl pathway probably used for formaldehyde oxidation, since they lack several core genes involved in methanogenesis including methyl-CoM reductases. Brockarchaeota also appear to play an important role in the breakdown of plant-derived polysaccharides, especially cellulose, starch and xylan. Their broad distribution and their capacity to use both C1 compounds and complex polysaccharides via anaerobic metabolism suggest that the Brockarchaeota occupy previously overlooked roles in carbon cycling.

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Section: Discussionmentioning

confidence: 99%

“…Phylogenetic analyses. A phylogenetic tree was generated as recently described in ref 46 . Briefly, 36 conserved marker proteins were extracted using phylosift 51 , in a genomic dataset containing 3,549 archaeal genomes including Brockarchaeota, and 40 bacterial genomes.…”

Section: Methodsmentioning

confidence: 99%

Brockarchaeota, a novel archaeal lineage capable of methylotrophy

Anda¹,

Chen²,

Dombrowski³

et al. 2020

Preprint

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“…Apart from well-documented lineages of Deltaproteobacteria and Archaeoglobi [6,21], faeA genes are reported here as also occurring in the class Dehalococcoidia within the phylum Chloro exi, the class Thermoplasmata within the phylum Euryarchaeota, and within the Asgard superphylum (Lokiarchaeota, Thorarchaeota, and Heimdallarchaeota). Current knowledge about archaea involved in anaerobic hydrocarbon degradation focuses mainly on oxidation of methane and other short alkane gases using methyl-CoM reductase or methyl-CoM reductase-like enzymes [25,44,45]. New archaeal diversity presented here for the degradation of longer alkanes opens up a wider perspective on the evolution and expansion of hydrocarbon-oxidizing pathways throughout the archaeal domain.…”

Section: Discussionmentioning

confidence: 99%

Marine Sediments Harbor Diverse Archaea and Bacteria With Potentials for Anaerobic Hydrocarbon Degradation via Fumarate Addition

Zhang¹,

Weng²,

Wei³

et al. 2020

Preprint

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Background: Marine sediments can contain large amounts of alkanes and methylated aromatic hydrocarbons that are introduced by natural processes or anthropogenic activities. These compounds can be biodegraded by anaerobic microorganisms via enzymatic addition of fumarate. Previous gene- and genome-based surveys have detected ubiquitous and novel fumarate-adding enzymes (FAE), but these were neither confirmed as occurring within full degradation pathways nor affiliated with known organisms. The identity and ecological roles of a significant fraction of anaerobic hydrocarbon degraders in marine sediments therefore remains unknown.Results: By combining phylogenetic reconstructions, protein homolog modelling, and functional profiling of publicly available and newly sequenced metagenomes and genomes, 61 draft bacterial and archaeal genomes encoding anaerobic hydrocarbon degradation via fumarate addition were obtained. Besides Deltaproteobacteria that are well-known to catalyze these reactions, Chloroflexi are dominant FAE-encoding bacteria in hydrocarbon-impacted sediments, potentially coupling sulfate reduction or fermentation to anaerobic hydrocarbon degradation. Among Archaea, besides Archaeoglobi previously shown to have this capability, genomes of Heimdallarchaeota, Lokiarchaeota, Thorarchaeota and Thermoplasmata also suggest fermentative hydrocarbon degradation using archaea-type FAE. The biogeography survey reveals these bacterial and archaeal hydrocarbon degraders occur in a wide range of marine sediments, including high abundances of FAE-encoding Asgard archaea associated with natural seeps and subseafloor ecosystems.Conclusions: Our results expand the knowledge of novel microbial lineages engaged in anaerobic degradation of alkanes and methylated aromatic hydrocarbons, and shed new light on the importance of marine sedimentary archaea in hydrocarbon degradation.

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“…The results showed that the richness of archaea in the GC environment was far greater than in the PC environment. These might be closely related to the water source and the length of aquaculture cycle (Zhong et al, 2016;Lu et al, 2016Lu et al, , 2019Baker e al., 2020). In addition, a total of 326 biomarkers with statistical differences were obtained in six groups by using LDA Effect Size (LEfSe) analysis, and the LDA values ranged from 3.3745 to 5.5156, and the relative abundances of microbiota in different growth stages of PC and GC environments showed signi cant differences (Fig.…”

Section: Annotation Analysis Of the Microbiotamentioning

confidence: 99%

Comparing environmental microbiota of different growth stages of fresh water turtle Chinemys reevesii in pond and greenhouse cultivation

Zhou¹,

Xie²,

Sun³

et al. 2020

Preprint

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The microbial community structure is an important indicator for evaluating the water quality of the aquaculture environment. In this study, V4 regions of 16S rRNA gene of pond (PC) and greenhouse cultured (GC) C. reevesii were sequenced. Results showed that a total of 1,993,090 high quality counts and 105,159 observed OUTs were obtained; and the Chao1 richness estimator of PC was significantly higher than that of GC groups. Beta-diversity showed that the microbiota of two groups were isolated from each other. In addition, the correlation analysis of environmental factors showed that NO2-N, PH, PO4-P, and stocking density played significant roles in the bacterial community composition. The dominant phyla in PC groups were cyanobacteria, proteobacteria, actinobacteria, bacteroidetes, verrucomicrobia, planctomycetes; and in GC groups were proteobacteria, bacteroidetes, firmicutes, cyanobacteria, chloroﬂexi, actinobacteria. The functional prediction showed that the top5 Picrust prediction gene functions were protein processing in endoplasmic reticulum, retinol metabolism, proteasome, glycan binding proteins, and stilbenoid, diarylheptanoid and gingerol biosynthesis. Meanwhile, the numbers and types of KEGG pathway annotations showed a significant difference between the two cultivation environments. The prediction of bacterial phenotype implied that the GC environment is more likely to deteriorate, and turtles are more susceptible to pathogens than those of PC environment. This is the first report to explore and understand the difference of microbiota characteristics between different cultivation environments in different growth stages of C. reevesii, which will provide basic data for water quality adjustment, disease prevention, and healthy breeding of turtle.

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Diversity, ecology and evolution of Archaea

Cited by 326 publications

References 190 publications

Brockarchaeota, a novel archaeal lineage capable of methylotrophy

Brockarchaeota, a novel archaeal lineage capable of methylotrophy

Marine Sediments Harbor Diverse Archaea and Bacteria With Potentials for Anaerobic Hydrocarbon Degradation via Fumarate Addition

Comparing environmental microbiota of different growth stages of fresh water turtle Chinemys reevesii in pond and greenhouse cultivation

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