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Commonly used 16S rRNA gene primers do not detect the full range of archaeal diversity present in the vertebrate gut. As a result, several questions regarding the archaeal component of the gut microbiota remain, including which Archaea are host-associated, the specificities of such associations and the major factors influencing archaeal diversity. Using 16S rRNA gene amplicon sequencing with primers that specifically target Archaea, we obtained sufficient sequence data from 185 gastrointestinal samples collected from 110 vertebrate species that span five taxonomic classes (Mammalia, Aves, Reptilia, Amphibia and Actinopterygii), of which the majority were wild. We provide evidence for previously undescribed Archaea–host associations, including Bathyarchaeia and Methanothermobacter, the latter of which was prevalent among Aves and relatively abundant in species with higher body temperatures, although this association could not be decoupled from host phylogeny. Host phylogeny explained archaeal diversity more strongly than diet, while specific taxa were associated with both factors, and cophylogeny was significant and strongest for mammalian herbivores. Methanobacteria was the only class predicted to be present in the last common ancestors of mammals and all host species. Further analysis indicated that Archaea–Bacteria interactions have a limited effect on archaeal diversity. These findings expand our current understanding of Archaea–vertebrate associations., Analysis of the archaeal gut microbiota of 110 vertebrate species spanning five taxonomic classes revealed that host phylogeny could explain archaeal diversity.

Metagenome assembled genomes (MAGs) and single amplified genomes (SAGs) affiliated with two distinct Methanobacterium lineages were recovered from subsurface fracture waters of the Samail Ophiolite, Sultanate of Oman. Lineage Type I was abundant in waters with circumneutral pH, whereas lineage Type II was abundant in hydrogen rich, hyperalkaline waters. Type I encoded proteins to couple hydrogen oxidation to CO2 reduction, typical of hydrogenotrophic methanogens. Surprisingly, Type II, which branched from the Type I lineage, lacked homologs of two key oxidative [NiFe]-hydrogenases. These functions were presumably replaced by formate dehydrogenases that oxidize formate to yield reductant and cytoplasmic CO2 via a pathway that was unique among characterized Methanobacteria, allowing cells to overcome CO2/oxidant limitation in high pH waters. This prediction was supported by microcosm-based radiotracer experiments that showed significant biological methane generation from formate, but not bicarbonate, in waters where the Type II lineage was detected in highest relative abundance. Phylogenetic analyses and variability in gene content suggested that recent and ongoing diversification of the Type II lineage was enabled by gene transfer, loss, and transposition. These data indicate that selection imposed by CO2/oxidant availability drove recent methanogen diversification into hyperalkaline waters that are heavily impacted by serpentinization.

The previously uncharted Afifi brine pool was discovered in the eastern shelf of the southern Red Sea. It is the shallowest brine basin yet reported in the Red Sea (depth range: 353.0 to 400.5 m). It presents a highly saline (228 g/L), thalassohaline, cold (23.3 °C), anoxic brine, inhabited by the bacterial classes KB1, Bacteroidia and Clostridia and the archaeal classes Methanobacteria and Deep Sea Euryarcheota Group. Functional assignments deduced from the taxonomy indicate methanogenesis and sulfur respiration to be important metabolic processes in this environment. The Afifi brine was remarkably enriched in dissolved inorganic carbon due to microbial respiration and in dissolved nitrogen, derived from anammox processes and denitrification, according to high δN values (+6.88‰, AIR). The Afifi brine show a linear increase in δO and δD relative to seawater that differs from the others Red Sea brine pools, indicating a non-hydrothermal origin, compatible with enrichment in evaporitic environments. Afifi brine was probably formed by venting of fossil connate waters from the evaporitic sediments beneath the seafloor, with a possible contribution from the dehydration of gypsum to anhydrite. Such origin is unique among the known Red Sea brine pools., This research was funded with King Abdullah University of Science and Technology funding through baseline funding and Red Sea Research Center competitive fund to C.M.D. and D.D. We thank J.C. Santamarina, M. Terzariol, K. Pigeon, A. Granados and J.M. Arrieta, and the crew of R/V Thuwal for their help.

Mixed microbial cultures have become a preferred choice of biocatalyst for chain elongation systems due to their ability to convert complex substrates into medium-chain carboxylates. However, the complexity of the effects of process parameters on the microbial metabolic networks is a drawback that makes the task of optimizing product selectivity challenging. Here, we studied the effects of small air contaminations on the microbial community dynamics and the product formation in anaerobic bioreactors fed with lactate, acetate and H2/CO2. Two stirred tank reactors and two bubble column reactors were operated with H2/CO2 gas recirculation for 139 and 116 days, respectively, at pH 6.0 and 32°C with a hydraulic retention time of 14 days. One reactor of each type had periods with air contamination (between 97 ± 28 and 474 ± 33 mL O2 L−1 d−1, lasting from 4 to 32 days), while the control reactors were kept anoxic. During air contamination, production of n-caproate and CH4 was strongly inhibited, whereas no clear effect on n-butyrate production was observed. In a period with detectable O2 concentrations that went up to 18%, facultative anaerobes of the genus Rummeliibacillus became predominant and only n-butyrate was produced. However, at low air contamination rates and with O2 below the detection level, Coriobacteriia and Actinobacteria gained a competitive advantage over Clostridia and Methanobacteria, and propionate production rates increased to 0.8–1.8 mmol L−1 d−1 depending on the reactor (control reactors 0.1–0.8 mmol L−1 d−1). Moreover, i-butyrate production was observed, but only when Methanobacteria abundances were low and, consequently, H2 availability was high. After air contamination stopped completely, production of n-caproate and CH4 recovered, with n-caproate production rates of 1.4–1.8 mmol L−1 d−1 (control 0.7–2.1 mmol L−1 d−1). The results underline the importance of keeping strictly anaerobic conditions in fermenters when consistent n-caproate production is the goal. Beyond that, micro-aeration should be further tested as a controllable process parameter to shape the reactor microbiome. When odd-chain carboxylates are desired, further studies can develop strategies for their targeted production by applying micro-aerobic conditions.

International audience; Coastal sediments are considered to be final receptacles for organic and inorganic contaminants. Characterizing those sediments and assessing their biodegradation potential have become a great challenge in recent years. In this study, the chemical composition, including the content in polycyclic aromatic hydrocarbons, the microbial community abundance and diversity (using culture-independent approaches targeting 16S rRNA genes), and the aerobic/anaerobic biodegradation potential of coastal sediments collected in the Sfax coastal area (Gulf of Gabès, Southern Mediterranean Sea) were investigated. The highest concentration of total polycyclic aromatic hydrocarbons (981 µg kg−1 dw) was recorded in Sidi Mansour harbor sediment, emphasized pyrogenic and petrogenic hydrocarbon sources. Organic matter, including total organic carbon, and the ultimate aerobic biodegradability, with 30% as the highest value in Sidi Salem channel sediment, were in a positive accordance with bacterial communities assigned within Actinobacteria, Clostridia and Flavobacteria classes. The correlation noticed between Thermocladium and Thermogladius genera and sulfate content explained that Sidi Mansour and PK4 sediments are located in terrestrial acid–sulfate areas. The highest cumulative methane produced with Marseille inoculum and Tunisian inoculum was recorded in Sidi Salem sediment and strongly correlated with methanogens among Methanobacteria, Methanococci and Methanomicobia classes showing the presence of industrial and municipal sources. The bioavailability of low and moderate polycyclic aromatic hydrocarbons in the current study may explain the occurrence of Methanobacterium which positively correlated with the anaerobic biodegradability using Tunisian inoculum with 50% as the highest value in Sidi Mansour sediment.

To date, there is an urgent need for implementing practical strategies to reduce CH4 emissions from ruminants. Lovastatin (Lv) is a specific inhibitor of methanogenic archaea. Due to the high cost of pure Lv, solid-state fermentation might be an economical bioprocess to produce Lv and facilitate its use in ruminant nutrition. The goal of this work was to assess the effects of supplementing fermented oat straw as a lovastatin carrier (FOS) to a high-grain ration on in vitro CH4 inhibition and rumen microbiota in beef cattle. The experimental design of in vitro rumen fermentation was completely randomized with four concentrations of Lv in the diet mixture. The supplementation with FOS to give Lv concentration of 100 and 150 mg L−1 in the ruminal fermentation medium significantly inhibited methanogenesis at similar levels. This suggested that less than 20% of FOS was required in the ration to achieve up to 38% of CH4 mitigation without affecting the chemical composition and nutritional value of the ration. Short-chain fatty acid (SCFA) production and profile showed that only the treatments with Lv at 100 and 150 mg L−1 decreased the concentration of total SCFAs; the molar ratio of propionate significantly increased with respect to that of the control. Treatment with Lv at 150 mg L−1 did not result in significant differences in the alpha and beta diversity indices compared to the control. However, significant changes in the relative abundance of some microorganisms were detected, such as an increase in Ruminococcus and a decrease in Prevotella. The predominant 99%+ MA in all controls, treatment, and inocula samples belonged to the Methanobrevibacter genus and very small (negligible) unclassified Methanobacterium genus (Euryarchaeota phylum). Interestingly, the reduction of relative abundance of MA was 39.17%, very close to the percent reduction of CH4 production, 38%. Our data showed that there was a parallel and similar percent decrease of both CH4 production and relative abundance of the predominant MA in our experiment, although the statistical significance was not complete. Finally, our results hold promise for significantly decreasing ruminal CH4 by 38%. Thus, our work is one step toward the sustainable management of the livestock sector.

Biogas production through co-digestion of second and third generation substrates is an environmentally sustainable approach. Green willow biomass, chicken manure waste and microalgae biomass substrates were combined in the anaerobic digestion experiments. Biochemical methane potential test showed that biogas yields of co-digestions were significantly higher compared to the yield when energy willow was the sole substrate. To scale up the experiment continuous stirred-tank reactors (CSRTs) are employed, digestion parameters are monitored. Furthermore, genome-centric metagenomics approach was employed to gain functional insight into the complex anaerobic decomposing process. This revealed the importance of Firmicutes, Actinobacteria, Proteobacteria and Bacteroidetes phyla as major bacterial participants, while Methanomicrobia and Methanobacteria represented the archaeal constituents of the communities. The bacterial phyla were shown to perform the carbohydrate hydrolysis. Among the representatives of long-chain carbohydrate hydrolysing microbes Bin_61: Clostridia is newly identified metagenome assembled genome (MAG) and Bin_13: DTU010 sp900018335 is common and abundant in all CSTRs. Methanogenesis was linked to the slow-growing members of the community, where hydrogenotrophic methanogen species Methanoculleus (Bin_10) and Methanobacterium (Bin_4) predominate. A sensitive balance between H2 producers and consumers was shown to be critical for stable biomethane production and efficient waste biodegradation.

BACKGROUND: The present study compared the performance and capability of thermophilic–mesophilic, temperature‐phased anaerobic digestion (TPAD) of wastewater sludge at 45 and 55 °C in terms of rate of hydrolysis and methanogenesis at two point interval times – December and January – with operational conditions kept constant (total solid content 6.5%, solids retention time 12.5 days). RESULTS: The reduction of volatile solids (VS) was 77% at 45 °C TPAD‐1 and 72% at 55 °C TPAD‐II. The accumulation of ammonia and volatile fatty acids (VFAs; propionic acid) were observed to be below the inhibitory range (>3000 mg L⁻¹), whereas the methane (CH₄) production (45 °C, 3.55 ± 0.47 L CH₄ L⁻¹ day⁻¹; 35 °C, 1.44 ± 0.12 L CH₄ L⁻¹ day⁻¹) remained considerably higher in TPAD‐I than TPAD‐II. Furthermore, the TPAD‐II system suffered from certain degree of instability due to high level of total VFAs (6087 ± 1578 mg L⁻¹), low buffering capacity, increased level of total NH₃ (2982 ± 219 mg L⁻¹) and free NH₃ (246 ± 25 mg L⁻¹), and relatively reduced CH₄ production (1.69 ± 0.1 L L⁻¹ day). The bacterial and archaeal population of the TPADs investigated by 454 pyrosequencing and Illumina sequencing showed, in both TPAD systems, a bacterial community dominated by Firmicutes, followed by Bacteriodetes, Proteobacteria, Synergistetes and Actiniobacteria. The archaeal community was dominated by Methanimicrobia (74–84% Methanosarcina) and Methanobacteria (15–27% Methanobacterium). A progression from genus Clostridium to Coprothermobacter and Tepidanaerobacter, and Methanocarcina to Methanothermobacter and Methanobacterium was observed in TPAD‐II. CONCLUSIONS: This study proved the processes driving the dynamics of key microbial population and its correlation with hydrolytic functionality of TPAD systems. © 2019 Society of Chemical Industry

The archaeal composition of permafrost samples taken during drilling of frozen marine sediments in the area of the Barentsburg coal mine on the east coast of Gronfjord Bay of Western Spitsbergen has been studied. The study was based on the analysis of the V4 region of the 16S rRNA gene, carried out using next generation sequencing. This is the second part of the work dedicated to the prokaryotic composition of the Western Spitsbergen, the fi rst part was devoted to the domain of Bacteria. The general phyla of the the Archaea domain were Euryarchaeota, Bathyarchaeota, Thaumarchaeota and Asgardarchaeota. As a result of phylogenetic analysis of the dominant operational taxonomic units, representatives of methanogenic methane- and ammonium-oxidizing archaea, as well as heterotrophic archaea were found. Methanobacteria class of methanogenic archaea was found in the controversial genesis, while methane-oxidizing archaea of the Methanomicrobia class of Methanosarcinales order were found in the marine permafrost of Cape Finneset: ANME-2a, -2b group was found in layers 8.6 and 11.7 m, and a group ANME-2d (Candidatus Methanoperedens) – in a layer of 6.5 m. Ammonium-oxidizing archaea of the phylum Thaumarchaeota was present in all types of permafrost, while Nitrososphaerales was detected in controversial genesis permafrost, and the order-Nitrosopumilales in the marine permafrost or controversial genesis ones. Representatives of phylum Bathyarchaeota were found in the stratigraphicly most ancient samples under this study. Superphylum Asgardarchaeota was met exclusively in the layers of permafrost with marine genesis and was represented by phyla Lokiarchaeota, Thorarchaeota and another group belonging to this superphylum that was not identified by us. The presence in the marine permafrost terrace of Cape Finneset at 11.7 m depth of methane, ethylene and ethane, as well as the composition of the archaeal community gives this layer to assume in it the presence of microbiological processes of the anaerobic oxidation of methane, probably received from Tertiary deposits before freezing. The results obtained are represented the permafrost of Spitsbergen as a rich archive of genetic information of little studied prokaryotic groups.

Anaerobic bacteria are known to produce neurotoxic methylmercury [MeHg] when elemental mercury [Hg(0)] is provided as the sole mercury source. In this study, we examined the formation of MeHg in anaerobic incubations of sediment collected from the San Jacinto River estuary (Texas, USA) amended with aqueous Hg(0) to investigate the microbial communities involved in the conversion of Hg(0) to MeHg. The results show that the addition of the methanogen inhibitor 2-bromoethanesulfonate (BES) significantly decreased MeHg production. The mercury methylation gene, hgcA, was detected in these sediments using archaeal specific primers, and 16S rRNA sequencing showed that a member of the Methanosarcinaceae family of methanogens was active. These results suggest that methanogenic archaea play an underappreciated role in the production of MeHg in estuarine sediments contaminated with Hg(0).

In addition to inhabiting extreme territories, Archaea are widely distributed in common environments spanning from terrestrial to aquatic environments. This study investigated and compared archaeal community structures from three different habitats (representing distinct environments): agriculture soils (from farming system trials FST, PA, United States), freshwater biofilms (from White Clay Creek, PA, United States), and estuary water (Chesapeake Bay, United States). High-throughput sequencing of 16S rRNA genes indicated that Thaumarchaeota, Euryarchaeota, Nanoarchaeota, Crenarchaeota, and Diapherotrites were the commonly found dominant phyla across these three environments. Similar to Bacteria, distinct community structure and distribution patterns for Archaea were observed in soils vs. freshwater vs. estuary. However, the abundance, richness, evenness, and diversity of archaeal communities were significantly greater in soils than it was in freshwater and estuarine environments. Indicator species (or amplicon sequence variants, ASVs) were identified from different nitrogen and carbon cycling archaeal groups in soils (Nitrososphaerales, Nitrosotaleales, Nitrosopumilales, Methanomassiliicoccales, Lainarchaeales), freshwater biofilms (Methanobacteria, Nitrososphaerales) and Chesapeake Bay (Marine Group II, Nitrosopumilales), suggesting the habitat-specificity of their biogeochemical contributions to different environments. Distinct functional aspects of Archaea were also confirmed by functional predictions (PICRUSt2 analysis). Further, co-occurrence network analysis indicated that only soil Archaea formed stable modules. Keystone species (ASVs) were identified mainly from Methanomassiliicoccales, Nitrososphaerales, Nitrosopumilales. Overall, these results indicate a strong habitat-dependent distribution of Archaea and their functional partitions within the local environments.

Substantial amounts of topsoil organic matter (OM) in Arctic Cryosols have been translocated by the process of cryoturbation into deeper soil horizons (cryoOM), reducing its decomposition. Recent Arctic warming deepens the Cryosols´ active layer, making more topsoil and cryoOM carbon accessible for microbial transformation. To quantify bacteria, archaea and selected microbial groups (methanogens – mcrA gene and diazotrophs – nifH gene) and to investigate bacterial and archaeal diversity, we collected 83 soil samples from four different soil horizons of three distinct tundra types located in Qikiqtaruk (Hershel Island, Western Canada). In general, the abundance of bacteria and diazotrophs decreased from topsoil to permafrost, but not for cryoOM. No such difference was observed for archaea and methanogens. CryoOM was enriched with oligotrophic (slow-growing microorganism) taxa capable of recalcitrant OM degradation. We found distinct microbial patterns in each tundra type: topsoil from wet-polygonal tundra had the lowest abundance of bacteria and diazotrophs, but the highest abundance of methanogens. Wet-polygonal tundra, therefore, represented a hotspot for methanogenesis. Oligotrophic and copiotrophic (fast-growing microorganism) genera of methanogens and diazotrophs were distinctly distributed in topsoil and cryoOM, resulting in different rates of nitrogen flux into these horizons affecting OM vulnerability and potential CO2 and CH4 release.

Prebiotic fermentation in the gut often leads to the coproduction of short-chain fatty acids (SCFAs) and gases. While excess gas production can be a potential problem for those with functional gut disorders, gas production is rarely considered during prebiotic design. In this study, we combined the use of theoretical models and an ex vivo experimental platform to illustrate that both the chemical composition of the prebiotic and the community composition of the human gut microbiota can affect the volume and content of gas production during prebiotic fermentation. Specifically, more prevalent metabolic processes such as hydrogen production were strongly affected by the oxidation state of the probiotic, while rare metabolisms such as methane production were less affected by the chemical nature of the substrate and entirely dependent on the presence of Methanobacteria in the microbiota., Prebiotics confer benefits to human health, often by promoting the growth of gut bacteria that produce metabolites valuable to the human body, such as short-chain fatty acids (SCFAs). While prebiotic selection has strongly focused on maximizing the production of SCFAs, less attention has been paid to gases, a by-product of SCFA production that also has physiological effects on the human body. Here, we investigate how the content and volume of gas production by human gut microbiota are affected by the chemical composition of the prebiotic and the community composition of the microbiota. We first constructed a linear system model based on mass and electron balance and compared the theoretical product ranges of two prebiotics, inulin and pectin. Modeling shows that pectin is more restricted in product space, with less potential for H2 but more potential for CO2 production. An ex vivo experimental system showed pectin degradation produced significantly less H2 than inulin, but CO2 production fell outside the theoretical product range, suggesting fermentation of fecal debris. Microbial community composition also impacted results: methane production was dependent on the presence of Methanobacteria, while interindividual differences in H2 production during inulin degradation were driven by a Lachnospiraceae taxon. Overall, these results suggest that both the chemistry of the prebiotic and the composition of the microbiota are relevant to gas production. Metabolic processes that are relatively prevalent in the microbiome, such as H2 production, will depend more on substrate, while rare metabolisms such as methanogenesis depend more strongly on microbiome composition.

Methanogenesis is the final step in the anaerobic degradation of organic matter. The most important substrates of methanogens are hydrogen plus carbon dioxide and acetate, but also the use of methanol, methylated amines, and aromatic methoxy groups appears to be more widespread than originally thought. Except for most members of the family Methanosarcinaceae, all methylotrophic methanogens require external hydrogen as reductant and therefore compete with hydrogenotrophic methanogens for this common substrate. Since methanogenesis from carbon dioxide consumes four molecules of hydrogen per molecule of methane, whereas methanogenesis from methanol requires only one, methyl-reducing methanogens should have an energetic advantage over hydrogenotrophic methanogens at low hydrogen partial pressures. However, experimental data on their hydrogen threshold is scarce and suffers from relatively high detection limits. Here, we show that the methyl-reducing methanogens Methanosphaera stadtmanae (Methanobacteriales), Methanimicrococcus blatticola (Methanosarcinales), and Methanomassiliicoccus luminyensis (Methanomassiliicoccales) consume hydrogen to partial pressures, Based on their extremely low hydrogen threshold, methylotrophic methanogens (MM) should always outcompete hydrogenotrophic methanogens (HM) for hydrogen, provided that methyl groups are available in sufficient amounts.

Methanogenesis, a biological process mediated by complex microbial communities, has attracted great attention due to its contribution to global warming and potential in biotechnological applications. The current study unveiled the core microbial methanogenic metabolisms in anaerobic vessel ecosystems by applying combined genome-centric metagenomics and metatranscriptomics. Here, we demonstrate that an enriched natural system, fueled only with acetate, could support a bacteria-dominated microbiota employing a multi-trophic methanogenic process. Moreover, significant changes, in terms of microbial structure and function, were recorded after the system was supplemented with additional H2. Methanosarcina thermophila, the predominant methanogen prior to H2 addition, simultaneously performed acetoclastic, hydrogenotrophic, and methylotrophic methanogenesis. The methanogenic pattern changed after the addition of H2, which immediately stimulated Methanomicrobia-activity and was followed by a slow enrichment of Methanobacteria members. Interestingly, the essential genes involved in the Wood-Ljungdahl pathway were not expressed in bacterial members. The high expression of a glycine cleavage system indicated the activation of alternative metabolic pathways for acetate metabolism, which were reconstructed in the most abundant bacterial genomes. Moreover, as evidenced by predicted auxotrophies, we propose that specific microbes of the community were forming symbiotic relationships, thus reducing the biosynthetic burden of individual members. These results provide new information that will facilitate future microbial ecology studies of interspecies competition and symbiosis in methanogenic niches.

International audience; The relevant microorganims driving efficiency changes in anaerobic digestion of phenol remains uncertain. In this study correlations were established between microbial population and the process performance in an anaerobic sequencing batch reactor (ASBR) treating increasing concentrations of phenol (from 120 to 1200 mg L −1). Sludge samples were taken at different operational stages and microbial community dynamics was analyzed by 16S rRNA sequencing. In addition, bamA gene was quantified in order to evaluate the dynamics of anaerobic aromatic degraders. The microbial community was dominated by Anaerolineae, Bacteroidia, Clostridia, and Methanobacteria classes. Correlation analysis between bamA gene copy number and phenol concentration were highly significant, suggesting that the increase of aromatic degraders targeted by bamA assay was due to an increase in the amount of phenol degraded over time. The incremental phenol concentration affected hydrogenotrophic archaea triggering a linear decrease of Methanobacterium and the growth of Methanobrevibacter. The best performance in the reactor was at 800 mg L −1 of phenol. At this stage, the highest relative abundances of Syntrophorhabdus, Chloroflexus, Smithella, Methanolinea and Methanosaeta were observed and correlated positively with initial degradation rate, suggesting that these microorganisms are relevant players to maintain a good performance in the ASBR.

In subseafloor sediment, microbial cell densities exponentially decrease with depth into the fermentation zone. Here, we address the classical question of 'why are cells dying faster than they are growing?’ from the standpoint of physiology. The stoichiometries of fermentative ATP production and consumption in the fermentation zone place bounds on the conversion of old cell biomass into new. Most fermentable organic matter in deep subseafloor sediment is amino acids from dead cells because cells are mostly protein by weight. Conversion of carbon from fermented dead cell protein into methanogen protein via hydrogenotrophic and acetoclastic methanogenesis occurs at ratios of ∼200:1 and 100:1, respectively, while fermenters can reach conversion ratios approaching 6:1. Amino acid fermentations become thermodynamically more efficient at lower substrate and product concentrations, but the conversion of carbon from dead cell protein into fermenter protein is low because of the high energetic cost of translation. Low carbon conversion factors within subseafloor anaerobic feeding chains account for exponential declines in cellular biomass in the fermentation zone of anoxic sediments. Our analysis points to the existence of a life–death transition zone in which the last biologically catalyzed life processes are replaced with purely chemical reactions no longer coupled to life., Physiological and stoichiometric calculations uncover extremely low carbon conversion factors within anaerobic feeding chains in subsurface fermentation zones of marine sediments, accounting for global declines in cellular subseafloor biomass with depth.

Microbial communities associated with plants are greatly influenced by water availability in soil. In flooded crops, such as rice, the impact of water management on microbial dynamics is not fully understood. Here, we present a comprehensive study of the rice microbiota investigated in an experimental field located in one of the most productive areas of northern Italy. The microbiota associated with paddy soil and root was investigated using 454 pyrosequencing of 16S, ITS and 18S rRNA gene amplicons under two different water managements, upland (non-flooded, aerobic) and lowland (traditional flooding, anaerobic), at three plant development stages. Results highlighted a major role of the soil water status in shaping microbial communities, while phenological stage had low impacts. Compositional shifts in prokaryotic and fungal communities upon water management consisted in significant abundance changes of Firmicutes, Methanobacteria, Chloroflexi, Sordariomycetes, Dothideomycetes and Glomeromycotina. A vicariance in plant beneficial microbes and between saprotrophs and pathotrophs was observed between lowland and upland. Moreover, through network analysis, we demonstrated different co-abundance dynamics between lowland and upland conditions with a major impact on microbial hubs (strongly interconnected microbes) that fully shifted to aerobic microbes in the absence of flooding.

Intestinal microbes play a key role in the energy metabolism of broiler chickens, participate in the development of the gastrointestinal tract, including the regulation of intestinal epithelial proliferation, vitamin synthesis and ion absorption, fermentation of carbohydrates and proteins, biotransformation of bile acids, protection from pathogens and modulation of the immune system. Metagenomic analysis of the gastrointestinal microbiota allows to find approaches to improve the growth and productivity of chickens by introducing a diet based on beneficial bacterial strains or their secondary metabolites. In this paper, we studied the effect of the total fraction of Bacillus subtilis GM5 lipopeptides on the growth parameters and formation of bacterial communities in the caecum of cross Cobb 500 broiler chickens. It was found that the addition of bacillary lipopeptides to the feed resulted in an increase in chicken weight by 12.7% and a decrease in feed conversion by 6.36% compared to the control (P < 0.05). It was also shown that the introduction of a feed additive in the form of a lipopeptide fraction modulates the structure of the bacterial microbiota of the caecum of chickens. Thus, the proportion of classes Bacteroidia, Negativicutes, Betaproteobacteria, Epsilonproteobacteria, Deltaproteobacteria, Synergistia in the caecal microbiota of chickens of the experimental group increases, and the proportion of Clostridia, Methanobacteria decreases in comparison with the control.

The dynamic change of microbial community during sludge acclimation from aerobic to anaerobic in a MBR for coking wastewater treatment was revealed by Illumina Miseq sequencing in this study. The diversity of both Bacteria and Archaea showed an increase-decrease trajectory during acclimation, and exhibited the highest at the domestication interim. Ignavibacteria changed from a tiny minority (less than 1%) to the dominant bacterial group (54.0%) along with acclimation. The relative abundance of Betaproteobacteria kept relatively steady, as in this class some species increased coupled with some other species decreased during acclimation. The dominant Archaea shifted from Halobacteria in initial aerobic sludge to Methanobacteria in the acclimated anaerobic sludge. The dominant bacterial and archaeal groups in different acclimation stages were indigenous microorganisms in the initial sludge, though some of them were very rare. This study supported that the species in "rare biosphere" might eventually become dominant in response to environmental change.

Microbial fuel cells (MFC) can effectively control the methane emissions from constructed wetland (CW). In this study, the effect of rhizosphere locations on the reduction of methane emission from CW by operating MFC was further studied. According to results, operating MFC in CW improved the COD removal and inhibited the methane emission from CW by 1/3. Plants (Cyperus alternifolius) roots at anode were more conducive to CW-MFC power generation. The highest power density (47.813 mW/m3) was observed in CW-MFC with rhizosphere at anode. The rhizosphere in cathode could improve CW-MFC COD removal. Operating MFC led to the competition between electrogens and methanogens, which changed the microbial community structure and biochemical processes in CW. Proteobacteria, as the main electricigen in CW-MFCs, were specifically enriched in CW-MFC with rhizosphere located in cathode. As the dominant archaea, methanobacteria and methanomicrobia were specifically enriched in CW-MFC with rhizosphere located in anode.

This paper aims to investigate the methane emissions from typical urban and rural constructed wetlands (CWs) associated with methanogen diversity using Illumina sequencing in microcosms from five different CWs planted with Cyperus alternifolius L. The results show that the average CH4 flux in summer in these five CWs was 0.33 gCH4 m−2 day−1, with a range of 0.01–1.52 g CH4 m−2 day−1 ((GWP: global warming potential) = 0.28–42.72 kg CO2eq m−2 year−1). Redundancy analysis (RDA) shows that methane fluxes were mostly impacted by local temperature (Ymethane = 4.66 Xtemp - 102.63, R2 = 0.81), which is considered to be a key environmental factor. The dissolved oxygen of all CWs showed a significantly negative correlation with CH4 emissions (R2 = −0.99, p = 0.01). Both the species richness index and species diversity index showed that Methanobacteria was the predominant class, with percentages ranging from 16.47% to 26.66% in the five CWs. The percentage of Methanomicrobia was 15.42–24.98% in the five CWs, and Methanococci was only found in the FengHuang constructed wetland. Other findings suggest that Methanomicrobiales in the Anlong Village constructed wetland was a dominant order and similar to a local paddy ecosystem in the Chengdu Plain.

The Taixinan Basin is one of the most potential gas hydrate bearing areas in the South China Sea and abundant gas hydrates have been discovered during expedition in 2013. In this study, geochemical and microbial methods are combinedly used to characterize the sediments from a shallow piston Core DH_CL_11 (gas hydrate free) and a gas hydrate-bearing drilling Core GMGS2-16 in this basin. Geochemical analyses indicate that anaerobic oxidation of methane (AOM) which is speculated to be linked to the ongoing gas hydrate dissociation is taking place in Core DH_CL_11 at deep. For Core GMGS2-16, AOM related to past episodes of methane seepage are suggested to dominate during its diagenetic process; while the relatively enriched δ 18O bulk-sediment values indicate that methane involved in AOM might be released from the “episodic dissociation” of gas hydrate. Microbial analyses indicate that the predominant phyla in the bacterial communities are Firmicutes and Proteobacteria (Gammaproteobacteria and Epsilonproteobacteria), while the dominant taxa in the archaeal communities are Marine_Benthic_Group_B (MBGB), Halobacteria, Thermoplasmata, Methanobacteria, Methanomicrobia, Group C3 and MCG. Under parallel experimental operations, comparable dominant members (Firmicutes and MBGB) are found in the piston Core DH_CL_11 and the near surface layer of the long drilling Core GMGS2-16. Moreover, these members have been found predominant in other known gas hydrate bearing cores, and the dominant of MBGB has even been found significantly related to gas hydrate occurrence. Therefore, a high possibility for the existing of gas hydrate underlying Core DH_CL_11 is inferred, which is consistent with the geochemical analyses. In all, combined geochemical and microbiological analyses are more informative in characterizing sediments from gas hydrate-associated areas in the South China Sea.

This study was conducted to investigate the phylogenetic diversity of archaea in the rumen of adult and elderly yaks. Six domesticated female yaks, 3 adult yaks ((5.3±0.6) years old), and 3 elderly yaks ((10.7±0.6) years old), were used for the rumen contents collection. Illumina MiSeq high-throughput sequencing technology was applied to examine the archaeal composition of rumen contents. A total of 92 901 high-quality archaeal sequences were analyzed, and these were assigned to 2 033 operational taxonomic units (OTUs). Among these, 974 OTUs were unique to adult yaks while 846 OTUs were unique to elderly yaks; 213 OTUs were shared by both groups. At the phylum level, more than 99% of the obtained OTUs belonged to the Euryarchaeota phylum. At the genus level, the archaea could be divided into 7 archaeal genera. The 7 genera (i.e., Methanobrevibacter, Methanobacterium, Methanosphaera, Thermogymnomonas, Methanomicrobiu, Methanimicrococcus and the unclassified genus) were shared by all yaks, and their total abundance accounted for 99% of the rumen archaea. The most abundant archaea in elderly and adult yaks were Methanobrevibacter and Thermogymnomonas, respectively. The abundance of Methanobacteria (class), Methanobacteriales (order), Methanobacteriaceae (family), and Methanobrevibacter (genus) in elderly yaks was significantly higher than in adult yaks. In contrast, the abundance of Thermogymnomonas in elderly yaks was 34% lower than in adult yaks, though the difference was not statistically significant. The difference in abundance of other archaea was not significant between the two groups. These results suggested that the structure of archaea in the rumen of yaks changed with age. This is the first study to compare the phylogenetic differences of rumen archaeal structure and composition using the yak model.

High-saturation (40–100%), microbial gas hydrates have been acquired by expedition GMGS2 from the Taixinan Basin. In this study, geochemical and microbial features of hydrate-containing sediments from the drilling cores (GMGS2-09 and GMGS2-16) were characterized to explore their relationships with gas hydrate formation. Results showed that the average TOC content of GMGS2-09 and GMGS2-16 were 0.45% and 0.63%, respectively. They could meet the threshold for in situ gas hydrate formation, but were not available for the formation of high-saturation gas hydrates. The dominant members of Bacteria at the class taxonomic level were Alphaproteobacteria, Bacilli, Bacteroidia, Epsilonproteobacteria and Gammaproteobacteria, and those in Archaea were Marine_Benthic_Group_B (MBGB), Miscellaneous_Crenarchaeotic_Group (MCG), Group C3, Methanomicrobia and Methanobacteria. Indicators of microbes associated with thermogenic organic matter were measured. These include: (1) most of the dominant microbes had been found dominant in other gas hydrates bearing sediments, mud volcanos as well as oil/coal deposits; (2) hydrogenotrophic methanogens and an oilfield-origin thermophilic, methylotrophic methanogen were found dominant the methanogen community; (3) hydrocarbon-assimilating bacteria and other hyperthermophiles were frequently detected. Therefore, thermogenic signatures were inferred existed in the sediments. This deduction is consistent with the interpretation from the seismic reflection profiles. Owing to the inconsistency between low TOC content and gas hydrates with high saturation, secondary microbial methane generated from the bioconversion of thermogenic organic matters (oil or coal) was speculated to serve as enhanced gas flux for the formation of high-saturation gas hydrates. A preliminary formation model of high-saturation biogenic gas hydrates was proposed, in which diagenesis processes, tectonic movements and microbial activities were all emphasized regarding to their contribution to gas hydrates formation. In short, this research helps explain how microbial act and what kind of organic matter they use in forming biogenic gas hydrates with high saturations.

A laboratory-scale controlling internal circulation (CIC) anaerobic reactor was developed to treat cassava wastewater. The hydraulic retention time (HRT), internal circulation ratio, and temperature were selected as main operating variables that could be optimized to increase efficiency of the reactor. Responses of microbial communities to changes in these parameters were investigated using high throughput sequencing (HTS) approach. With increasing internal circulation ratio, the COD removal efficiencies and gas production rates also increased. On the other hand, decreasing temperature to 20 °C resulted to increase in the effluent COD concentration to 1000 mg L−1, with low gas production rate of 0.10 m3CH4 kg−1·COD−1. Upon starting the internal circle of the CIC reactor, species diversity was reduced while species abundance increased. Specifically, Methanosarcinales increased from 32.82% to 39.69%, and Methanobacteriales from 33.72% to 54.77%. However, when the CIC reactor temperature was further reduced to 25 °C, the abundance of Methanobacteria decreased to 33.35%. Results showed the microbial community shift was observed at different internal circulation ratio and temperature, influencing the pollutants removal rate and gas production rate.

The aim of this study was to observe how the effluents from a massive poultry farming facility influence the microbial community in the sediment of the nearby constructed wetland, which functions as a reservoir for poultry wastes. The microbial community structures and compositions in the two neighboring constructed wetlands of Louisiana (named Big Pond and Corner Pond) were characterized and compared through a metagenomics approach using the high-throughput sequence data of a conserved 16S rDNA region (V4 region) obtained from the sediment DNA samples and the metagenomics analysis tool QIIME. Big Pond is connected to a poultry farming facility, directly influenced by the poultry wastes, while its neighboring Corner Pond is separated from the poultry house. Among the 74 phyla of prokaryotes detected from the sediments of the two wetlands, four phyla (Acidobacteria, Chloroflexi, Euryarchaeota, and Proteobacteria) were predominant in both conditions. Proteobacteria, the most predominant phylum in both wetlands, was not significantly different in its relative abundance between the two conditions. However, Alphaproteobacteria, one of the four major classes within Proteobacteria, was almost depleted in Big Pond. Within another major phylum Euryarchaeota, all the three classes known as methanogenic organisms (Methanobacteria, Methanomicrobia, and Thermoplasmata) were more abundant in Big Pond. In addition, the relative abundance of Acidobacteria was significantly reduced in Big Pond, while that of the class Dehalococcoidetes within the phylum Chloroflexi was significantly higher in Big Pond compared to Corner Pond. Wastes released from an intensive poultry farming facility change significantly the relative abundance of some taxonomic groups of microorganisms in the microbial community of the wetland sediment. This study provided valuable information about the global changes of microbial community in the wetland sediments caused by the infusion of poultry wastes at various taxonomic levels.

Anaerobic digestion, the principal method of stabilizing biosolids in wastewater treatment plants (WWTPs), can efficiently and largely attenuate the antibiotic resistances in biosludge. This study aims to investigate the effect of oxidative pretreatment with ultrasound irradiation combined with ozone (US/O3) on the mesophilic and thermophilic anaerobic digestion (MAD and TAD) for the biosludge bearing trace fluoroquinolones contaminants-levofloxacin (LEVO) which was widely used in recent years. During the oxidation, the trace-level LEVO was almost completely degraded. The methanogenic activity in US/O3 pretreated TAD dosed 0.1 mg/L LEVO was much higher than those in single MAD and TAD, therefore leading to a remarkable increase in biogas production. The identification of levofloxacin intermediates during chemical degradation was analyzed using LCMS technique and the reaction pathway based on them was proposed. Hydroxyl radicals provided by US/O3 contributed to oxidative ring opening of LEVO as well as degradation of other biomacromolecules in the biosludge. Besides, the quinoline resistance genes-qnrA and qnrS declined significantly by 1–2 orders of magnitude in US/O3-pretreated TAD, indicating that the active radicals produced by US/O3 oxidized and degraded LEVO and therefore inactivated the antibiotic resistant bacteria or genes in the biosolids. Meanwhile, the composition and structure of the microbial community altered and the diversity and richness of total bacterial and potential human pathogens decreased, the pattern of which was correlated with LEVO-resistant genes. Among the well-known AD-related phylum including Bacteroidetes, Firmicutes, Methanobacteria as well as Thermotogae which has been previously detected in TAD and performed organic hydrolysis and degradation, the potential LEVO-resistant bacteria were probably affiliated to Actinobacteria, Bacteroidetes, Proteobacteria, Thermotogae. This study revealed the contribution of US/O3 pretreatment to the anaerobic digestion in terms of ARGs reduction for trace-LEVO- exposed biosludge and could provide useful guidance for controlling the dissemination of ARB and ARGs in sewage sludge.

Due to the activity of methane-oxidizing bacteria, forest soils are usually net sinks for the greenhouse gas methane (CH4). Despite several hints that CH4 balances might be influenced by vegetation, there are only few investigations dealing with this connection. Therefore, we studied this soil–plant–microbe interaction by using mesocosm experiments with forest soil and Larix decidua, a common coniferous tree species within the Alps. Gas measurements showed that the presence of L. decidua significantly reduced CH4 oxidation of the forest soil by ∼10% (−0.95 µmol m−2 h−1 for soil vs −0.85 µmol m−2 h−1 for soil plus L. decidua) leading to an increased net CH4 balance. Increased light intensity was used to intensify the influence of the plant on the soil's CH4 balance. The increase in light intensity strengthened the effect of the plant and led to a greater reduction of CH4 oxidation. Besides, we examined the impact of L. decidua and light on the abundance of methanogens and methanotrophs in the rhizosphere as compared with bulk soil. The abundance of both methane-oxidizing bacteria and methanogenic archaea was significantly increased in the rhizosphere compared with bulk soil but no significant response of methanogens and methanotrophs upon light exposure was established.

The Atacama Desert, the oldest and driest desert on Earth, displays significant rains only once per decade. To investigate how microbial communities take advantage of these sporadic wet events, we carried out a geomicrobiological study a few days after a heavy rain event in 2015. Different physicochemical and microbial community analyses were conducted on samples collected from playas and an alluvial fan from surface, 10, 20, 50, and 80 cm depth. Gravimetric moisture content peaks were measured in 10 and 20 cm depth samples (from 1.65 to 4.1% w/w maximum values) while, in general, main anions such as chloride, nitrate, and sulfate concentrations increased with depth, with maximum values of 13-1,125; 168-10,109; and 9,904-30,952 ppm, respectively. Small organic anions such as formate and acetate had maximum concentrations from 2.61 to 3.44 ppm and 6.73 to 28.75 ppm, respectively. Microbial diversity inferred from DNA analysis showed Actinobacteria and Alphaproteobacteria as the most abundant and widespread bacterial taxa among the samples, followed by Chloroflexi and Firmicutes at specific sites. Archaea were mainly dominated by Nitrososphaerales, Methanobacteria, with the detection of other groups such as Halobacteria. Metaproteomics showed a high and even distribution of proteins involved in primary metabolic processes such as energy production and biosynthetic pathways, and a limited but remarkable presence of proteins related to resistance to environmental stressors such as radiation, oxidation, or desiccation. The results indicated that extra humidity in the system allows the microbial community to repair, and prepare for the upcoming hyperarid period. Additionally, it supplies biomarkers to the medium whose preservation potential could be high under strong desiccation conditions and relevant for planetary exploration.

Huge numbers of microorganisms reside in livestock faeces and constitute one of the most complex microbial ecosystems. Here, faecal microbial communities of three typical livestock in Xilingol steppe grassland, i.e. sheep, cattle, and horse, were investigated by Illumina MiSeq sequencing and quantitative real-time polymerase chain reaction (qPCR). Firmicutes and Bacteroidetes comprised the majority of bacterial communities in three livestock faeces. Sordariomycetes, Leotiomycetes, and Dothideomycetes were dominant in fungal communities, as well as Methanobacteria and Methanomicrobia were dominant in archaeal communities in three livestock faeces. Similar fungal community dominated in these samples, with 95.51% of the sequences falling into the overlap of three livestock faeces. In contrast, bacterial communities were quite variable among three different livestock faeces, but a similar community was observed in sheep and cattle faeces. Nearly all the archaea were identified as methanogens, whilst the most diverse and abundant methanogens were detected in cattle faeces. Potential pathogens including Bacteroides spp., Desulfovibrio spp., and Fusarium spp. were also detected in livestock faeces. Overall, this study provides the first detailed microbial comparison of typical livestock faeces dwelling on single grassland, and may be help guide management strategies for livestock grazing and grassland restoration.

Shallow hydrothermal systems (SHS) around the Eolian Islands (Italy), related to both active and extinct volcanism, are characterized by high temperatures, high concentrations of CO2 and H2S, and low pH, prohibitive for the majority of eukaryotes which are less tolerant to the extreme conditions than prokaryotes. Archaea and bacteria are the key elements for the functioning of these ecosystems, as they are involved in the transformation of inorganic compounds released from the vent emissions and are at the basis of the hydrothermal system food web. New extremophilic archaea (thermophilic, hyperthermophilic, acidophilic, alkalophilic, etc.) have been isolated from vents of Vulcano Island, exhibiting interesting features potentially valuable in biotechnology. Metagenomic analyses, which mainly involved molecular studies of the 16S rRNA gene, provided different insights into microbial composition associated with Eolian SHS. Archaeal community composition at Eolian vent sites results greatly affected by the geochemistry of the studied vents, principally by hypersaline conditions and declining temperatures. Archaeal community in sediments was mostly composed by hyperthermophilic members of Crenarchaeota (class Thermoprotei) and Euryarchaeota (Thermococci and Methanococci) at the highest temperature condition. Mesophilic Euryarchaeota (Halobacteria, Methanomicrobia, and Methanobacteria) increased with decreasing temperatures. Eolian SHS harbor a high diversity of largely unknown archaea, and the studied vents may be an important source of new isolates potentially useful for biotechnological purposes.

Previous studies showed that exoelectrogenic bacteria in paddy soil could suppress methanogens and methanogenesis after they were enriched by application of Fe3+ or running microbial fuel cells (MFCs). However, the relationship between exoelectrogenic bacteria and methanogens without the enrichment process is unknown. Our study was conducted in three paddy fields in China and over three seasons. We explored novel MFC-based sensors to in situ detect voltage signals that were generated from paddy soil within 10 min. The voltage and methane emission flux were determined as an indicator of the exoelectrogenic activity and methanogenic activity, respectively. The abundance of exoelectrogenic bacteria was assessed by quantifying five exoelectrogenic bacterial-associated genera including Geobacter, Shewanella, Anaeromyxobacter, Desulfovibrio and Clostridium, while the methanogens were studied by quantifying and sequencing the mcrA gene. The results showed that the abundance of exoelectrogenic bacteria and the voltage signals were positively correlated to the abundance of mcrA gene and methane emission flux, respectively. Moreover, non-metric dimensional scaling reveals that the abundance of Geobacter, Desulfovibrio and Clostridium significantly correlated with that of Methanomassiliicoccus, Methanoregula and Methanolinea. The present study suggests that the voltage signals might act as a novel indicator of methane emission flux in paddy fields.

Petroleum contaminants are exposed to weathering when released into environment, resulting in the alteration of their chemical composition. Here, we investigated microbial communities through the soil profile at an industrial site, which was exposed to various petroleum products for over 50 years. The petroleum is present as light non-aqueous phase liquid (LNAPL) and is undergoing natural source zone depletion (NSZD). Microbial community composition was compared to the contaminant type, concentration, and its depth of obtained soil cores. A large population of Archaea, particularly Methanomicrobia and Methanobacteria and indication of complex syntrophic relationships of methanogens, methanotrophs and bacteria were found in the contaminated cores. Different families were enriched across the LNAPL types. Results indicate methanogenic or anoxic conditions in the deeper and highly contaminated sections of the soil cores investigated. The contaminant was highly weathered, likely resulting in the formation of recalcitrant polar compounds. This research provides insight into the microorganisms fundamentally associated with LNAPL, throughout a soil depth profile above and below the water table, undergoing NSZD processes at a legacy petroleum site. It advances the potential for integration of microbial community effects on bioremediation and in response to physicochemical partitioning of LNAPL components from different petroleum types.

Microbial communities perform crucial biogeochemical cycles in distinct ecosystems. Halophilic microbial communities are enriched in the saline areas. Hence, haloarchaea have been primarily studied in salterns and marine biosystems with the aim to harness haloarcheal carotenoids biosynthesis. In this study, sediment from several distinct biosystems (mangrove, seashore, estuary, river, lake, salt pan and island) across the Arabian coastal region of India were collected and analyzed though 16s rRNA metagenomic and whole genome approach to elucidated the dominant representative genre, haloarcheal diversity, and the prevalence of Crtl and CruF genes. We found that the microbial diversity in mangrove sediment (794 OTUs) was highest and lowest in lake and river (558-560 OTUs). Moreover, the bacterial domain dominated in all biosystems (96.00-99.45%). Top 10 abundant genera were involved in biochemical cycles such as sulfur, methane, ammonia, hydrocarbon degradation, and antibiotics production. The Archaea was mainly composed of Haloarchaea, Methanobacteria, Methanococci, Methanomicrobia and Crenarchaeota. Carotenoid gene, Crtl, was observed in a major portion (abundance 60%; diversity 45%) of microbial community. Interestingly, we found that all species under haloarcheal class that were represented in fresh as well as marine biosystems encodes CruF gene (bacterioruberin carotenoid). Our study demonstrates the high microbial diversity in various ecosystems, enrichment of Crtl gene, and also shows that Crtl and CruF genes are highly abundant in haloarcheal genera. The finding of ecosystems specific Crtl and CruF encoding genera opens up a promising area in bioprospecting the carotenoid derivatives from the wide range of natural biosystems.

We carried out a regional survey on the archaea composition from surface waters of > 300 high-altitude Pyrenean lakes (average altitude 2300 m, pH range 4.4-10.1) by 16S rRNA gene tag sequencing. Relative Archaea abundances ranged between 0% and 6.3% of total prokaryotes amplicons in the polymerase chain reaction (PCR) mixture, and we detected 769 operational taxonomic units (OTUs; grouped at 97% identity) that split into 13 different lineages, with altitude and pH having a significant effect on the community composition. Woesearchaeota and Pacearchaeota (formerly Euryarchaeota DHVEG-6 cluster) dominated the data set (83% of total OTUS), showed a high occurrence (presence in c. 75% of the lakes) and had relative abundances significantly and positively correlated with the phylogenetic diversity of bacterial communities. Micrarchaeota-Diapherotrites (formerly Euryarchaeota MEG cluster), Methanomicrobia, Thermoplasmata and ammonia-oxidizing thaumarchaeota (AOA) showed relative abundances between 1% and 3% and occurrences between 14% and 26%. Minor lineages were SM1K20, Aenigmarchaeota (formerly Euryarchaeota DSEG cluster), Methanobacteria, Bathyarchaeota and SCG. Environmental preferences substantially differed among lineages, with Aenigmarchaeota and Methanomicrobia having the largest habitat breadth, and Thermoplasmata, AOA and Micrarchaeota having the smallest. Pacearchaeota and Woesearchaeota had been mostly reported from saline habitats and sediments, but surface waters of oligotrophic alpine lakes are suitable environments for such ecologically spread and genetically diverse archaeal lineages.

Pentachlorophenol (PCP) is a common residual persistent pesticide in paddy soil and has resulted in harmful effect on soil ecosystem. The anaerobic microbial transformation of PCP, therefore, has been received much attentions, especially the functional microbial communities for the reductive transformation. However, the key functional microorganisms for PCP mineralization in the paddy soil still remain unknown. In this work, DNA-based stable isotope probing (SIP) was applied to explore the key microorganisms responsible for PCP mineralization in paddy soil. The SIP results indicated that the dominant bacteria responsible for PCP biodegradation belonged to the genus Dechloromonas of the class β-Proteobacteria. In addition, the increased production of (13)CH4 and (13)CO2 indicated that the addition of lactate enhanced the rate of biodegradation and mineralization of PCP. Two archaea classified as the genera of Methanosaeta and Methanocella of class Methanobacteria were enriched in the heavy fraction when with lactate, whereas no archaea was detected in the absence of lactate. These findings provide direct evidence for the species of bacteria and archaea responsible for anaerobic PCP or its breakdown products mineralization and reveal a new insight into the microorganisms linked with PCP degradation in paddy soil.

Benthic Archaea play a crucial role in the biogeochemical cycles and food webs, however, their spatiotemporal distribution and environmental drivers are not well investigated in brackish sediments. The composition and abundances of benthic archaeal communities were examined from a coastal lagoon; Chilika (India) which is experiencing an intense pressure from anthropogenic and natural factors. High-throughput sequencing of 16S rRNA genes revealed that sediment (n = 96) archaeal communities were largely composed of Crenarchaeota (18.76%), Euryarchaeota (18.34%), Thaumarchaeota (13.45%), Woesearchaeota (10.05%), and Pacearchaeota (4.21%). Archaeal taxa affiliated to methanogens, sulfate-reducers, and ammonia-oxidizers were detected suggesting that carbon, sulfur, and nitrogen cycles might be prominent in benthic sediments. Salinity, total organic carbon, available nitrogen, available phosphorus, macrophyte (Phragmites karka) and inter-taxa relationships between community members and with bacterial communities played steering roles in structuring the archaeal communities. Marine sites with mesohaline-polyhaline regime were dominated by Nitrosopumilus and Thaumarchaeota. In contrast, riverine sites with oligohaline regime demonstrated a higher abundance of Thermoprotei. Macrophyte dominated zones were enriched in Methanomicrobia and Methanobacteria in their rhizosphere sediments, whereas, bulk (un-vegetated) sediments were dominated by Nitrosopumilus. Spatial patterns in archaeal communities demonstrated ‘distance-decay’ patterns which were correlated with changes in physicochemical factors over geographical distances. Heterotrophic microbial communities showed much higher metabolic diversity and activity in their carbon utilization profiles in rhizosphere sediments than the bulk sediments. This baseline information on benthic archaea and their environmental drivers would be useful to assess the impact of anthropogenic and natural pressures on these communities and associated biogeochemical cycles.

Methanogens are among the oldest forms of life on Earth and are detectable in a wide range of environments, but our knowledge of their overall diversity and functioning is limited. Peatlands in particular host a broad range of methanogens that contribute large amounts of methane to the atmosphere, but are largely under-represented in pure cultures. Here, we anaerobically enriched peat with common growth substrates, supplements and antibiotics to identifying novel methanogen sequences and potential growth conditions. Over 3 years, we obtained 28 new mcrA sequences from taxa that have remained previously uncultured and undescribed beyond distantly related clones or sequences detected in environmental samples. Evidence suggests that the novel methanogens, representing five of the seven known orders, were capable of growing on H2 as well as acetate and at temperatures ranging from 6 to ca. 22°C. Methods involving the use of ampicillin proved useful, although obtaining high methane production in the absence of H2 was difficult. Our results also indicate that many methanogens may rely on bacterial symbionts (commonly Clostridium spp.). Such enrichment approaches represent a useful intermediary between maker-gene detection and isolation, allowing us to broaden our understanding of methanogen physiological ecology while potentially providing valuable sequence data.

The rhizosphere microbiome is known to play a crucial role in promoting plant growth, partly by countering soil-borne phytoparasites and by improving nutrient uptake. The abundance and composition of the rhizosphere and root-associated microbiota are influenced by several factors, including plant species and genotype. We hypothesize that crop domestication might influence the composition and diversity of plant-associated microbiomes. We tested the contribution of domestication to the bacterial and archaeal root and soil composition associated with six genotypes of domesticated Setaria italica and four genotypes of its wild ancestor, S. viridis. The bacterial microbiome in the rhizoplane and root endophyte compartments, and the archaea in the endophyte compartment, showed major composition differences. For instance, members of the Betaproteobacteria and Firmicutes were overrepresented in S. italica root samples compared to S. viridis. Metagenomic analysis of samples that contained both root surface-bound (rhizoplane) and inside-root (endophytic) bacteria defined two unique microbial communities only associated with S. italica roots and one only associated with S. viridis roots. Root endophytic bacteria were found in six discernible communities, of which four were primarily on S. italica and two primarily on S. viridis. Among archaea, Methanobacteria, and Methanomicrobia exhibited species-associated differences in the rhizosphere and root compartments, but most detected archaea were not classified more specifically than at the level of phylum. These results indicate a host genetic contribution to the microbial composition in Setaria, and suggest that domestication has selected for specific associations in the root and in the rhizosphere.

BACKGROUND Shared traits between prokaryotes and eukaryotes are helpful in the understanding of the tree of life evolution. In bacteria and eukaryotes, it has been shown a particular organisation of tRNA genes as clusters, but this trait has not been explored in the archaea domain. OBJECTIVE Explore the occurrence of tRNA gene clusters in archaea. METHODS In-silico analyses of complete and draft archaeal genomes based on tRNA gene isotype and synteny, tRNA gene cluster content and mobilome elements. FINDINGS We demonstrated the prevalence of tRNA gene clusters in archaea. tRNA gene clusters, composed of archaeal-type tRNAs, were identified in two Archaea class, Halobacteria and Methanobacteria from Euryarchaeota supergroup. Genomic analyses also revealed evidence of the association between tRNA gene clusters to mobile genetic elements and intra-domain horizontal gene transfer. MAIN CONCLUSIONS tRNA gene cluster occurs in the three domains of life, suggesting a role of this type of tRNA gene organisation in the biology of the living organisms.