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Journal articles on the topic 'Phylum Bathyarchaeota'

Author: Grafiati

Published: 4 June 2021

Last updated: 18 February 2022

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1

Evans, P. N., D. H. Parks, G. L. Chadwick, et al. "Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics." Science 350, no. 6259 (2015): 434–38. http://dx.doi.org/10.1126/science.aac7745.

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2

Berghuis, Bojk A., Feiqiao Brian Yu, Frederik Schulz, Paul C. Blainey, Tanja Woyke, and Stephen R. Quake. "Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens." Proceedings of the National Academy of Sciences 116, no. 11 (2019): 5037–44. http://dx.doi.org/10.1073/pnas.1815631116.

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Methanogenic archaea are major contributors to the global carbon cycle and were long thought to belong exclusively to the euryarchaeal phylum. Discovery of the methanogenesis gene cluster methyl-coenzyme M reductase (Mcr) in the Bathyarchaeota, and thereafter the Verstraetearchaeota, led to a paradigm shift, pushing back the evolutionary origin of methanogenesis to predate that of the Euryarchaeota. The methylotrophic methanogenesis found in the non-Euryarchaota distinguished itself from the predominantly hydrogenotrophic methanogens found in euryarchaeal orders as the former do not couple met

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3

Lv, Liu, Han, et al. "The Effect of Nitrogen Content on Archaeal Diversity in an Arctic Lake Region." Microorganisms 7, no. 11 (2019): 543. http://dx.doi.org/10.3390/microorganisms7110543.

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The function of Arctic soil ecosystems is crucially important for the global climate, and nitrogen (N) is the major limiting nutrient in these environments. This study assessed the effects of changes in nitrogen content on archaeal community diversity and composition in the Arctic lake area (London Island, Svalbard). A total of 16S rRNA genes were sequenced to investigate archaeal community composition. First, the soil samples and sediment samples were significantly different for the geochemical properties and archaeal community composition. Thaumarchaeota was an abundant phylum in the nine so

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4

Butterfield, Cristina N., Zhou Li, Peter F. Andeer, et al. "Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone." PeerJ 4 (November 8, 2016): e2687. http://dx.doi.org/10.7717/peerj.2687.

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Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms present, and this link to causative agents is necessary to predict the results of perturbations on the system. We collected soil samples at two sub-root depths (10–20 cm and 30–40 cm) before and after a rainfall-driven nutrient perturbation event in a Northern California grassland that experiences a Mediterranean climate. From ten sample

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5

Zheng, Pengfei, Chuantao Wang, Xiaoli Zhang, and Jun Gong. "Community Structure and Abundance of Archaea in a Zostera marina Meadow: A Comparison between Seagrass-Colonized and Bare Sediment Sites." Archaea 2019 (November 18, 2019): 1–11. http://dx.doi.org/10.1155/2019/5108012.

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Seagrass colonization alters sediment physicochemical properties by depositing seagrass fibers and releasing organic carbon and oxygen from the roots. How this seagrass colonization-induced spatial heterogeneity affects archaeal community structure and abundance remains unclear. In this study, we investigated archaeal abundance, diversity, and composition in both vegetated and adjacent bare surface sediments of a Zostera marina meadow. High-throughput sequencing of 16S rDNA showed that Woesearchaeota, Bathyarchaeota, and Thaumarchaeota were the most abundant phyla across all samples, accountin

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6

Martino, Amanda, Matthew E. Rhodes, Rosa León-Zayas, Isabella E. Valente, Jennifer F. Biddle, and Christopher H. House. "Microbial Diversity in Sub-Seafloor Sediments from the Costa Rica Margin." Geosciences 9, no. 5 (2019): 218. http://dx.doi.org/10.3390/geosciences9050218.

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The exploration of the deep biosphere continues to reveal a great diversity of microorganisms, many of which remain poorly understood. This study provides a first look at the microbial community composition of the Costa Rica Margin sub-seafloor from two sites on the upper plate of the subduction zone, between the Cocos and Caribbean plates. Despite being in close geographical proximity, with similar lithologies, both sites show distinctions in the relative abundance of the archaeal domain and major microbial phyla, assessed using a pair of universal primers and supported by the sequencing of s

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7

Li, Cheng-Peng, Ya-Ping Li, Qing-Qing Huo, et al. "Comparison of Prokaryotic Communities Associated with Different TOC Concentrations in Dianchi Lake." Water 12, no. 9 (2020): 2557. http://dx.doi.org/10.3390/w12092557.

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The effect of total organic carbon (TOC) on the prokaryotic community structure in situ has been rarely known. This study aimed to determine the effect of TOC level on the composition and networks of archaeal and bacterial communities in the sediments of Dianchi Lake, one of the most eutrophic lakes in China. Microbial assemblages showed significantly associations with TOC. Moreover, relatively high and low TOC formed taxonomic differences in prokaryotic assemblages. According to the results, the most abundant bacteria across all samples were identified as members of the phyla Proteobacteria,

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8

Zhang, Xiaoke, Huili Wang, Zhifei Li, Jun Xie, and Jiajia Ni. "Hydrological and soil physiochemical variables determine the rhizospheric microbiota in subtropical lakeshore areas." PeerJ 8 (September 29, 2020): e10078. http://dx.doi.org/10.7717/peerj.10078.

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Background Due to intensive sluice construction and other human disturbances, lakeshore vegetation has been destroyed and ecosystems greatly changed. Rhizospheric microbiota constitute a key part of a functioning rhizosphere ecosystem. Maintaining rhizosphere microbial diversity is a central, critical issue for sustaining these rhizospheric microbiota functions and associated ecosystem services. However, the community composition and abiotic factors influencing rhizospheric microbiota in lakeshore remain largely understudied. Methods The spatiotemporal composition of lakeshore rhizospheric mic

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9

Yuan, Bo, Wei Wu, Mengjing Guo, Xiaode Zhou, and Shuguang Xie. "Spatial-temporal dynamics and influencing factors of archaeal communities in the sediments of Lancang River cascade reservoirs (LRCR), China." PLOS ONE 16, no. 6 (2021): e0253233. http://dx.doi.org/10.1371/journal.pone.0253233.

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The spatial and temporal distribution of the archaeal community and its driving factors in the sediments of large-scale regulated rivers, especially in rivers with cascade hydropower development rivers, remain poorly understood. Quantitative PCR (qPCR) and Illumina MiSeq sequencing of the 16S rRNA archaeal gene were used to comprehensively investigate the spatiotemporal diversity and structure of archaeal community in the sediments of the Lancang River cascade reservoirs (LRCR). The archaeal abundance ranged from 5.11×104 to 1.03×106 16S rRNA gene copies per gram dry sediment and presented no

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10

Hervé, Vincent, Pengfei Liu, Carsten Dietrich, et al. "Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites." PeerJ 8 (February 13, 2020): e8614. http://dx.doi.org/10.7717/peerj.8614.

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“Higher” termites have been able to colonize all tropical and subtropical regions because of their ability to digest lignocellulose with the aid of their prokaryotic gut microbiota. Over the last decade, numerous studies based on 16S rRNA gene amplicon libraries have largely described both the taxonomy and structure of the prokaryotic communities associated with termite guts. Host diet and microenvironmental conditions have emerged as the main factors structuring the microbial assemblages in the different gut compartments. Additionally, these molecular inventories have revealed the existence o

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11

He, Y., M. Li, V. Perumal, et al. "Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments." Nature Microbiology 1, no. 6 (2016). http://dx.doi.org/10.1038/nmicrobiol.2016.35.

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12

L. Bräuer, Suzanna, Nathan Basiliko, Henri M. P. Siljanen, and Stephen H. Zinder. "Methanogenic archaea in peatlands." FEMS Microbiology Letters 367, no. 20 (2020). http://dx.doi.org/10.1093/femsle/fnaa172.

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ABSTRACT Methane emission feedbacks in wetlands are predicted to influence global climate under climate change and other anthropogenic stressors. Herein, we review the taxonomy and physiological ecology of the microorganisms responsible for methane production in peatlands. Common in peat soils are five of the eight described orders of methanogens spanning three phyla (Euryarchaeota, Halobacterota and Thermoplasmatota). The phylogenetic affiliation of sequences found in peat suggest that members of the thus-far-uncultivated group Candidatus Bathyarchaeota (representing a fourth phylum) may be i

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13

Suominen, Saara, Daan M. van Vliet, Irene Sánchez-Andrea, Marcel T. J. van der Meer, Jaap S. Sinninghe Damsté, and Laura Villanueva. "Organic Matter Type Defines the Composition of Active Microbial Communities Originating From Anoxic Baltic Sea Sediments." Frontiers in Microbiology 12 (May 5, 2021). http://dx.doi.org/10.3389/fmicb.2021.628301.

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Carbon cycling in anoxic marine sediments is dependent on uncultured microbial communities. Niches of heterotrophic microorganisms are defined by organic matter (OM) type and the different phases in OM degradation. We investigated how OM type defines microbial communities originating from organic-rich, anoxic sediments from the Baltic Sea. We compared changes in the sediment microbial community, after incubation with different stable isotope labeled OM types [i.e., particulate algal organic matter (PAOM), protein, and acetate], by using DNA stable isotope probing (DNA-SIP). Incorporation of 13

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14

Chen, Ying, Kairui Qiu, Ziyuan Zhong, and Tao Zhou. "Influence of Environmental Factors on the Variability of Archaeal Communities in a Karst Wetland." Frontiers in Microbiology 12 (September 3, 2021). http://dx.doi.org/10.3389/fmicb.2021.675665.

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Archaea are ubiquitous and play an important role in elemental cycles in Earth’s biosphere; but little is known about their diversity, distribution, abundance, and impact in karst environments. The present study investigated the effect of environmental factors on the variability of archaeal communities in the sediment of the Huixian karst wetland, the largest karst wetland in South China. Sediment cores were obtained from four sampling sites with different water depths and macrophyte inhabitants in both the winter of 2016 and the summer of 2018. The community analysis was based on PacBio seque

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15

Loh, Hui Qi, Vincent Hervé, and Andreas Brune. "Metabolic Potential for Reductive Acetogenesis and a Novel Energy-Converting [NiFe] Hydrogenase in Bathyarchaeia From Termite Guts – A Genome-Centric Analysis." Frontiers in Microbiology 11 (February 3, 2021). http://dx.doi.org/10.3389/fmicb.2020.635786.

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Symbiotic digestion of lignocellulose in the hindgut of higher termites is mediated by a diverse assemblage of bacteria and archaea. During a large-scale metagenomic study, we reconstructed 15 metagenome-assembled genomes of Bathyarchaeia that represent two distinct lineages in subgroup 6 (formerly MCG-6) unique to termite guts. One lineage (TB2; Candidatus Termitimicrobium) encodes all enzymes required for reductive acetogenesis from CO2 via an archaeal variant of the Wood–Ljungdahl pathway, involving tetrahydromethanopterin as C1 carrier and an (ADP-forming) acetyl-CoA synthase. This include

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16

Bird, Jordan T., Eric D. Tague, Laura Zinke, et al. "Uncultured Microbial Phyla Suggest Mechanisms for Multi-Thousand-Year Subsistence in Baltic Sea Sediments." mBio 10, no. 2 (2019). http://dx.doi.org/10.1128/mbio.02376-18.

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ABSTRACTEnergy-starved microbes in deep marine sediments subsist at near-zero growth for thousands of years, yet the mechanisms for their subsistence are unknown because no model strains have been cultivated from most of these groups. We investigated Baltic Sea sediments with single-cell genomics, metabolomics, metatranscriptomics, and enzyme assays to identify possible subsistence mechanisms employed by unculturedAtribacteria,Aminicenantes,Actinobacteriagroup OPB41,Aerophobetes,Chloroflexi,Deltaproteobacteria,Desulfatiglans,Bathyarchaeota, andEuryarchaeotamarine group II lineages. Some functi

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17

Wong, Hon Lun, Fraser I. MacLeod, Richard Allen White, Pieter T. Visscher, and Brendan P. Burns. "Microbial dark matter filling the niche in hypersaline microbial mats." Microbiome 8, no. 1 (2020). http://dx.doi.org/10.1186/s40168-020-00910-0.

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Abstract Background Shark Bay, Australia, harbours one of the most extensive and diverse systems of living microbial mats that are proposed to be analogs of some of the earliest ecosystems on Earth. These ecosystems have been shown to possess a substantial abundance of uncultivable microorganisms. These enigmatic microbes, jointly coined as ‘microbial dark matter’ (MDM), are hypothesised to play key roles in modern microbial mats. Results We reconstructed 115 metagenome-assembled genomes (MAGs) affiliated to MDM, spanning 42 phyla. This study reports for the first time novel microorganisms (Zi

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