To increase the permeability of the cell wall and obtain a good amplification signal, a 10-min 0.01 M HCl treatment may be employed (Kuboetal.2012). It has been suggested that Bathyarchaeota is one of the cosmopolitan groups frequently detected in the freshwater and marine sediments (68% of all sediments analyzed), accounting for a large proportion of the sediment microbial communities (average 36 22%) (Filloletal.2016). The Bathyarchaeota formerly known as the Miscellaneous Crenarchaeotal Group is an evolutionarily diverse group of microorganisms found in a wide 3A). The major bathyarchaeotal community comprises Subgroups-1, -8, -12 and -15, and is relatively stable during the hypoxic/oxic change, thus being independent of the sedimentary chemistry change, such as manganese and iron redox cycling during different seasons (Devereuxetal.2015). Details of markers refer to Supplementary Table S1 available online. The distinct bathyarchaeotal subgroups diverged to adapt to marine and freshwater environments. Consequently, CO2 appears to be the only electron acceptor mediating AOM, like in a reverse acetoclastic methanogenesis (Hallametal.2004; Wangetal.2014). Taxonomic classification revealed that between 0.1 and 2% of all classified sequences were assigned to Bathyarchaeota. Jacquemet A, Barbeau J, Lemiegre L et al. Species abundance distribution analysis indicates that Bathyarchaeota is one of the persistent and abundant core lineages of the sediment archaeal communities, showing, to some extent, habitat-specific distribution (Filloletal.2016). In a recent study exploring the stratified distribution of archaeal groups in a tropical water column, the analysis of archaeal 16S rRNA community distribution was combined with isoprenoid glycerol dialkyl glycerol tetraether lipid abundance information to reveal that glycerol dibiphytanyl glycerol tetraether lacking the cyclopentane rings [GDGT(0)] likely originated from the Bathyarchaeota-enriched layer in the water column (Bucklesetal.2013). [43] (Figure 4). Evans PN, Parks DH, Chadwick GL et al. Thus, this systematic nomenclature based on clear monophyletic or phylogenetically stable subgroups not only facilitates further sequence assignment, but also provides useful information for understanding the evolutionary separation of specific lineages subjected to natural selection (Filloletal.2016). However, because of the high intragroup diversity and potential heterogeneous metabolic properties and adaptive strategies within the bathyarchaeotal subgroups, investigation into the subgroup distribution patterns at a fine-sorted phylotype level was recommended. 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 Ta stands for qPCR annealing temperature, Ta,e stands for annealing and extension temperature of two-step qPCR. The discovery of BchG of archaeal origin in the genomic content of Bathyarchaeota also suggests that an archaeon-based photosynthetic pathway might exist in nature, and that photosynthesis might have evolved before the divergence of bacteria and archaea (Mengetal.2009). Here we reported the abundance of Bathyarchaeota members across different ecosystems and their correlation with environmental factors by constructing 16S However, due to the great diversity of them, there is limited genomic information that accurately encompasses the metabolic potential of the entire archaeal phylum. Genomic fragments of the fosmid clone 75G8 harbor a putative methyl-accepting chemotaxis protein- and 4-carboxymuconolactone decarboxylase-encoding genes, suggesting that this bathyarchaeotal member (Subgroup-8) is able to utilize aromatic compounds. 4) (Evansetal.2015; Heetal.2016; Lazaretal.2016). Amend JP, McCollom TM, Hentscher M et al. 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). Lineage (full): cellular organisms; Archaea; TACK group. A pair of primers (Bathy-442F/Bathy-644R) was recently designed to target Subgroups-15 and -17; the in silico primer testing indicates that Bathy-442F can also adequately cover Subgroups-2, -4, -9 and -14, with Bathy-644R covering nearly all subgroups, except for Subgroups-6 and -11 (Yuetal.2017). Bathyarchaeota occupied about 60% of the total archaea in the Jiulong River, China (Li et al. 2). The assignment of bathyarchaeotal subgroups was made based on either having been formerly defined or being monophyletic, using both distance and maximum-likelihood estimations (Kuboetal.2012). JCYJ20170818091727570). On the other hand, the subgroups MCG-18 and MCG-19 were also named in Fillol et al.s research (Filloletal.2016). To cover all bathyarchaeotal subgroups that are characterized by high intragroup diversity while retaining bathyarchaeotal sequence specificity is necessary but challenging. 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. A recent study found that the refractory aromatic polymer lignin stimulated the growth of Bathyarchaeota (Subgroup-8) and they incorporated CO2 as a carbon source autotrophically and utilized lignin as an energy source (Yuetal.2018). Given the substrate specificity of this MCR type in utilizing butane instead of methane, and amino acid divergence of this MCR type from its methane metabolizing related counterparts, it is possible that the MCR clusters in some members of Bathyarchaeota are responsible for butane oxidation instead of methane metabolism (Laso-Prezetal.2016). The wide availability of buried organic matter in the marine subsurface would favor the heterotrophic feeding of Bathyarchaeota. 2017KZDXM071), and the Science and Technology Innovation Committee of Shenzhen (Grant No. 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 < with 12C-acetate added); this indicated that the acetate might participate in microbial biosynthesis rather than being used for energy production (Naetal.2015). This is the first ever genomic evidence for homoacetogenesis, the ability to solely utilize CO2 and H2 to generate acetate, in an archaeal genome and of distinct archaeal phylogenetic origin other than that of Bacteria (Heetal.2016). Metabolic pathways of the Along with the widespread distribution of Bathyarchaeota, i.e. Gene arrangement in these two fosmid clones, together with the previously recovered bathyarchaeotal fosmid sequences, confirmed low collinearity with other known archaeal genomes. Combinations of MCG242dF with MCG678R or MCG732R were recommended for targeting relatively long 16S rRNA gene fragments to obtain more phylogenetic information; these might be used in clone library construction or for denaturing gradient gel electrophoresis-based community fingerprinting analysis. Sequences longer than 940 bp were first used to construct the backbone of the tree, and additional sequences were then added without altering the general tree topology. (2016), it appears that these microbes rely on the acetyl-CoA synthetase (Acd) to generate acetate (Heetal.2016). 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). S. butanivorans forms a distinct cluster with those of Bathyarchaeota origin, separately from other methanogens and methanotrophs (Laso-Prezetal.2016). Recent genomic evidence suggests that Bathyarchaeota might potentially be involved in methane metabolism, a property that had only been confirmed to date in the Euryarchaeota domain (Evansetal.2015; Lloyd 2015). Members of Bathyarchaeota are able to use CO2 and H2 from natural sources and fermentation products to fuel acetogenesis (Heetal.2016; Martinetal.2016). The picked genomes are of high completeness (>70%) and good quality (excluding genomes with numerous long breaking parts with N). 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. Ancestral state reconstruction was used to estimate the diversification of bathyarchaeotal lineages previously subjected to the saline/freshwater transition. More importantly, the first-ever bacteriochlorophyll a synthase (BchG) of archaeal origin was identified in the archaeal portion of the genomic fragment, and its function confirmed by producing BchG in a heterologous expression system (Mengetal.2009). The syntrophic relationship between Bathyarchaeota and SRB would be similar to the anaerobic methane-oxidizing archaea (ANME)/SRB consortium, and acetate would be maintained at a low level as a transient intermediate (Boetiusetal.2000; Hinrichs and Boetius 2002). The archaeal phylum Bathyarchaeota, which is composed of a large number of diverse lineages, is widespread and abundant in marine sediments.
Archaea While Subgroups-18 and -19 were named to be consistent with subgroups MCG-18 and MCG-19 as proposed in two previous reports (Lazaretal.2015; Filloletal.2016), Subgroup-20 was renamed to replace the subgroup MCG-19 in Fillol et al.s tree (Filloletal.2016). 2. For full access to this pdf, sign in to an existing account, or purchase an annual subscription. 2012 ). Based on the genomic evidence, the authors concluded that some lineages of Bathyarchaeota are similar to bona fide bacterial homoacetogens, with pathways for acetogenesis and fermentative utilization of a variety of organic substrates (Heetal.2016). 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. The possibility of the replacement of the AOM function of ANME by Bathyarchaeota was also suggested by a microbial community composition in a study of the microbial colonization within an artificial micro-niche, basaltic glass imposed by hydrothermal conditions (Callacetal.2013). The concatenated ribosomal protein (RP) alignment contained 12 RPs, and those genomes with <25% RPs were excluded from tree construction. 2). 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). The identification of key genes of the MCR complex (mcrA, mcrB and mcrG), and the presence of hdrABC and mcvhADG responsible for the cycling of coenzyme M (CoM) and coenzyme B (CoB), suggest their role in the methanogenesis machinery that mediates the CoM-S-S-CoB cycling, similar to Euryarchaeota methanogens (Evansetal.2015). Bathyarchaeota possesss a bona fide homoacetogenesis pathway of archaeal phylogenetic origin, as confirmed by functional studies, indicating a distinct evolutionary pathway of acetogenesis in archaea, different from horizontal transfer from bacteria (Heetal.2016). Fosmid clone 37F10 containing a genome fragment originating from a bathyarchaeotal member was isolated from a metagenomic library constructed from Pearl River sediment samples (Mengetal.2009); its G + C content indicated that this genomic fragment had two portions: an archaeon-like portion (42.2%) and a bacterium-like portion (60.1%) (Mengetal.2009; Lietal.2012). Oxford University Press is a department of the University of Oxford. Bathyarchaeota was the most abundant archaeal phylum in most samples, accounting for 13.8164.14% of archaeal sequences (Fig. 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). Heetal. The groups of B24 and B25 (Heetal.2016) were added into the tree representing Subgroups-21 and -22, respectively. BA1 (Subgroup-3) genome contains many genes of the reductive acetyl-CoA (WoodLjungdahl) pathway and key genes of the methane metabolism pathway. Newberry CJ, Webster G, Cragg BA et al. In a recent global evaluation of the archaeal clone libraries from various terrestrial environmental settings, permutational analysis that tested the relationship between Bathyarchaeota and environmental factors suggested that salinity, total organic carbon and temperature are the most influential factors impacting community distribution across different terrestrial habitats (Xiangetal.2017). The three methods described above may be used for the quantification of bathyarchaeotal abundance based on DNA and RNA targets. 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). 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). The Bathyarchaeota formerly known as the Miscellaneous Crenarchaeotal Group is an evolutionarily diverse group of microorganisms found in a wide range of A group called Peat MCG (pMCG) (Xiangetal.2017) was also listed on the tree; however, because there was only one represented sequence after dereplication at 90% similarity of all bathyarchaeotal 16S rRNA gene sequences, we did not list pMCG as a separate subgroup in this tree (Fig.
Genomic and enzymatic evidence for acetogenesis among Methane metabolism in the archaeal phylum Subgroup-5 thrives in the euxinic bottom water layer, characterized as anoxic and sulfide-rich, with accumulated inorganic and organic reduced compounds; Subgroup-6 is a group of generalists that are adapted to both planktonic and sediment habitats with a wide range of sulfidic conditions. The phylum Bathyarchaeota, which has high species and functional diversity, is abundant and widespread in marine sediments. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide, This PDF is available to Subscribers Only. Subgroup-6 genome was reconstructed from the surficial sulfate reduction zone, harboring genes encoding enzymes with predicted functions in the degradation of extracellular plant-derived mono- and polysaccharides. 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). The currently available bathyarchaeotal genomes shared 63.5% similarity on average, indicating a wide phylogenetic diversity at the genome scale (Fig. No methane metabolism genes were recovered from bathyarchaeotal genomic bins or any contigs from the WOR estuarine sediments, in contrast to an earlier study (Evansetal.2015). Bathy-15 (36.4% of all archaea), Introduction. 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. Because of the universal distribution and predominance of Bathyarchaeota, not only in the marine sediments but also in terrestrial sediments and various other eco-niches, and because of their versatile metabolism (including acetogenesis, methane metabolism, and dissimilatory nitrate and sulfate reduction) and potential interactions with ANME archaea, acetoclastic methanogens and heterotrophic bacteria, the ecological importance of this group of generalists has entered the limelight and needs further exploration. 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.