facts about bathyarchaeota
It is evident that the phylogenetically diverse subgroups are heterotrophs with metabolism centralized around acetyl-CoA generation. This suggests that methane metabolism might have evolved before the divergence of the ancient archaeal lineages of Bathyarchaeota and Euryarchaeota, in agreement with the assumption that methanogenesis might represent one of the earliest metabolic transformations (Battistuzzi, Feijao and Hedges 2004; Ferry and House 2006; Evansetal.2015; Lloyd 2015). with 12C-acetate added); this indicated that the acetate might participate in microbial biosynthesis rather than being used for energy production (Naetal.2015). 4), although these might not necessarily exist in all bathyarchaeotal subgroups (Fig. Phylogenetic analysis of the Pta and Ack coding sequences in He et al.s study revealed that these genes form a monophyletic clade and are different from all other know sequences, indicating that they evolved independently of the currently known bacterial counterparts (Heetal.2016). 1 and Table S 5 ), and the average proportion of Bathyarchaeota in the mangrove sediments (43.32%, sd = 0.106) was significantly higher than that in the mud flat sediments (36.47%, sd = 0.084) ( p < Characteristics of the Bathyarchaeota community in Although the accumulated information paves the way for further clarification of the adaptation of different lineages to various environments, systematic understanding of the distribution pattern of bathyarchaeotal subgroups and influential factors is still needed. However, the ecological knowledge of Bathyarchaeota is limited in peatland ecosystems. Buckles LK, Villanueva L, Weijers JWH et al. High-throughput sequencing of the archaeal communities and the analysis of the relationship between the distribution pattern of bathyarchaeotal subgroups and the physicochemical parameters of study sites revealed that sediment depth and sulfate concentration were important environmental factors that shape the distribution of bathyarchaeotal subgroups; Subgroup-8 was shown to be predominantly distributed in the reducing and deeper sediment layers, while Subgroup-10 was preferentially distributed in the relatively more oxidizing and shallow sediment layers (Yuetal.2017). Membrane lipids are an informative indicator of the distribution and activity of living microbial cells, independently of their culturing (Sturtetal.2004; Jacquemetetal.2009; Lipp, Liu and Hinrichs 2009). Draft Genome Sequence of " Candidatus In this tree, the Subgroups-1 to -17 were the same as Kubo's tree (Kuboetal.2012), and Subgroup-5 was divided into Subgroups-5a, -5b and -5bb as suggested in Fillol et al.s research (Filloletal.2016). The exclusive archaeal origin of the Ack-Pta homoacetogenesis pathway is different from other archaeal acetogenesis systems but shares functional similarity with its bacterial origin counterparts, although it is phylogenetically divergent (Heetal.2016). the classification proposed by Zhou et al. The novel Bathyarchaeota lineage possesses an incomplete methanogenesis pathway lacking the methyl co-enzyme M reductase complex and encodes a non-canonical acetogenic pathway potentially coupling methylotrophy to acetogenesis via the methyl branch of Wood-Ljundahl pathway. Diverse Bathyarchaeotal Lineages Dominate Archaeal The current genomic and physiological information of these subgroups also suggests their potential ecological strategies and functions in specific habitats, further highlighting their important roles in global biogeochemical cycling (Xiangetal.2017). Our results provide an overview of the archaeal population, Bathyarchaeota, a recently proposed archaeal phylum, is globally distributed and highly abundant in anoxic sediments. This study represents the first report on the diversity and spatial distribution of microbial communities in methane-rich tropical shallow water ecosystems, highlighting the most abundant archaea detected, the Bathyarchaeia Class. Further, a close co-occurrence of Bathyarchaeota and Methanomicrobia hinted at a syntrophic association between them; the acetate production/consumption relationship between the two might be responsible for such a scenario, as proposed by metabolic predictions (Heetal.2016; Xiangetal.2017). Evans PN, Parks DH, Chadwick GL et al. Future experiments investigating substrate specificity of these proteins and analyses of the intermediate metabolites will help establish their actual functions. The diversity of bathyarchaeotal community turns out to be similar in the four cultivation treatments (basal medium, addition of an amino acid mix, H2-CO2 headspace and initial aerobic treatment). The Miscellaneous Crenarchaeotal Group (MCG) archaea were firstly detected from a hot spring (Barnsetal.1996) and later proposed with a name in a study surveying 16S rRNA gene sequences from marine subsurface sediments (Inagakietal.2003). Logares R, Brate J, Bertilsson S et al. In surface and shallow subsurface sediments (surficial to 10 cm deep) of an intertidal mudflat of Brouage in the Bay of Marennes-Olron, however, the abundances of Subgroup-15 and other bathyarchaeotal subgroups are stable, while the total abundance of Euryarchaeota sequences increases in the same depth range (Hlneetal.2015). To compare the coverage and specificity of analysis using the qPCR primer pairs MCG242dF/MCG678R and MCG528F/MCG732R for freshwater and marine sediment samples, amplicons obtained with these two primer pairs were analyzed and community structures compared (Filloletal.2015). Bathyarchaeotal SAGs also encode pathways for the intracellular breakdown of amino acids. Three fosmid clones harboring bathyarchaeotal genomic fragments were screened from the South China Sea sediments (05 cm depth) (Lietal.2012). A meta-analysis of the distribution of sediment archaeal communities towards environmental eco-factors (7098 archaeal operational taxonomic units from 207 sediment sites worldwide) was performed and a multivariate regression tree was constructed to depict the relationship between archaeal lineages and the environmental origin matrix (Filloletal.2016). Diversity, metabolism and cultivation of archaea 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 involved in methane cycling, either anaerobic oxidation of methane and/or methanogenesis, as at least a few organisms within this group contain the essential These indicative subgroups are the dominant ones in the environment, as evaluated by relatively abundant fraction of Bathyarchaeota in corresponding archaeal communities (on average 44% among all studies). Two highly abundant MCR variants were detected in Ca. The deduced last common ancestor of Bathyarchaeota might be a saline-adapted organism, which evolved from saline to freshwater habitats during the diversification process, with the occurrence of few environmental transitional events. WebInteresting Archaebacteria Facts: Archaebacteria are believed to have emerged approximately 3.5 billion years ago. Subgroups were assigned from the corresponding 16S rRNA gene phylogenic tree (Fig. WebHost. This group of lipids has not been found in natural environments or microorganism enrichments dominated by methanotrophic archaea before (Rosseletal.2008; Kellermannetal.2012), nor have they been detected after re-analyzing lipid extracts from the above two studies using the same method in the study (Meadoretal.2015). 2). Diverse Bathyarchaeotal Lineages Dominate Archaeal The emergence of freshwater-adapted lineages, including freshwater-indicative Subgroups-5, -7, -9 and -11, occurred after the first salinefreshwater transition event (Filloletal.2016). During the enriching process with lignin addition, the Subgroup-8 abundance climbed over 10 times compared with the initial stage and became the most dominant archaeal species. (2016) reconstructed six nearly complete bathyarchaeotal genomes (Subgroups-13, -15, -16, -18 and -19) from the Guaymas Basin subsurface sediment. Surprisingly, these genes fall closely to the Bathyarchaeota mcr genes. The subgroups MCG-18, -19 and -20 were firstly named in Lazar et al.s study, but only MCG-19 was represented in the phylogenetic tree (Lazaretal.2015). Further, based on genomic inferences, Evansetal. Kuboetal. In summary, there are a total of 25 subgroups of Bathyarchaeota based on all available 16S rRNA gene sequences at this moment, and the former names for each subgroup are also labeled in the tree (Fig. In this study, the abundance and S. butanivorans protein extracts; they are probably responsible for the initial step of butane activation to generate butyl-CoM. Genomic inferences from SAGs and genome-resolved metagenomic bins provide further genomic support for the heterotrophic lifestyle of Bathyarchaeota, rendering them capable of adapting to various environments and becoming one of the most successful lineages globally (Fig. Bathyarchaeota is of great interest to microbial ecologists for its wide distribution, high abundance, and diversity, as well as its potential ability to degrade detrital organic matter in aquatic environments and drive global elements cycling . Four genomes (Subgroups-1, -6, -7 and -15) were recovered from the sediment metagenome. Considering the relative abundance of lineages in the separated leaves, Bathyarchaeota accounted for the greatest proportion of lineage variance in the freshwater and saline environments. WebEtymology: Gr. Individual metagenome assemblies Future efforts should be encouraged to address the fundamental issues of the diversity and distribution patterns of Bathyarchaeota, and their vital roles in global carbon cycling. It is one of the predominant groups in the marine subsurface archaeal community (Fryetal.2008; Teske and Srensen 2008; Lloydetal.2013). Details of markers refer to Supplementary Table S1 available online. Eight subgroups were delineated based on the freshwater/saline segregation, as suggested by the significant IndVal values (P < 0.01) pointing to freshwater/marine sediment distribution. They are able to use a variety of substrates, including (i) detrital proteins, (ii) polymeric carbohydrates, (iii) fatty acids/aromatic compound, (iv) methane (or short alkane) and methylated compounds, and/or (v) potentially other organic matter to generate acetyl-CoA, subsequently using it to obtain energy or assimilate it in biosynthetic processes. The IndVal species with statistical support in terrestrial environments indicated by this study were pMCG and Subgroup-5b in peat; Subgroup-5a in hot springs; Subgroup-6 in the soil; Subgroups-3, -4, -13 and -16 in estuaries; and Subgroup-15 in mangroves. Some of these Crenarchaeota were able to assimilate all 13C-organic compounds tested, including acetate, glycine, urea, simple biopolymers (extracted algal lipids) and complex biopolymers (ISOGRO), while others were only detected in specific substrates (acetate or urea). Meanwhile, the ability to utilize a wide variety of substrates could have allowed Bathyarchaeota to avoid a direct competition with other substrate specialists, such as methanogens and sulfate reducers; in contrast, organic matter degradation to generate acetate might be more energetically favorable for Bathyarchaeota than for other bacterial acetogens, as the former do not need to invest in ATP to activate formate; subsequently, Bathyarchaeota plays the role of active carbon transformers, especially in the subsurface sediments, to fuel the heterotrophy and acetoclastic methanogenesis processes and facilitate coupled carbon cycling (Fig. Thauer RK, Kaster A-K, Seedorf H et al. High occurrence of Bathyarchaeota (MCG) in the deepsea Markers for individual pathway/function were scanned against genomes using the HMM and KEGG databases (Anantharamanetal.2016; Kanehisa, Sato and Morishima 2016; Spang, Caceres and Ettema 2017). Archaea are abundant in lake sediments [14].Particularly, members of the phylum Bathyarchaeota and the class Thermoplasmata are widespread and considered as core generalists in sediment habitats [], where they have been recognized as key players in the carbon cycle [69].Archaea are also common 2). Peat MCG group was represented with one sequence at 90% cutoff level (Xiangetal.2017). Although the Pta-Ack pathway has been previously identified in the methanogenic genus Methanosarcina, it was shown that the encoding pta-ack gene pair might be derived from a horizontal transfer of genes of bacterial origin (Fournier and Gogarten 2008). 3) (Lloydetal.2013; Evansetal.2015; Lazaretal.2015; Heetal.2016; Lazaretal.2016; Lever 2016). is bathyarchaeota multicellular. Furthermore, genes encoding ATP sulfurylase, for the reduction of sulfate to adenosine 5-phosphosulfate, and adenylyl-sulfate reductase, for the reduction of adenosine 5-phosphosulfate to sulfite, were identified in a metagenomic assembly of Bathyarchaeota TCS49 genome from the Thuwal cold seep brine pool of the Red Sea; this suggests that specific bathyarchaeotal members might harbor a dissimilatory sulfate reduction pathway, indicating the existence of additional potential metabolic capacities of Bathyarchaeota (Zhangetal.2016). Recently, Subgroup-15 was widely detected in both freshwater and marine benthic sediments; its persistent distribution along the sediment depth profile, with higher abundance within active archaeal communities, provides additional hints linking its members physiological traits to habitat preferences (Liuetal.2014). After incubation with 13C-acetate, the archaeal population within a sulfate reduction zone, detected on the basis of 13C-DNA, was almost entirely dominated by Bathyarchaeota (65% by Subgroup-8 and 30% by Subgroup-15) (Websteretal.2010). Furthermore, one new subgroup (Subgroup-23) was proposed in this study (Fig. The 13C-depleted nature of butanetriol dibiphytanyl glycerol tetraethers found in the study implied that members of Bathyarchaeota might be autotrophs or fueled by 13C-depleted organic substrates (Meadoretal.2015). In addition to the global distribution, expanding prokaryotic community investigations of deep ocean drilling sediments revealed that members of Bathyarchaeota occupy considerable fractions of the archaeal communities (Teske 2006). Bathyarchaeota, formerly known as the Miscellaneous Crenarchaeotal Group, is a phylum of global generalists that are widespread in anoxic sediments, which host relatively high abundance archaeal communities. Recently, two bathyarchaeotal genome bins (BA1 and BA2) were recovered from the formation waters of coal-bed methane wells within the Surat Basin (Evansetal.2015). Community, Distribution, and Ecological Roles In one study, small amounts of stable isotope-labeled substrates, including glucose, acetate and CO2, were introduced multiple times into slurries from different biogeochemical depths of tidal sediments from the Severn estuary (UK) to better reflect the in situ environmental conditions (Websteretal.2010). All sequences were aligned using SINA v1.2.11 (vision 21227) with SSU ARB database version 128, and poorly aligned columns (gaps in 50% or more of the sequences) were deleted by using trimAl v1.4.rev15 (Ludwigetal.2004; Capella-Gutirrez, Silla-Martnez and Gabaldn 2009; Pruesse, Peplies and Gloeckner 2012). Multiple genomic and physiological traits of these microorganisms have been coming to light in recent decades with the advent of stable isotope labeling and metagenomic profiling methods. masc. Among the presently recognized 25 bathyarchaeotal subgroups, eight are delineated as significantly niche-specific based on their marine/freshwater segregation. The wide availability of buried organic matter in the marine subsurface would favor the heterotrophic feeding of Bathyarchaeota. Furthermore, a principal coordinate analysis also clearly separates the bathyarchaeotal community into freshwater and saline sediment groups. Genomic characterization and metabolic potentials of Bathyarchaeota. However, their life strategies have remained largely elusive. (Kuboetal.2012), and the outgroup sequences of Crenarchaeota, YNPFFA group and Korarchaeota were added. Fryetal. Methane would be oxidized in a stepwise manner to methyl-tetrahydromethanopterin (CH3-H4MPT); the methyl group of CH3-H4MPT and CO2 would then be subjected to a CO dehydrogenase/acetyl-CoA synthase (CODH/ACS complex); CO2 would be fixed by a reverse CO dehydrogenation to CO, and then coupled with a methyl group and CoA to generate acetyl-CoA; ATP would be generated in the course of substrate-level phosphorylation from ADP, with one acetate molecule simultaneously generated by a reverse ADP-forming acetyl-CoA synthase. Beyond methane The members of the Bathyarchaeota are the most abundant archaeal components of the transitional zone between the freshwater and saltwater benthic sediments along the Pearl River, with a central position within the co-occurrence network among other lineages (Liuetal.2014). The results indicate that the phylum Bathyarchaeota shares a core set of metabolic pathways, including protein degradation, glycolysis, and the reductive acetyl neut. A subsequent heterologous expression and activity assays of the bathyarchaeotal acetate kinase gene ack demonstrated the ability of these bathyarchaeotal members to grow as acetogens. Metabolic versatility of freshwater sedimentary archaea feeding The capability to utilize a wide variety of substrates might comprise an effective strategy for competing with substrate specialists for energy sources in various environments (Lietal.2015), such as detrital protein-rich deep seafloor sediments and estuarine sediments containing various carbohydrates. Subgroup-5 is divided into Subgroups-5a and -5b, each with intragroup similarity >90% according to a maximum-likelihood estimation. In the White Oak River estuary, the abundance of Bathyarchaeota decreases with decreasing reductive redox conditions of the sediment (Lazaretal.2015). Furthermore, bathyarchaeotal members have wide metabolic capabilities, including acetogenesis, methane metabolism, and dissimilatory nitrogen and sulfur reduction, and they also have potential interactions with anaerobic methane-oxidizing archaea, acetoclastic methanogens and heterotrophic bacteria. 4) (Evansetal.2015; Heetal.2016; Lazaretal.2016). The concatenated ribosomal protein (RP) alignment contained 12 RPs, and those genomes with <25% RPs were excluded from tree construction. Combined with the aforementioned specific heterotrophic metabolic potentials of members within bathyarchaeotal subgroups and their occurrence in sediment layers of distinct biogeochemical properties (Lazaretal.2015), it was proposed that the acquisition of diverse physiological capacities by Bathyarchaeota is driven by adaptation to specific habitats rather than there being a common metabolic capacity. Genomic inferences from the two reconstructed bathyarchaeotal genomic bins from the coal-bed methane wells suggest that some Bathyarchaeota are methylotrophic methanogens feeding on a wide variety of methylated compounds, possessing an additional ability to ferment peptides, glucose and fatty acids (Evansetal.2015). The metabolic properties are also considerably diverse based on genomic analysis (Fig. The analysis of the stable isotopic-probed microcosms from Cheesequake salt marsh sediment revealed that all Crenarchaeota groups, which still include Bathyarchaeota and Thaumarchaeota (formerly Crenarchaeota MG 1.a) and other Crenarchaeota groups, are heterotrophic and do not incorporate 13C-bicarbonate (Seyler, McGuinness and Kerkhof 2014). In a recent study, Bathyarchaeota and ANME were shown to predominate on the flange of a hydrothermal chimney wall in the Soria Moria Vent field, where the local energy condition favors anaerobic methane oxidizers (Dahleetal.2015). BA1 (Subgroup-3) genome contains many genes of the reductive acetyl-CoA (WoodLjungdahl) pathway and key genes of the methane metabolism pathway. Currently available bathyarchaeotal genomes (from GenBank, 29 November 2017 updated) with 16S rRNA gene sequences were labeled in the tree. 2) based on currently available bathyarchaeotal 16S rRNA gene sequences from SILVA SSU 128 by adding the information from pervious publications (Kuboetal.2012; Lazaretal.2015; Filloletal.2016; Heetal.2016; Xiangetal.2017). Bathyarchaeota was initially proposed to form a distinct cluster closely related to Aigarchaeota and hyperthermophilic Crenarchaeota; because of their terrestrial origin (Barnsetal.1996) (such as freshwater lakes and hot springs), the name Terrestrial MCG was temporarily proposed (Takaietal.2001). Barns SM, Delwiche CF, Palmer JD et al. This primer pair shows good specificity toward Bathyarchaeota; it allowed amplification of 10100 times more bathyarchaeotal 16S rRNA gene sequences from the sediment samples from the South China Sea, and the Atlantic and Antarctic Oceans than the MCG242dF/MCG678R primers (Yuetal.2017). Acetyl-CoA might be involved in acetate generation in a fermentative pathway; however, genomic evidence suggests that Subgroup-1 cells might rely on both fermentative and respiratory metabolism (a simple respiratory metabolism based on a membrane-bound hydrogenase). The branching order of Subgroups-13 to -17 was unstable when analyzed by different tree-construction methods, and they were presented as multifurcated branches. Metabolic potential of Bathyarchaeota and their interactive relationships with other microorganisms. Inagaki F, Nunoura T, Nakagawa S et al. However, due to the great diversity of them, there is limited genomic information that accurately encompasses the metabolic potential of the entire archaeal phylum. Obtaining direct physiological evidence for the generation or oxidization of methane by Bathyarchaeota in the future is also important. 3). ( 2012) conducted a comprehensive analysis of the biogeographical distribution of Bathyarchaeota and found that it was the dominant archaeal population in anoxic, low-activity subsurface sediments. For full access to this pdf, sign in to an existing account, or purchase an annual subscription. It also contains typical methane metabolism genes (hdrABC and mvhADG) but lacks hdrE, similar to Methanomassiliicoccales genomes (Evansetal.2015). Since these two genomic bins represent only a small fraction of all bathyarchaeotal lineages, and no evidence of methanogenic machinery is apparent in the recent parallel genomic binning data, the ability to metabolize methane might not be shared by all subgroup lineages (Lloydetal.2013; Mengetal.2014; Heetal.2016; Lazaretal.2016). BA1 also lacks other genes for energy-conserving complexes, including F420H2 dehydrogenase, energy-converting hydrogenases A and B, Rhodobacter nitrogen fixation complex and V/A-type ATP synthase. Because of their high sequence coverage and bathyarchaeotal sequence specificity, MCG528 and MCG732 primers are recommended for the detection and quantification of Bathyarchaeota (Kuboetal.2012); nevertheless, this primer pair is not suitable for quantifying Bathyarchaeota in freshwater columns and sediments (Filloletal.2015). Introduction. Physiological incubation experiments with stable isotopic probing demonstrated that members of Bathyarchaeota are able to assimilate a wide variety of the tested 13C-organic compounds, including acetate, glycine, urea, simple biopolymers (extracted algal lipids) and complex biopolymers (ISOGRO) (Websteretal.2010; Seyler, McGuinness and Kerkhof 2014). Stahl DA, Flesher B, Mansfield HR et al. Microbial communities of deep marine subsurface sediments: molecular and cultivation surveys, Methanogenic archaea: ecologically relevant differences in energy conservation, Methylotrophic methanogenesis discovered in the archaeal phylum, Methanotrophic archaea possessing diverging methane-oxidizing and electron-transporting pathways, Prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin, Prokaryotic functional diversity in different biogeochemical depth zones in tidal sediments of ?the Severn Estuary, UK, revealed by stable-isotope probing, Enrichment and cultivation of prokaryotes associated with the sulphate-methane transition zone of diffusion-controlled sediments of Aarhus Bay, Denmark, under heterotrophic conditions, The physiology and habitat of the last universal common ancestor, Distribution of Bathyarchaeota communities across different terrestrial settings and their potential ecological functions, Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences, A large-scale evaluation of algorithms to calculate average nucleotide identity, High occurrence of Bathyarchaeota (MCG) in the deep-sea sediments of South China Sea quantified using newly designed PCR primers, Growth of sedimentary Bathyarchaeota on lignin as an energy source, Genomic and transcriptomic evidence for carbohydrate consumption among microorganisms in a cold seep brine pool, This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (, Illuminating the Oral Microbiome and its Host Interactions: Animal models of disease, Engineering lanthipeptides by introducing a large variety of RiPP modifications to obtain new-to-nature bioactive peptides, Meat fermentation at a crossroads: where the age-old interplay of human, animal, and microbial diversity and contemporary markets meet, Incorporation, fate, and turnover of free fatty acids in cyanobacteria, Ruminococcus gnavus: friend or foe for human health, About the Federation of European Microbiological Societies, GLOBAL DISTRIBUTION AND HIGH DIVERSITY OF BATHYARCHAEOTA, DISTRIBUTION PATTERN AND MOLECULAR DETECTION, PHYSIOLOGICAL AND GENOMIC CHARACTERIZATION, ECOLOGICAL FUNCTIONS AND EVOLUTION OF BATHYARCHAEOTA, https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model, Receive exclusive offers and updates from Oxford Academic, Copyright 2023 Federation of European Microbiological Societies.
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