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). Taxonomic classification revealed that between 0.1 and 2% of all classified sequences were assigned to Bathyarchaeota. Considering the ubiquity and frequent predominance of Bathyarchaeota in marine sediments, as well as the high abundance and potential activity of extracellular peptidases that they encode, it has been proposed that Bathyarchaeota may play a previously undiscovered role in protein remineralization in anoxic marine sediments. Specific lipids, exclusively synthesized by certain archaea, can serve as a supplementary biomarker for tracing the existence and abundance of targeted archaeal groups; their isotopic composition can be used to indicate specific carbon acquisition pathways (Schouten, Hopmans and Damste 2013). The ability to use a wide range of substrates for energy conservation and biosynthesis, rather than a single reductive acetyl-CoA pathway, enhances the survival of Bathyarchaeota in energy-limited environments (Lazaretal.2016). Furthermore, in contrast to the consistent vertical distribution of all archaeal lineages in freshwater sediments with almost no abundance changes, the total abundance of all Bathyarchaeota and the fraction of Subgroup-15 increase along with the depths of sediments, with significantly high abundance within the archaeal community (Liuetal.2014). 2. For us, phenotypical and genotypical information on subgroups whose existing patterns have only been sporadically reported still remains elusive and more explicit investigations are lacking. Bathyarchaeota, reflecting its phylogenetic position as deeply branching with Aigarchaeota and Thaumarchaeota, and its prevalence in subsurface sediments (Mengetal.2014). Characteristics of the Bathyarchaeota community in Moreover, the carbonyl branch of the WoodLjungdahl pathway might reduce CO2 into acetyl-CoA. Metabolic potential of Bathyarchaeota and their interactive relationships with other microorganisms. 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). 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). Schematic figure representing major eco-niches of Bathyarchaeota. Bathyarchaeotal subgroups analyzed here acquired an almost complete EmbdenMeyerhof Parnas glycolysis pathway. Growth of sedimentary Bathyarchaeota on lignin as an Furthermore, both BA1 and BA2 lack ATP-synthase, indicating that they are restricted to substrate-level phosphorylation for energy, which was first found in methanogenic archaea (Evansetal.2015). 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. In the case of Subgroup-15, which branched away from other groups, MCG242dF would be associated with a relatively low coverage efficiency in the absence of nucleotide mismatches, but high (above 80%) coverage efficiency with 1 or 2 nucleotide mismatches; similarly, MCG678R would be associated with a limited coverage efficiency in the absence of nucleotide mismatches, but the coverage efficiency increases considerably with 1 or 2 nucleotide mismatches. is bathyarchaeota multicellular. It has been proposed that the deduced last common ancestor was most likely a saline-adapted organism, and the evolutionary progression occurred most likely in the saline-to-freshwater direction, with few environmental transitional events. Ta stands for qPCR annealing temperature, Ta,e stands for annealing and extension temperature of two-step qPCR. (iii) The relatively small 13C signature of the archaeal intact polar lipids in comparison with the archaeal biomass suggests that the C isotopic fractionation during lipid biosynthesis is different from that of typical methylotrophic methanogens (Summons, Franzmann and Nichols 1998). Among these are Subgroups-1 and -8 with high IndVal values in marine sediments, and Subgroups-5 and -11 with high IndVal values in fresh sediments (Filloletal.2016). We also highlighted the unique genomic features and potential adaptation strategies of estuarine archaea, pointing out major unknowns in the field and scope for future research. 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. 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. Their results agree well and reflect the relatively higher bathyarchaeotal fraction in marine sediments with sulfate penetration (>0.15 m below seafloor) (Kuboetal.2012). The concatenated ribosomal protein (RP) alignment contained 12 RPs, and those genomes with <25% RPs were excluded from tree construction. Details of markers refer to Supplementary Table S1 available online. 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). However, after allowing for a single nucleotide mismatch, the coverage efficiency markedly increased, to around 8090%. The production of a putative 4-carboxymuconolactone decarboxylase was evident when the mangrove sediments were supplemented with protocatechuate, further suggesting the capacity of certain bathyarchaeotal members to degrade aromatic compounds (Mengetal.2014). However, in a study investigating the archaeal lipidome in the White Oak River estuary, the presence of the recently discovered butanetriol dibiphytanyl glycerol tetraethers correlated well with bathyarchaeotal abundance along the sediment depth (Meadoretal.2015). ( 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. Beyond methane Bathyarchaeota occupied about 60% of the total archaea in the Jiulong River, China (Li et al. The primer pair MCG242dF/MCG528R may potentially be used for the determination of the bathyarchaeotal community abundance, with relatively high subgroup coverage and specificity in silico; however, experimental tests are needed to confirm this. 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). 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). The potential AOM metabolic capacity of Bathyarchaeota could help to fully address the isotopic relationship between the archaeal biomass and the ambient environmental carbon pools, as follows. The BA2 (Subgroup-8) genome contains MCR-encoding genes and additional genes of typical methane metabolism, like BA1, reflecting a similar methylotrophic methanogenesis activity. The group was termed miscellaneous because of its occurrence in diverse habitats; it is not only abundant in marine sediments but is also widely distributed in terrestrial, freshwater, hot spring, hydrothermal, etc., environments (Kuboetal.2012). Peptidases targeting d-amino acids, which are highly enriched in the peptidoglycan of bacterial cell walls, are encoded as well, indicating that Bathyarchaeota may have acquired the capacity to degrade recalcitrant components of bacterial cell walls, i.e. Bathyarchaeota, a recently proposed archaeal phylum, is globally distributed and highly abundant in anoxic sediments. Furthermore, another study demonstrated that the archaeal communities of the sulfatemethane transition zone at diffusion-controlled sediments of Aarhus Bay (Denmark) contain considerable amounts of Bathyarchaeota; the overall archaeal community structure did not change greatly during the experimentits diversity was lower after 6 months of incubation under heterotrophic conditions, with periodic modest sulfate and acetate additions (Websteretal.2011). pl. The phylum Bathyarchaeota, which has high species and functional diversity, is abundant and widespread in marine sediments. 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). 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). It was proposed that reduced ferredoxin generated by peptide and/or glucose might be used for the reduction of methyl groups on methylated compounds to subsequently generate methane (Evansetal.2015). Bathyarchaeota was the dominant archaeal taxon in the sediment samples from 3400 to 02 (40.67%) and CJ-00a (34.17%), which have the shallowest water Our results provide an overview of the archaeal population, It harbors methyl-coenzyme M reductase (MCR)-encoding genes, and many identified and unidentified methyltransferase-encoding genes for the utilization of various methylated compounds, but lacks most of the genes encoding the subunits of Na+-translocating methyl-H4MPT:coenzyme M methyltransferase, suggesting that the organism does not engage in hydrogenotrophic methanogenesis. A model based on the thermodynamic considerations of chemicals and temperatures may be used to offer a framework linking the distribution of microbial groups and energy landscapes (Amendetal.2011; LaRowe and Amend 2014; Dahleetal.2015). [43] (Figure 4). Callac N, Rommevaux-Jestin C, Rouxel O 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). 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). A successful enrichment, with nearly pure biomass of certain subgroups of Bathyarchaeota, would enable a more efficient investigation of their metabolic capacities using stable isotope-labeled substrates, and establishing a direct link between the genotype and phenotype. Bathyarchaeota are believed to have roles in the carbon cycle in marine systems. The results indicate that the phylum Bathyarchaeota shares a core set of metabolic pathways, including protein degradation, glycolysis, and the reductive acetyl The uptake and breakdown of polymeric hydrocarbons is facilitated by extracellular hydrolases; Bathyarchaeota also acquired the EmbdenMeyerhof Parnas/EntnerDoudoroff glycolysis and gluconeogenesis pathway for the core hydrocarbon utilization metabolism. In the two recent metagenomic bathyarchaeotal binning studies, nearly all the identified bins placed H4MPT as a C1-carrier in the WoodLjungdahl pathway, which is often used by the methanogenic archaea for carbon fixation (Heetal.2016; Lazaretal.2016). their relatively high abundance in the global marine subsurface ecosystem (Kuboetal.2012; Lloydetal.2013), they are also metabolically active in the subsurface sediments across geological time scales. Hallam SJ, Putnam N, Preston CM et al. Barns SM, Delwiche CF, Palmer JD et al. OTUs classified within Bathyarchaeota and Chloroflexi (Dehalococcoidia) showed positive correlation with methane concentrations, sediment depth and oxidation-reduction potential. This was confirmed by a permutational analysis of variance, with salinity as the best explanatory variable for the variance within the bathyarchaeotal community (R2 = 0.04, P < 0.001) (Filloletal.2016). Bathyarchaeota is characterized by high intragroup diversity, with most subgroups showing within-sequence similarity <92% (Kuboetal.2012; Filloletal.2016). PubChem BioAssay. Members of the archaeal phylum Bathyarchaeota are widespread and abundant in the energy-deficient marine subsurface sediments. 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). 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. Genome labels are according to panel (B). Characterization of Bathyarchaeota genomes assembled from Yuetal. To alleviate the nomenclature confusion, we constructed an updated RAxML tree (Fig. Lomstein BA, Langerhuus AT, DHondt S et al. Methanogenic archaea in peatlands The wide availability of buried organic matter in the marine subsurface would favor the heterotrophic feeding of Bathyarchaeota. 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. 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). Genomic and enzymatic evidence for acetogenesis among Inagaki F, Nunoura T, Nakagawa S et al. More recently, Heetal. 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). Bathyarchaeota the most persistent detrital matter in marine sediments (Lomsteinetal.2012; Lloydetal.2013). In some flange subsamples, Bathyarchaeota were even more dominant than ANME; however, compared with the well-studied metabolism of ANME, the exact function of Bathyarchaeota in that ecological setting remains unknown. Biddle JF, Fitz-Gibbon S, Schuster SC et al. Candidatus Bathyarchaeota Click on organism name to get more information. Metabolic versatility of freshwater sedimentary archaea feeding Metabolic pathways of the Metagenomic evidence of sulfate reductase-encoding genes in the upper region of SMTZ of the OPD site 1229 provides more hints to the potential synergistic metabolism of AOM coupled with sulfate reduction (Biddleetal.2008). Archaea Facts for Kids | KidzSearch.com 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 archaeal phylum Bathyarchaeota, which is composed of a large number of diverse lineages, is widespread and abundant in marine sediments. 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). This could be explained by the versatile pathways of organic matter assimilation present in the majority of Bathyarchaeota, reflected by inferences from genomic data. More recently, acetogenesis, a metabolic process deemed to be restricted to the domain bacteria, was also suggested to take place in some lineages of Bathyarchaeota (Heetal.2016; Lazaretal.2016), expanding the metabolic potential of archaea. According to that hypothesis, the proto-mitochondrion bacterium was capable of both respiration and anaerobic H2-producing fermentation; anaerobic syntrophy with respect to H2 brought about a physical association with an H2-dependent host and initiated a symbiotic association with the host; this led to endosymbiosis, after engulfment by the host cell (Martin and Muller 1998; Martinetal.2016). Furthermore, a principal coordinate analysis also clearly separates the bathyarchaeotal community into freshwater and saline sediment groups. Bathyarchaeia occurrence in rich methane sediments from Moreover, with the rapid development and application of 16S rRNA-based high-throughput sequencing techniques for microbial ecological profiling, and 16S rRNA-independent microbial metagenomic profiling that avoids the issue of polymerase chain reaction (PCR) primer bias, a much clearer distribution pattern of diverse bathyarchaeotal subgroups can be expected; at the same time, higher resolution of local physicochemical characteristics will facilitate classification of ecological niches of bathyarchaeotal subgroups into more detailed geochemical categories. Diverse Bathyarchaeotal Lineages Dominate Archaeal In experiments towards cultivating Bathyarchaeota from the White Oak River estuary sediments, the abundance of Bathyarchaeota in control groups (basal medium) and in experimental groups containing various substrate additives and submitted to various culture processing steps were compared (Gagenetal.2013). Considering that the marine subseafloor environment is one of the largest reservoirs of the prokaryotic biomass on Earth, with an estimated microbial abundance of 2.9 1029 cells and harboring ca 9.131.5% of all prokaryotes on Earth (Kallmeyeretal.2012), the predominance and activity of Bathyarchaeota in the marine subsurface sediments indicates that these microbes might play a crucial role in global biogeochemical nutrient cycling. Uncultured archaea in deep marine subsurface sediments: have we caught them all? Several sets of PCR primers and probes have been developed to detect and quantify Bathyarchaeota in natural community (Table 1). The picked genomes are of high completeness (>70%) and good quality (excluding genomes with numerous long breaking parts with N). This study is also a contribution to the Deep Carbon Observatory. Community, Distribution, and Ecological Roles Based on the lineage distribution pattern analysis of the archaeal community of seven major eco-niches, it is also evident that the different evolutionary lineages are habitat-specific, and salinity rather than temperature is the primary driving force of the variation of global archaea distribution, with a similar pattern also evident for the global bacterial distribution (Lozupone and Knight 2007; Auguet, Barberan and Casamayor 2010). 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). (2018) described a predominance of the phylum Bathyarchaeota (now class Bathyarchaeia from phylum Crenarchaeota) in mid-latitude estuaries, Furthermore, the lack of genes for ATPases and membrane-bound electron transport enzymes in the two genomic bins (BA1 and BA2) and the presence of the ion pumping, energy-converting hydrogenase complex (only in BA1), which might allow solute transportation independently of energy-generation mechanisms, suggest that the soluble substrate transportation is solely responsible for energy conservation (Evansetal.2015). 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). 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). WebBathyarchaeota are abundant in sediments, and they may involve in sedimentary organic matter degradation, acetogenesis, and, potentially, methane metabolism, based on genomics. The currently available bathyarchaeotal genomes shared 63.5% similarity on average, indicating a wide phylogenetic diversity at the genome scale (Fig. adj. The in silico tests revealed that primers MCG528, MCG493, MCG528 and MCG732 cover 87, 79, 44 and 27% of sequences of Subgroups-1 to -12 on average, respectively. Genomic characterization and metabolic potentials of Bathyarchaeota. WebArchaea are tiny, simple organisms. Bathyarchaeia occurrence in rich methane sediments Further, based on genomic inferences, Evansetal. However, due to the great diversity of them, there is limited genomic information that accurately encompasses the metabolic potential of the entire archaeal phylum. Following the four treatments, the viable bathyarchaeotal communities mainly comprised Subgroups-4 and -8, thus indicating that these two subgroups could tolerate the initial aerobic conditions (Gagenetal.2013). 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). Y He, et al., Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments. Nat Microbiol 1, 16035 (2016). L Jiang, Y Zheng, J Chen, X Xiao, F Wang, Stratification of achaeal communities in shallow sediments of the Pearl River Estuary, Southern China. Because of the high diversity of Bathyarchaeota and various independent analyses of samples from diverse environments, the nomenclature for this archaeal group in previous reports was very complex. Summary. The Bathyarchaeota formerly known as the Miscellaneous Crenarchaeotal Group is an evolutionarily diverse group of microorganisms found in a wide Td stands for dissociation temperature for RNA slot-bolt. 2). 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). facts about bathyarchaeota The gene for cytoplasmic flavin adenine dinucleotide-containing dehydrogenase (glcD) co-located with hdrD, indicating that BA1 uses lactate to reduce heterodisulfide in methanogenesis. Along with the widespread distribution of Bathyarchaeota, i.e. Among the presently recognized 25 bathyarchaeotal subgroups, eight are delineated as significantly niche-specific based on their marine/freshwater segregation. Fryetal. Currently available bathyarchaeotal genomes (from GenBank, 29 November 2017 updated) with 16S rRNA gene sequences were labeled in the tree. 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). This would be supported by a coupled AOM and syntrophic SRB metabolism, with methane consumed by Bathyarchaeota through reverse acetoclastic methanogenesis with the production of acetate, which is readily oxidized by sulfate in SRB. Liu et al. (B) The dendrogram and genome similarity heatmap based on pairwise OrthoANIu values of 24 bathyarchaeotal genomes (Yoonetal.2017). The reconstructed bathyarchaeotal genomes (except for Subgroup-15) also encode proteins with the ability to import extracellular carbohydrates. Further membrane lipid characterization of enriched or pure bathyarchaeotal cultures will help to validate this discovery. They also acquired some subunits of coenzyme F420 hydrogenase; this enzyme generates reduced ferredoxin, with hydrogen as the electron donor, as an alternative to MvhADG in many Methanomicrobiales (Thaueretal.2008; Lazaretal.2016; Sousaetal.2016). 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). 2). No bathyarchaeotal species have as yet been successfully cultured in pure cultures, despite their widespread distribution in the marine, terrestrial and limnic environments (Kuboetal.2012), which hampers their direct physiological characterization. In this study, the abundance and Considering the bathyarchaeotal community structure, depth is the first variable responsible for the high degree of absolute subgroup separation, followed by sulfide concentration (reflecting the redox conditions), which is responsible for a low degree of subgroup separation (Lazaretal.2015). Interestingly, one of the highly abundant McrA subunits of Ca. 4) (Evansetal.2015; Heetal.2016; Lazaretal.2016). These physiological, ecological and evolutionary features place Bathyarchaeota in the spotlight of current microbial ecology studies, encouraging further explorations of their impact on global and local biogeochemical carbon cycling. (2016) demonstrated that half of the bathyarchaeotal genomes encode a set of phosphate acetyltransferase (Pta) and acetate kinase (Ack) for acetate production or assimilation, usually observed in bacteria. Kallmeyer J, Pockalny R, Adhikari RR et al. 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). Study sites and sampling The members of Bathyarchaeota were positively and strongly correlated especially with the acetoclastic Methanosaeta; however, the second most abundant archaeal group, MG-I (subordinate to Thaumarchaeota) is negatively correlated with other groups, probably indicating segregation corresponding to two distinct lifestyles in this case (Liuetal.2014). Thaumarchaeota MG-I was present in the 12C-DNA library in the corresponding zone but was not detected in the 13C-DNA library, suggesting that these microbes are not able to use 13C-acetate (Websteretal.2010). 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). 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).