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Acid mine drainage (AMD) harbors all three life forms in spite of its toxic and hazardous nature. In comparison to bacterial diversity, an in-depth understanding of the archaeal diversity in AMD and their ecological significance remain less explored. Archaeal populations are known to play significant roles in various biogeochemical cycles within the AMD ecosystem, and it is imperative to have a deeper understanding of archaeal diversity and their functional potential in AMD system. The present study is aimed to understand the archaeal diversity of an AMD sediment of Malanjkhand Copper Project, India through archaea specific V6 region of 16S rRNA gene amplicon sequencing. Geochemical data confirmed the acidic, toxic, heavy metal-rich nature of the sample. Archaea specific V6-16S rRNA gene amplicon data showed a predominance of Thermoplasmata (BSLdp215, uncultured Thermoplasmata, and Thermoplasmataceae) and Nitrososphaeria (Nitrosotaleaceae) members constituting ~ 95% of the archaeal community. Uncultured members of Bathyarchaeia, Group 1.1c, Hydrothermarchaeota, and Methanomassiliicoccales along with Methanobacteriaceae, Methanocellaceae, Haloferaceae, Methanosaetaceae, and Methanoregulaceae constituted the part of rare taxa. Analysis of sequence reads indicated that apart from their close ecological relevance, members of the Thermoplasmata present in Malanjkhand AMD were mostly involved in chemoheterotrophy, Fe/S redox cycling, and with heavy metal resistance, while the Nitrososphaeria members were responsible for ammonia oxidation and fixation of HCO3− through 3-hydroxypropionate/4-hydroxybutyrate cycle at low pH and oligotrophic environment which subsequently played an important role in nitrification process in AMD sediment. Overall, the present study elucidated the biogeochemical significance of archaeal populations inhabiting the toxic AMD environment.

Recent discoveries of mcr and mcr-like genes in genomes from diverse archaeal lineages suggest that methane metabolism is an ancient pathway with a complicated evolutionary history. One conventional view is that methanogenesis is an ancestral metabolism of the class Thermoplasmata. Through comparative genomic analysis of 12 Thermoplasmata metagenome-assembled genomes (MAGs) basal to the Methanomassiliicoccales, we show that these microorganisms do not encode the genes required for methanogenesis. Further analysis of 770 Ca. Thermoplasmatota genomes/MAGs found no evidence of mcrA homologues outside of the Methanomassiliicoccales. Together, these results suggest that methanogenesis was laterally acquired by an ancestor of the Methanomassiliicoccales. The 12 analysed MAGs include representatives from four orders basal to the Methanomassiliicoccales, including a high-quality MAG that likely represents a new order, Ca. Lunaplasma lacustris ord. nov. sp. nov. These MAGs are predicted to use diverse energy conservation pathways, including heterotrophy, sulfur and hydrogen metabolism, denitrification, and fermentation. Two lineages are widespread among anoxic, sedimentary environments, whereas Ca. Lunaplasma lacustris has thus far only been detected in alpine caves and subarctic lake sediments. These findings advance our understanding of the metabolic potential, ecology, and global distribution of the Thermoplasmata and provide insight into the evolutionary history of methanogenesis within the Ca. Thermoplasmatota.

International audience; Studies on microbial communities, and their associated organic biomarkers, that are found thriving in the aphotic euxinic waters in modern stratified ecosystems are scarce compared to those undertaken in euxinic photic zones. The Dziani Dzaha (Mayotte,Indian Ocean) is a tropical, saline, alkaline crater lake that has recently been presentedas a modern analog of Proterozoic Oceans due to its thalassohaline classification (having water of marine origin) and specific biogeochemical characteristics. Continuous intense photosynthetic production and microbial mineralization keep most of the water column permanently aphotic and anoxic preventing the development of a euxinic (sulfidic and anoxic) photic zone despite a high sulfide/sulfate ratio and the presence of permanent or seasonal haloclines. In this study, the molecular composition of the organic matter in Lake Dziani Dzaha was investigated and compared to the microbial diversity evaluated through 16S rRNA gene amplicon sequencing, over two contrasting seasons (rainy vs. dry) that influence water column stratification. Depth profiles of organic biomarker concentrations (chlorophyll-a and lipid biomarkers) and bacterial and archaeal OTU abundances appeared to be strongly dependent on the presence of aphotic haloclines and euxinia. OTU abundances revealed theimportance of specific haloalkaliphilic bacterial and archaeal assemblages in phytoplanktonic biomass recycling and the biogeochemical functioning of the lake, suggesting new haloalkaline non-phototrophic anaerobic microbial precursors for some of the lipid biomarkers. Uncultured Firmicutes from the family Syntrophomonadaceae (Clostridiales), and Bacteroidetes from the ML635J-40 aquatic group, emerged as abundant chemotrophic bacterial members in the anoxic or euxinic waters and were probably responsible for the production of short-chain n-alkenes, wax esters, diplopterol, and tetrahymanol. Halocline-dependent euxinia also had a strong impact on the archaeal community which was dominated by Woesearchaeota in the sulfide-free waters. In the euxinic waters, methanogenic Euryarchaeota from the Methanomicrobia, Thermoplasmata, and WSA2 classes dominated and were likely at the origin of common hydrocarbon biomarkers of methanogens (phytane, pentamethyl-eicosenes, and partially hydrogenated squalene).

This study describes the community composition and functions of the gut microbiome of the freshwater omnivorous pufferfish based on metagenomic approach. Metagenome sequence data showed a dominance of the class Gammaproteobacteria followed by Fusobacteria, Actinobacteria, Anerolineae, Betaproteobacteria, Deinococci, Clostridia and Deltaproteobacteria. At the order level, the most abundant groups were Aeromonadales, Fusobacteriales, Enterobacterales, Synechococcales. The genus Aeromonas was the most predominant followed by Plesiomonas and Cetobacterium. Additionally, within the domain Archaea, class Methanomicrobia was most abundant followed by Hadesarchaea, Thermoplasmata, Candidatus Altiarchaeales, Candidatus Bathyarchaeota and Thermoprotei. The metabolic profile of the bacterial community exhibited a high prevalence of genes associated with core housekeeping functions, such as synthesis of cofactors, vitamins, prosthetic groups, pigments, amino acids and its derivatives, carbohydrate and protein metabolism. Comparative analysis with other fish gut microbiome showing similarity in protein metabolism with carnivorous Salmon and carbohydrate metabolism with herbivorous grass carp respectively. This study describes the bacterial community compositions are influenced by the trophic level.

Depth-dependent distribution patterns of bacterial and archaeal communities in deep sea water column around the Ninetyeast Ridge in the Indian Ocean were investigated using 16S rRNA gene profiling. Sampling was conducted at the northern Ninetyeast Ridge (1°59.89'N-9°59.70'S, 87°58.90'E-88°00.03'E) from September to November 2016 where samples were collected from the bathyal (1 000 m) to bathypelagic depths (>4 000 m) in four different stations. A total of 1 565 405 clean data falling into 6 712 bacterial OTUs and 1 452 727 clean data falling into 806 archaeal OTUs based on 97% similarity level were analyzed. Most of the bacterial 16S rRNA gene sequences were affiliated with Gammaproteobacteria, followed by Alphaproteobacteria and Bacteroidia. The archaeal 16S rRNA gene sequences mostly affiliated to Nitrososphaeria (Thaumarchaeota) dominated with relative abundances ranging from 52.68% to 97.2%, followed by Thermoplasmata (Euryarchaeota). Vertical partitioning of bacterial and archaeal communities among different water layers was observed. Canonical correspondence analysis (CCA) and Spearman's correlations revealed that depth (P=0.003), dissolved oxygen (P=0.019), and nitrite (P=0.033) were the main environmental factors affecting bacterial community structure at genus level in the Ninetyeast Ridge. On the other hand, the first two CCA axes accounted for 74.4% of the explained total variance, it seems that the archaeal communities at genus level were heavily influenced by the environmental variables including depth, dissolved oxygen (DO), nitrite, salinity, phosphate, ammonia, nitrate, and silicate, but none of them exhibited any significant correlation on the structuring (P>0.1).

Recent omics studies have provided invaluable insights into the metabolic potential, adaptation, and evolution of novel archaeal lineages from a variety of extreme environments. We utilized a genome-resolved metagenomic approach to recover eight medium- to high-quality metagenome-assembled genomes (MAGs) that likely represent a new order ("Candidatus Sysuiplasmatales") in the class Thermoplasmata from mine tailings and acid mine drainage (AMD) sediments sampled from two copper mines in South China. 16S rRNA gene-based analyses revealed a narrow habitat range for these uncultured archaea limited to AMD and hot spring-related environments. Metabolic reconstruction indicated a facultatively anaerobic heterotrophic lifestyle. This may allow the archaea to adapt to oxygen fluctuations and is thus in marked contrast to the majority of lineages in the domain Archaea, which typically show obligately anaerobic metabolisms. Notably, "Ca. Sysuiplasmatales" could conserve energy through degradation of fatty acids, amino acid metabolism, and oxidation of reduced inorganic sulfur compounds (RISCs), suggesting that they may contribute to acid generation in the extreme mine environments. Unlike the closely related orders Methanomassiliicoccales and "Candidatus Gimiplasmatales," "Ca. Sysuiplasmatales" lacks the capacity to perform methanogenesis and carbon fixation. Ancestral state reconstruction indicated that "Ca. Sysuiplasmatales," the closely related orders Methanomassiliicoccales and "Ca. Gimiplasmatales," and the orders SG8-5 and RBG-16-68-12 originated from a facultatively anaerobic ancestor capable of carbon fixation via the bacterial-type H4F Wood-Ljungdahl pathway (WLP). Their metabolic divergence might be attributed to different evolutionary paths. IMPORTANCE A wide array of archaea populate Earth's extreme environments; therefore, they may play important roles in mediating biogeochemical processes such as iron and sulfur cycling. However, our knowledge of archaeal biology and evolution is still limited, since the majority of the archaeal diversity is uncultured. For instance, most order-level lineages except Thermoplasmatales, Aciduliprofundales, and Methanomassiliicoccales within Thermoplasmata do not have cultured representatives. Here, we report the discovery and genomic characterization of a novel order, "Ca. Sysuiplasmatales," within Thermoplasmata in extremely acidic mine environments. "Ca. Sysuiplasmatales" are inferred to be facultatively anaerobic heterotrophs and likely contribute to acid generation through the oxidation of RISCs. The physiological divergence between "Ca. Sysuiplasmatales" and closely related Thermoplasmata lineages may be attributed to different evolutionary paths. These results expand our knowledge of archaea in the extreme mine ecosystem.

Identifying species interactions in a microbial community and how this relates to community function is a key challenge. Towards addressing this challenge, we present here an extensive genome-resolved, longitudinal dataset and associated metadata. We collected weekly samples of microbial communities and recorded operating conditions from industrial methane producing anaerobic digestion reactors for a year. This allowed us to recover 2240 dereplicated metagenome assembled genomes (dMAGs), together with their coverage dynamics and functional annotations from which functional traits were inferred. Of these dMAGs, 1910 were novel species, with 22 representing novel orders and classes. Methanogenic communities are expected to be strongly structured by syntrophic and other associations between the methanogens and syntrophs that produce their substrates. We identified 450 potential syntrophic dMAGs by searching for pairs of methanogenic and non-methanogenic dMAGs that had highly correlated time-series. Genomes of potential syntrophs were enriched for oxidoreductases and sugar transport genes and there was a strong taxonomic signal in their associations with methanogens. Of particular note, we found that Bathyarchaeiea associated specifically with methanogens from the Thermoplasmata, and Thermococci classes. Same syntrophic associations were only rarely observed across multiple reactors, suggesting that syntrophies might be facultative, with particular strains within a species forming syntrophic associations only sometimes and not necessarily always with the same methanogenic partner. The presented results show that longitudinal metagenomics is a highly valuable approach for identifying species and their interactions in microbial communities.One Sentence SummaryLongitudinal study of microbial communities identifies novel species and predicts their interactions and role in community function.

Huguangyan Maar Lake is a typical maar lake in the southeast of China. It is well preserved and not disturbed by anthropogenic activities. In this study, microbial community structures in sediment and water samples from Huguangyan Maar Lake were investigated using a high–throughput sequencing method. We found significant differences between the microbial community compositions of the water and the sediment. The sediment samples contained more diverse Bacteria and Archaea than did the water samples. Actinobacteria, Betaproteobacteria, Cyanobacteria, and Deltaproteobacteria predominated in the water samples while Deltaproteobacteria, Anaerolineae, Nitrospira, and Dehalococcoidia were the major bacterial groups in the sediment. As for Archaea, Woesearchaeota (DHVEG–6), unclassified Archaea, and Deep Sea Euryarchaeotic Group were detected at higher abundances in the water, whereas the Miscellaneous Crenarchaeotic Group, Thermoplasmata, and Methanomicrobia were significantly more abundant in the sediment. Interactions between Bacteria and Archaea were common in both the water column and the sediment. The concentrations of major nutrients ( $$\text{NO}_3^-$$ , $$\text{PO}_4^{3-}$$ , $$\text{SiO}_3^{2-}$$ and $$\text{NH}_4^+$$ ) shaped the microbial population structures in the water. At the higher phylogenetic levels including phylum and class, many of the dominant groups were those that were also abundant in other lakes; however, novel microbial populations (unclassified) were often seen at the lower phylogenetic levels. Our study lays a foundation for examining microbial biogeochemical cycling in sequestered lakes or reservoirs.

Marine Benthic Group D (MBG-D) archaea, discovered by 16S rRNA gene survey decades ago, are ecologically important, yet understudied and uncultured sedimentary archaea. In this study, a comprehensive meta-analysis based on the 16S rRNA genes of MBG-D archaea showed that MBG-D archaea are one of the most frequently found archaeal lineages in global sediment with widespread distribution and high abundance, including 16 subgroups in total. Interestingly, some subgroups show significant segregations toward salinity and methane seeps. Co-occurrence analyses indicate significant non-random association of MBG-D archaea with Lokiarchaeota (in both saline and freshwater sediments) and Hadesarchaea, suggesting potential interactions among these archaeal groups. Meanwhile, based on four nearly complete metagenome-assembled genomes (MAGs) and corresponding metatranscriptomes reconstructed from mangrove and intertidal mudflat sediments, we provide insights on metabolic potentials and ecological functions of MBG-D archaea. MBG-D archaea appear to be capable of transporting and assimilating peptides and generating acetate and ethanol through fermentation. Metatranscriptomic analysis suggests high expression of genes for acetate and amino acid utilization and for peptidases, especially the M09B-type extracellular peptidase (collagenase) showing high expression levels in all four mangrove MAGs. Beyond heterotrophic central carbon metabolism, the MBG-D genomes include genes that might encode two autotrophic pathways: Wood-Ljundahl (WL) pathways using both H4MPT and H4folate as C1 carriers, and an incomplete dicarboxylate/4-hydroxybutyrate cycle with alternative bypasses from pyruvate to malate/oxaloacetate during dicarboxylation. These findings reveal MBG-D archaea as an important ubiquitous benthic sedimentary archaeal group with specific mixotrophic metabolisms, so we proposed the name Thermoprofundales as a new Order within the Class Thermoplasmata. Globally, Thermoprofundales and other benthic archaea might synergistically transform benthic organic matter, possibly playing a vital role in sedimentary carbon cycle.

In this study, the abundance and composition of prokaryotic communities associated with the inner tissue of fruiting bodies of Suillus bovinus, Boletus pinophilus, Cantharellus cibarius, Agaricus arvensis, Lycoperdon perlatum, and Piptoporus betulinus were analyzed using culture-independent methods. Our findings indicate that archaea and bacteria colonize the internal tissues of all investigated specimens and that archaea are prominent members of the prokaryotic community. The ratio of archaeal 16S rRNA gene copy numbers to those of bacteria was >1 in the fruiting bodies of four out of six fungal species included in the study. The largest proportion of archaeal 16S rRNA gene sequences belonged to thaumarchaeotal classes Terrestrial group, Miscellaneous Crenarchaeotic Group (MCG), and Thermoplasmata. Bacterial communities showed characteristic compositions in each fungal species. Bacterial classes Gammaproteobacteria, Actinobacteria, Bacilli, and Clostridia were prominent among communities in fruiting body tissues. Bacterial populations in each fungal species had different characteristics. The results of this study imply that fruiting body tissues are an important habitat for abundant and diverse populations of archaea and bacteria. acceptedVersion

The obstacle to optimal utilization of biogas technology is poor understanding of biogas microbiomes diversities over a wide geographical coverage. We performed random shotgun sequencing on twelve environmental samples. Randomized complete block design was utilized to assign the twelve treatments to four blocks, within eastern and central regions of Kenya. We obtained 42 million paired-end reads that were annotated against sixteen reference databases using two ENVO ontologies, prior to β-diversity studies. We identified 37 phyla, 65 classes and 132 orders. Bacteria dominated and comprised 28 phyla, 42 classes and 92 orders, conveying substrate’s versatility in the treatments. Though, Fungi and Archaea comprised 5 phyla, the Fungi were richer; suggesting the importance of hydrolysis and fermentation in biogas production. High β-diversity within the taxa was largely linked to communities’ metabolic capabilities. Clostridiales and Bacteroidales, the most prevalent guilds, metabolize organic macromolecules. The identified Cytophagales, Alteromonadales, Flavobacteriales, Fusobacteriales, Deferribacterales, Elusimicrobiales, Chlamydiales, Synergistales to mention but few, also catabolize macromolecules into smaller substrates to conserve energy. Furthermore, δ-Proteobacteria, Gloeobacteria and Clostridia affiliates syntrophically regulate PH2 and reduce metal to provide reducing equivalents. Methanomicrobiales and other Methanomicrobia species were the most prevalence Archaea, converting formate, CO2(g), acetate and methylated substrates into CH4(g). Thermococci, Thermoplasmata and Thermoprotei were among the sulfur and other metal reducing Archaea that contributed to redox balancing and other metabolism within treatments. Eukaryotes, mainly fungi were the least abundant guild, comprising largely Ascomycota and Basidiomycota species. Chytridiomycetes, Blastocladiomycetes and Mortierellomycetes were among the rare species, suggesting their metabolic and substrates limitations. Generally, we observed that environmental and treatment perturbations influenced communities’ abundance, β-diversity and reactor performance largely through stochastic effect. Understanding diversity of biogas microbiomes over wide environmental variables and its’ productivity provided insights into better management strategies that ameliorate biochemical limitations to effective biogas production.

Complex microbial communities facilitate iron and methane transformations in anoxic methanic sediments of freshwater lakes, such as Lake Kinneret (the Sea of Galilee, Israel). The phylogenetic and functional diversity of these consortia are not fully understood, and it is not clear which lineages perform iron reduction and anaerobic oxidation of methane (AOM). Here, we investigated microbial communities from both natural Lake Kinneret iron-rich methanic sediments (>20 cm depth) and iron-amended slurry incubations from this zone using metagenomics, focusing on functions associated with iron reduction and methane cycling. Analyses of the phylogenetic and functional diversity indicate that consortia of archaea (mainly Bathyarchaeia, Methanomicrobia, Thermoplasmata, and Thermococci) and bacteria (mainly Chloroflexi (Chloroflexota), Nitrospirae (Nitrospirota), and Proteobacteria) perform key metabolic reactions such as amino acid uptake and dissimilation, organic matter fermentation, and methanogenesis. The Deltaproteobacteria, especially Desulfuromondales (Desulfuromonadota), have the potential to transfer electrons extracellularly either to iron mineral particles or to microbial syntrophs, including methanogens. This is likely via transmembrane cytochromes, outer-membrane hexaheme c-type cytochrome (OmcS) in particular, or pilin monomers (PilA), all of which were attributed to this lineage. Bona fide anaerobic oxidizers of methane (ANME) and denitrifying methanotrophs Methylomirabilia (NC10) may mediate AOM in these methanogenic sediments; however we also consider the role of methanogens in active AOM or back flux of methanogenesis. Putative aerobes, such as methane-oxidizing bacteria Methylomonas and their methylotrophic syntrophs Methylotenera, are found among the anaerobic lineages in Lake Kinneret iron-amended slurries and are also involved in the oxidation of methane or its intermediates, as suggested previously. We propose a reaction model for the metabolic interactions in these sediments, linking the potential players that interact via intricate metabolic tradeoffs and direct electron transfer between species. Our results highlight the metabolic complexity of microbial communities in an energy-limited environment, where aerobe and anaerobe communities may co-exist and facilitate AOM as one strategy for survival.

Marine sediments can contain large amounts of alkanes and methylated aromatic hydrocarbons that are introduced by natural processes or anthropogenic activities. These compounds can be biodegraded by anaerobic microorganisms via enzymatic addition of fumarate. However, the identity and ecological roles of a significant fraction of hydrocarbon degraders containing fumarate-adding enzymes (FAE) in various marine sediments remains unknown. By combining phylogenetic reconstructions, protein homolog modelling, and functional profiling of publicly available metagenomes and genomes, 61 draft bacterial and archaeal genomes encoding anaerobic hydrocarbon degradation via fumarate addition were obtained. Besides Desulfobacterota (previously known as Deltaproteobacteria) that are well-known to catalyze these reactions, Chloroflexi are dominant FAE-encoding bacteria in hydrocarbon-impacted sediments, potentially coupling sulfate reduction or fermentation to anaerobic hydrocarbon degradation. Among Archaea, besides Archaeoglobi previously shown to have this capability, genomes of Heimdallarchaeota, Lokiarchaeota, Thorarchaeota and Thermoplasmata also suggest fermentative hydrocarbon degradation using archaea-type FAE. These bacterial and archaeal hydrocarbon degraders occur in a wide range of marine sediments, including high abundances of FAE-encoding Asgard archaea associated with natural seeps and subseafloor ecosystems. Our results expand the knowledge of diverse archaeal and bacterial lineages engaged in anaerobic degradation of alkanes and methylated aromatic hydrocarbons.

Thermoplasmata is a widely distributed and ecologically important archaeal class in the phylum Euryarchaeota. Because few cultures and genomes are available, uncharacterized Thermoplasmata metabolisms remain unexplored. In this study, we obtained four medium- to high-quality archaeal metagenome-assembled genomes (MAGs) from the filamentous fragments of black-odorous aquatic sediments (Foshan, Guangdong, China). Based on their 16S rRNA gene and ribosomal protein phylogenies, the four MAGs belong to the previously unnamed Thermoplasmata UBA10834 clade. We propose that this clade (five reference genomes from the Genome Taxonomy Database (GTDB) and four MAGs from this study) be considered a new order, Candidatus Gimiplasmatales. Metabolic pathway reconstructions indicated that the Ca. Gimiplasmatales MAGs can biosynthesize isoprenoids and nucleotides de novo. Additionally, some taxa have genes for formaldehyde and acetate assimilation, and the Wood-Ljungdahl CO2 -fixation pathway, indicating a mixotrophic lifestyle. Sulfur reduction, hydrogen metabolism, and arsenic detoxification pathways were predicted, indicating sulfur-, hydrogen-, and arsenic-transformation potentials. Comparative genomics indicated that the H4 F Wood-Ljungdahl pathway of both Ca. Gimiplasmatales and Methanomassiliicoccales was likely obtained by the interdomain lateral gene transfer from the Firmicutes. Collectively, this study elucidates the taxonomic and potential metabolic diversity of the new order Ca. Gimiplasmatales and the evolution of this subgroup and its sister lineage Methanomassiliicoccales.

The microbial communities in mining impacted areas rely on a variety of mechanisms to survive in such extreme environments. In this work, a meta-taxonomic approach using 16S rRNA gene sequences was used to investigate the prokaryotic diversity of sediment samples from water bodies affected by acid mine drainage at the Sao Domingos mining area in the south of Portugal. Samples were collected in summer and winter from the most contaminated sites from where the water flows downstream to the freshwater of Chanca's river reservoir. The prokaryotic diversity on water bodies' sediments allowed us to distinguish the highly contaminated sites (pH approximate to 2) from sites with intermediate levels of contamination (pH approximate to 3-6.5), and from sites without contamination (pH approximate to 7.5). The abundances of acidophiles of generaAcidiphilium, Acidibacter, Acidobacterium and Acidocellain the sediments were correlated with the level of acid mine drainage contamination. The two first genera were among the 30 most abundant prokaryotes in all contaminated samples, including one (SS2w), where the contamination was very diluted, thereby emphasizing the impact that such type of pollution can have in the microbial communities of sediments. In addition, the high abundances of archaeal taxa from classThermoplasmataand of bacteria from family RCP1-48 in the sediments from the most contaminated site corroborate their importance in such ecosystems and a putative role in the generation of acid mine drainage. Portuguese national funds from the Foundation for Science and Technology (FCT) [UIDB/04326/2020] FCTPortuguese Foundation for Science and TechnologyEuropean Commission [29251] Algarve's Regional Operational Program (CRESC Algarve 2020), through Portugal 2020 European Regional Development Fund (FEDER)European Commission European Regional Development Fund ERDFEuropean Commission [0483_PROBIOMA_5_E] info:eu-repo/semantics/publishedVersion

We provide a 16S rRNA gene dataset of prokaryotic assemblages of a subantarctic marine ecosystem. Samples were collected at 2 stations (one near Ushuaia Bay and the other close to Bridges islands in the Beagle Channel). At each station, 2 depths (subsurface and bottom waters) were sampled in february, march, may and september during 2018, giving a total of 10 samples. 16S rRNA gene amplicon sequencing (V4 hypervariable region) was performed with the Illumina MiSeq platform. A total of 1116 amplicon sequence variants (ASVs) were recovered from the dataset. The sequences were taxonomically assigned to Alphaproteobacteria (23 ± 2%, mean ± standard error), Gammaproteobacteria (17 ± 1.5%), Flavobacteriia (8 ± 2%), Deltaproteobacteria (3.7 ± 0.5%), Acidimicrobiia (1.7 ± 0.1%), Planctomycetia (1.9 ± 0.4%), and AB16 group (1.7 ± 0.3%). Sequences affiliated with Archaea were abundant, reaching one third of analyzed sequences, mainly Thaumarchaeota (22 ± 3%), and Thermoplasmata (10 ± 1%). Together, sequences assigned to all these groups accounted for more than 90% of the sequences. This dataset constitutes a valuable resource for future scientific research aiming to unveil the role of these communities in ecosystem services such as carbon and nutrient cycling, and pollutants degradation. This will turn into benefits for future environmental monitoring and preservation actions, considering the tangible heritage of Ushuaia Bay and surrounding waters. Fil: Rodriguez Florez, Clara Natalia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Austral de Investigaciones Científicas; Argentina Fil: Malits, Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Austral de Investigaciones Científicas; Argentina Fil: Lozada, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Biología de Organismos Marinos; Argentina

The obstacle to optimal utilization of biogas technology is poor understanding of biogas’ microbiome diversities over a wide geographical coverage. We performed random shotgun sequencing on twelve environmental samples. A randomized complete block design was utilized to assign the twelve biogas reactor treatments to four blocks, within eastern and central regions of Kenya. We obtained 42 million paired-end reads that were annotated against sixteen reference databases using two ENVO ontologies, prior to β-diversities studies. We identified 37 phyla, 65 classes and 132 orders of micro-organisms. Bacteria dominated the microbiome and comprised of 28 phyla, 42 classes and 92 orders, conveying substrate’s versatility in the treatments. Though, fungi and Archaea comprised of only 5 phyla, the fungi were richer; suggesting the importance of hydrolysis and fermentation in biogas production systems. High β-diversity within the taxa was largely linked to communities’ metabolic capabilities. Clostridiales and Bacteroidales, the most prevalent guilds, metabolize organic macromolecules. The identified affiliates of Cytophagales, Alteromonadales, Flavobacteriales, Fusobacteriales, Deferribacterales, Elusimicrobiales, Chlamydiales, Synergistales to mention but few, also catabolize macromolecules into smaller substrates to conserve energy. Furthermore, δ-Proteobacteria, Gloeobacteria and Clostridia affiliates syntrophically regulate PH2 and reduce metal to provide reducing equivalents. Methanomicrobiales and other Methanomicrobia species were the most prevalence Archaea, converting formate, CO2(g), acetate and methylated substrates into CH4(g). Thermococci, Thermoplasmata and Thermoprotei were among the sulfur and other metal reducing Archaea that contributed to redox balancing and other metabolism within treatments. Eukaryotes, mainly fungi were the least abundant guild, comprised largely Ascomycota and Basidiomycota species. Chytridiomycetes, Blastocladiomycetes and Mortierellomycetes were among the rare species, suggesting their metabolic and substrates limitations. Generally, we observed that environmental and treatment perturbations influenced communities’ abundance, β-diversity and reactor performance largely through stochastic effect. The study of the diversity of the biogas’ microbiomes over wide environmental variables and the productivity of biogas reactor systems has provided insights into better management strategies that may ameliorate biochemical limitations to effective biogas production.Author SummaryThe failure of biochemical reactions in biogas producing systems is a common problem and results from poor functioning of the inhabiting micro-organisms. A poor understanding of the global diversities of these micro-organisms and lack of information on the link between environmental variables, biogas production, and community composition, contrains the development of strategies that can ameliorate these biochemical issues. We have integrated sequencing-by-synthesis technology and intensive computational approaches to reveal metacommunities in the studied reactor treatments. The identified communities were compared with the treatment’s phenotypic and environmental data in an attempt to fill the existing knowledge gaps on biogas microbiomes and their production capacities. We present 132 biogas taxonomic profiles systematically and comparatively, linking the abundance with the identified environmental variables. The local composition of microbiome and variations in abundance were also linked to the observed differences in biogas productivity, suggesting the possible cause of the observed variations. The detailed information presented in this study can aid in the genetic manipulation or formulation of optimal microbial ratios to improve their effectiveness in biogas production.

Recent discoveries of mcr and mcr-like complexes in genomes from diverse archaeal lineages suggest that methane (and more broadly alkane) metabolism is an ancient pathway with complicated evolutionary histories. The conventional view is that methanogenesis is an ancestral metabolism of the archaeal class Thermoplasmata. Through comparative genomic analysis of 12 Thermoplasmata metagenome-assembled genomes (MAGs), we show that these microorganisms do not encode the genes required for methanogenesis, which suggests that this metabolism may have been laterally acquired by an ancestor of the order Methanomassiliicoccales. These MAGs include representatives from four orders basal to the Methanomassiliicoccales, including a high-quality MAG (95% complete) that likely represents a new order, Ca. Lunaplasma lacustris ord. nov. sp. nov. These MAGs are predicted to use diverse energy conservation pathways, such as heterotrophy, sulfur and hydrogen metabolism, denitrification, and fermentation. Two of these lineages are globally widespread among anoxic, sedimentary environments, with the exception of Ca. Lunaplasma lacustris, which has thus far only been detected in alpine caves and subarctic lake sediments. These findings advance our understanding of the metabolic potential, ecology, and global distribution of the Thermoplasmata and provide new insights into the evolutionary history of methanogenesis within the Thermoplasmata.

Members of the phylum Bathyarchaeota and the class Thermoplasmata are widespread in marine and freshwater sediments where they have been recognized as key players in the carbon cycle. Here, we tested the responsiveness of archaeal communities on settled plant debris and sediment from a karstic lake to different organic carbon amendments (amino acids, plant-derived carbohydrates, and aromatics) using a lab-scale microcosm. Changes in the composition and abundance of sediment and biofilm archaeal communities in both DNA and RNA fractions were assessed by 16S rRNA gene amplicon sequencing and qPCR, respectively, after 7 and 30 days of incubation. Archaeal communities showed compositional changes in terms of alpha and beta diversity in relation to the type of carbon source (amino acids vs. plant-derived compounds), the nucleic acid fraction (DNA vs. RNA), and the incubation time (7 vs. 30 days). Distinct groups within the Bathyarchaeota (Bathy-15 and Bathy-6) and the Thermoplasmata (MBG-D) differently reacted to carbon supplements as deduced from the analysis of RNA libraries. Whereas Bathyarchaeota in biofilms showed a long-term positive response to humic acids, their counterparts in the sediment were mainly stimulated by the addition of tryptophan, suggesting the presence of different subpopulations in both habitats. Overall, our work presents an in vitro assessment of the versatility of archaea inhabiting freshwater sediments towards organic carbon and introduces settled leaf litter as a new habitat for the Bathyarchaeota and the Thermoplasmata.

Bacterial and archaeal community structure of five microbial communities, developing at different salinities in Baja California Sur, Mexico, were characterized by 16S rRNA sequencing. The response of the microbial community to artificial changes in salinity-sulfate concentrations and to addition of trimethylamine was also evaluated in microcosm experiments. Ordination analyses of the microbial community structure showed that microbial composition was distinctive for each hypersaline site. Members of bacteria were dominated by Bacteroidetes and Proteobacteria phyla, while Halobacteria of the Euryarchaeota phylum was the most represented class of archaea for all the environmental samples. At a higher phylogenetic resolution, methanogenic communities were dominated by members of the Methanosarcinales, Methanobacteriales and Methanococcales orders. Incubation experiments showed that putative hydrogenotrophic methanogens of the Methanomicrobiales increased in abundance only under lowest salinity and sulfate concentrations. Trimethylamine addition effectively increased the abundance of methylotrophic members from the Methanosarcinales, but also increased the relative abundance of the Thermoplasmata class, suggesting the potential capability of these microorganisms to use trimethylamine in hypersaline environments. These results contribute to the knowledge of microbial diversity in hypersaline environments from Baja California Sur, Mexico, and expand upon the available information for uncultured methanogenic archaea in these ecosystems.

We characterized the rich Archaea microbiome of shallow inland lakes (Monegros Desert, NE Spain) by 16S rRNA gene tag sequencing covering a wide salinity range (0.1-40% w/v) along three years. Up to 990 OTUs (370 OTUs each), followed by Halobacteria (105), Nanohaloarchaeota (62) and Thermoplasmata (19). Overall, the distribution of genetic richness was strongly correlated with environmental niche amplitude, but not with occurrence. We unveiled high occurrence for a very rich Woesearchaeota assemblage, and an unexpected positive correlation of Pacearchaeota abundance with salinity at >15% dissolved salt content. The estimated dynamic behaviour (temporal “turnover” rates of presence/absence data) unveiled Thaumarchaeota and Halobacteria as the most dynamic groups, and Aenigmarchaeota and Thermoplasmata as the most stable. The DPANN Pacearchaeota, Woesearchaeota, and Nanohaloarchaeota showed intermediate rates, suggesting higher resilience to environmental perturbations. A rich and dynamic Archaea microbiome was unveiled including unseen ecological traits for relevant members of the still largely unknown DPANN group, supporting a strong ecological differentiation between Pacearchaeota and Woesearchaeota., Funding was provided by grant BRIDGES, CGL2015-69043-P from the Spanish Office of Science (MINECO) and European funding (ERDF) to EOC and DA. MMS was funded by the Spanish FPI PhD scholarships program (BRIDGES MINECO)

Physicochemical and microbiological characteristics of formation waters low-temperature heavy oil reservoirs (Russia) were investigated. The Chernoozerskoe, Yuzhno-Suncheleevskoe, and Severo-Bogemskoe oilfields, which were exploited without water-flooding, were shown to harbor scant microbial communities, while microbial numbers in the water-flooded strata of the Vostochno-Anzirskoe and Cheremukhovskoe oilfields was as high as 106 cells/mL. The rates of sulfate reduction and methanogenesis were low, not exceeding 1982 ng S2–/(L day) and 9045 nL СН4/(L day), respectively, in the samples from water-flooded strata. High-throughput sequencing of microbial 16S rRNA gene fragments in the community of injection water revealed the sequences of the Proteobacteria (74.7%), including Betaproteobacteria (40.2%), Alphaproteobacteria (20.7%), Gammaproteobacteria (10.1%), Deltaproteobacteria (2.0%), and Epsilonproteobacteria (1.6%), as well as Firmicutes (7.9%), Bacteroidetes (4.1%), and Archaea (0.2%). DGGE analysis of microbial mcrA genes in the community of injection water revealed methanogens of the genera Methanothrix, Methanospirillum, Methanobacterium, Methanoregula, Methanosarcina, and Methanoculleus, as well as unidentified Thermoplasmata. Pure cultures of bacteria of the genera Rhodococcus, Pseudomonas, Gordonia, Cellulomonas, etc., capable of biosurfactant production when grown on heavy oil, were isolated. Enrichment cultures of fermentative bacteria producing significant amounts of volatile organic acids (acetic, propionic, and butyric) from sacchariferous substrates were obtained. These acids dissolve the carbonates of oil-bearing rock efficiently. Selection of the efficient microbial technology for enhanced recovery of heavy oil from terrigenous and carbonate strata requires model experiments with microbial isolates and the cores of oil-bearing rocks.

Microbial communities play crucial roles in mine drainage generation and remediation. Despite the wide distribution of archaea in the mine ecosystem, their diversity and ecological roles remain less understood than bacteria. Here, we retrieved 56 archaeal metagenome-assembled genomes from a river impacted by rare earth element (REE) mining activities in South China. Genomic analysis showed that archaea represented four distinct lineages, including phyla of Thaumarchaeota, Micrarchaeota, Nanoarchaeota and Thermoplasmata. These archaea represented a considerable fraction (up to 40%) of the total prokaryote community, which might contribute to nitrogen and sulfur cycling in the REE mine drainage. Reconstructed metabolic potential among diverse archaea taxa revealed that archaea were involved in the network of ammonia oxidation, denitrification, sulfate redox reaction, and required substrates supplied by other community members. As the dominant driver of ammonia oxidation, Thaumarchaeota might provide substrates to support the survival of two nano-sized archaea belonging to Micrarchaeota and Nanoarchaeota. Despite the absence of biosynthesis pathways for amino acids and nucleotides, the potential capacity for nitrite reduction (nirD) was observed in Micrarchaeota, indicating that these nano-sized archaea encompassed diverse metabolisms. Moreover, Thermoplasmata, as keystone taxa in community, might be the main genetic donor for the other three archaeal phyla, transferring many environmental resistance related genes (e.g., V/A-type ATPase and Vitamin B12-transporting ATPase). The genetic interactions within archaeal community through horizontal gene transfer might be the key to the formation of archaeal resistance and functional partitioning. This study provides putative metabolic and genetic insights into the diverse archaea taxa from community-level perspectives, and highlights the ecological roles of archaea in REE contaminated aquatic environment.

We lack a predictive understanding of the environmental drivers determining the structure and function of archaeal communities as well as the proteome associated with these important soil organisms. Here, we characterized the structure (by 16S rRNA gene sequencing) and function (by metaproteomics) of archaea from 32 soil samples across terrestrial ecosystems with contrasting climate and vegetation types. Our multi-“omics” approach unveiled that genes from Nitrosophaerales and Thermoplasmata dominated soils collected from four continents, and that archaea comprise 2.3 ± 0.3% of microbial proteins in these soils. Aridity positively correlated with the proportion of Nitrosophaerales genes and the number of archaeal proteins. The interaction of climate x vegetation shaped the functional profile of the archaeal community. Our study provides novel insights into the structure and function of soil archaea across climates, and highlights that these communities may be influenced by increasing global aridity.

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.

Summary Salar de Uyuni (SdU), with a geological history that reflects 50,000 years of climate change, is the largest hypersaline salt flat on Earth and is estimated to be the biggest lithium reservoir in the world. Its salinity reaches saturation levels for NaCl, a kosmotropic salt, and high concentrations of MgCL2 and LiCl, both salts considered important chaotrophic stressors. In addition, extreme temperatures, anoxic conditions, high UV irradiance, high albedo, and extremely low concentrations of phosphorous, make SdU a unique natural extreme environment in which to contrast hypotheses about limiting factors of life diversification. Geophysical studies of brines from different sampling stations show that water activity is rather constant along SdU. Geochemical measurements show significant differences in magnesium concentration, ranging from 0.2 to 2M. This work analyses the prokaryotic diversity and community structure at four SdU sampling stations, selected according to their location and ionic composition. Prokaryotic communities were composed of both Archaea (with members of the classes Halobacteria, Thermoplasmata and Nanohaloarchaea, from the Euryarchaeota and Nanohaloarcheota phyla respectively) and Bacteria (mainly belonging to Bacteroidetes and Proteobacteria phyla). The important differences in composition of microbial communities inversely correlate with Mg2+ concentration, suggesting that prokaryotic diversity at SdU is chaotropic dependent. This article is protected by copyright. All rights reserved.

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.

[Background] The current view suggests that in low-temperature acidic environments, archaea are significantly less abundant than bacteria. Thus, this study of the microbiome of Parys Mountain (Anglesey, UK) sheds light on the generality of this current assumption. Parys Mountain is a historically important copper mine and its acid mine drainage (AMD) water streams are characterised by constant moderate temperatures (8–18 °C), extremely low pH (1.7) and high concentrations of soluble iron and other metal cations., [Results] Metagenomic and SSU rRNA amplicon sequencing of DNA from Parys Mountain revealed a significant proportion of archaea affiliated with Euryarchaeota, which accounted for ca. 67% of the community. Within this phylum, potentially new clades of Thermoplasmata were overrepresented (58%), with the most predominant group being “E-plasma”, alongside low-abundant Cuniculiplasmataceae, ‘Ca. Micrarchaeota’ and ‘Terrestrial Miscellaneous Euryarchaeal Group’ (TMEG) archaea, which were phylogenetically close to Methanomassilicoccales and clustered with counterparts from acidic/moderately acidic settings. In the sediment, archaea and Thermoplasmata contributed the highest numbers in V3-V4 amplicon reads, in contrast with the water body community, where Proteobacteria, Nitrospirae, Acidobacteria and Actinobacteria outnumbered archaea. Cultivation efforts revealed the abundance of archaeal sequences closely related to Cuniculiplasma divulgatum in an enrichment culture established from the filterable fraction of the water sample. Enrichment cultures with unfiltered samples showed the presence of Ferrimicrobium acidiphilum, C. divulgatum, ‘Ca. Mancarchaeum acidiphilum Mia14’, ‘Ca. Micrarchaeota’-related and diverse minor (, [Conclusion] Contrary to expectation, our study showed a high abundance of archaea in this extremely acidic mine-impacted environment. Further, archaeal populations were dominated by one particular group, suggesting that they are functionally important. The prevalence of archaea over bacteria in these microbiomes and their spatial distribution patterns represents a novel and important advance in our understanding of acidophile ecology. We also demonstrated a procedure for the specific enrichment of cell wall-deficient members of the archaeal component of this community, although the large fraction of archaeal taxa remained unculturable. Lastly, we identified a separate clustering of globally occurring acidophilic members of TMEG that collectively belong to a distinct order within Thermoplasmata with yet unclear functional roles in the ecosystem., The work of OVG, PNG and SVT was supported by the Royal Society UK-Russia Exchange Grant #IE 160224 (RFBR 16-54-10072 КО project). OVG and PNG acknowledge ERA Net IB2 Project MetaCat through UK Biotechnology and Biological Sciences Research Council (BBSRC) Grant BB/M029085/1 and the support of the Centre of Environmental Biotechnology Project funded by the European Regional Development Fund (ERDF) through the Welsh Government. RB and PNG acknowledge the support of the Supercomputing Wales project, which is part-funded by the European Regional Development Fund (ERDF) via the Welsh Government. The work of AAK and IVK was supported by the Russian Science Foundation grant # 18-44-04024. MF acknowledges grants PCIN-2014-107 (within ERA NET IB2 grant ERA-IB-14-030—MetaCat), PCIN-2017-078 (within the Marine Biotechnology ERA-NET (ERA-MBT) funded under the European Commission’s Seventh Framework Programme, 2013-2017, Grant agreement 604814), BIO2014-54494-R and BIO2017-85522-R from the Spanish Ministry of Economy and Competitiveness.

Increasing attention has been attracted to host microbiota, due to their vital impact on host health. Little is known about the microbiota of the Chinese giant salamander (Andrias davidianus), in spite of the high economic and scientific value of this endangered species. This study was designed to characterise and compare the gut and lung prokaryotic communities of the Chinese giant salamander by high-throughput sequencing. Our study showed that the giant salamander had a lung prokaryotic community that clustered separately from its intestinal microbiota. Statistical analysis (LEfSe) revealed that the bacterial populations were dominated by Geobacter, Sulfurimonas, and Dechloromonas from Proteobacteria phylum, and Corynebacterium from Actinobacteria phylum in the lung, while Parabacteroides, Bacteroides, and PW3 from Bacteroidetes phylum, and Oscillospira from Firmicutes phylum were predominant in the intestine. A particularly innovative finding was the fairly high abundance of Archaea, especially methanogenic Euryarchaeota. The gut dominant Archaea were Methanocorpusculum and Thermoplasmata vadinCA11, while Methanosaeta and Methanoculleus were the main Archaea in the lung. PICRUSt analysis revealed differentiated functional profiles between the intestinal miacrobiota and the lung microbiota. Specially, some microbial metabolic functions were significantly more active in the intestinal microbiota, while the functional genes involved in infectious diseases were much richer in the lung microbiota. This study characterized the prokaryotic microbial community profiles in the gut and lung of the Chinese giant salamander, providing foundational support for future study seeking to understand microbiota of the giant salamander and the role of its microbiota on infectious diseases.

Last decade advances on methane microbial ecology in natural environments and man-made systems have introduced possibilities and challenges to biogas-producing processes. Mostly restricted to anaerobic environments, methanogens have also been detected in aerobic desertic soils, and their presence in extreme environments, such as hydrothermal vents, soda lakes, and Antarctic sediments, shows how ubiquitous and adapted they are to different environmental conditions. Most known methanogens belong to Euryarchaeota classes, producing methane from acetoclastic, hydrogenotrophic, or methylotrophic pathways. Recently discovered representatives in Thermoplasmata and Halobacteria classes, as well as in Bathyarchaeota and Vestretearchaeota, Phyla brought new insights on methanogenic diversity and their metabolic pathways. Biotechnological application of methanogens has been studied in bioreactors used for treatment of wastewater and waste. These bioreactors can be operated with acidogenesis and methanogenesis occurring in one stage or, with phase separation, acidogenesis followed by methanogenesis, with suspended and/or attached cells. Several factors have been studied to understand and optimize biogas production in bioreactors, such as temperature, organic load, and type of wastewater input. The biogas-producing communities received special attention following the development of metagenomics, metatranscriptomics, and single-cell genomic approaches. Coupled to the discovery of new methanogenic lineages, these methods revealed the complexity of microbial community structure and functions in both natural environments and bioreactors. However, a comprehensive view of these communities is still needed to improve current biogas-producing processes.

It has been suggested that condensed tannin (CT) fractions of different molecular weights (MWs) affect the level of methane (CH 4 ) production in ruminant by altering the ruminal methanogenic diversity. In this study, the effects of unfractionated CTs (F0) and five CT fractions (F1⿿F5) of different MWs from Leucaena leucocephala hybrid-Rendang (LLR) on the population and diversity of rumen methanogenic archaea in vitro were investigated using real-time PCR and high throughput sequencing. Real-time PCR analysis showed that higher-MW CT fractions (fractions F1 and F2) significantly ( P Methanobacteriales than the control (without CTs), unfractionated CTs F0 and lower-MW CT fractions (fractions F3-F5). Population of methanogens from the order Methanomicrobiales was not significantly ( P > 0.05) different among all CT fractions and the control. Amplification of archaeal 16S RNA genes (targeting the V3 region) of seven samples (obtained from in vitro gas production test) using Illumina Miseq sequencer, recovered 642,244 sequences (mean of 91,763 sequences per sample) which consisted of a number of OTUs ranging from 91 to 155 and were assigned to 12 genera. Bioinformatic analysis illustrated that the natural rumen archaeal community of a cattle (without supplementation of CTs) was predominated by an unclassified genus, VadinCA11 gut group which is Thermoplasmata -associated (56.3% of the total sequence reads), followed by Methanobrevibacter (25.1%) and Methanomicrobium (15.3%), while the remaining genera were below 1% of relative abundance. Relative abundance of the unclassified Thermoplasmata -associated group (VadinCA11 gut group) increased significantly ( P Methanobrevibacter was significantly ( P P Methanomicrobium . Condensed tannin fractions of different MWs from LLR could alter the size of populations and diversity of rumen methanogenic archaea in vitro , which could contribute to the reduction of CH 4 production, and the impact was more pronounced for CT fractions with higher-MWs.

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.

Archaea are ubiquitous in terrestrial and marine environments and play an important role in biogeochemical cycles. Although air acts as the primary medium for their dispersal among different habitats, their diversity and abundance is not well characterized. The main reason for this lack of insight is that archaea are difficult to culture, seem to be low in number in the atmosphere, and have so far been difficult to detect even with molecular genetic approaches. However, to better understand the transport, residence time, and living conditions of microorganisms in the atmosphere as well as their effects on the atmosphere and vice versa, it is essential to study all groups of bioaerosols. Here we present an in-depth analysis of airborne archaea based on Illumina sequencing of 16S rRNA genes from atmospheric coarse and fine particulate matter samples and show seasonal dynamics and discuss anthropogenic influences on the diversity, composition, and abundance of airborne archaea.The relative proportions of archaea to bacteria, the differences of the community composition in fine and coarse particulate matter, and the high abundance in coarse matter of one typical soil related family, the Nitrososphaeraceae, point to local phyllosphere and soil habitats as primary emission sources of airborne archaea.We found comparable seasonal dynamics for the dominating Euryarchaeota classes and Crenarchaeota orders peaking in summer and fall. In contrast, the omnipresent Cenarchaeales and the Thermoplasmata occur only throughout summer and fall. We also gained novel insights into archaeal composition in fine particulate matter (Nitrosopumilus as the dominating taxa.The seasonal dynamics of methanogenic Euryarchaeota point to anthropogenic activities, such as fertilization of agricultural fields with biogas substrates or manure, as sources of airborne archaea. This study gains a deeper insight into the abundance and composition of archaea in the atmosphere, especially within the fine particle mode, which adds to a better understanding of the overall atmospheric microbiome.

This paper presents study on the microbiome of a unique extreme environment - saline and alkaline lime, a by-product of soda ash and table salt production in Janikowo, central Poland. High-throughput 16S rDNA amplicon sequencing was used to reveal the structure of bacterial and archaeal communities in the lime samples, taken from repository ponds differing in salinity (2.3–25.5% NaCl). Surprisingly abundant and diverse bacterial communities were discovered in this extreme environment. The most important geochemical drivers of the observed microbial diversity were salinity, calcium ions, nutrients, and water content. The bacterial and archaeal communities in saline, alkaline lime were similar to those found in natural haloalkaline environments. Although the archaeal contribution to the whole microbial community was lower than 4%, the four archaeal genera Natronomonas, Halorubrum, Halobellus, and Halapricum constituted the core microbiome of saline, alkaline lime - a set of OTUs (> 0.1% of total archaeal relative abundance) present in all samples under study. The high proportion of novel, unclassified archaeal and bacterial sequences (not identified at 97% similarity level) in the 16S rRNA gene libraries indicated that potentially new genera, especially within the class of Thermoplasmata inhabit this unique environment.

Archaea are abundant in extreme environments but they are also a prevalent component of microbial communities in soils, marine or freshwater plankton and sediments. Many studies highlighted the prominent role of marine sedimentary Archaea in global nutrient cycles. Less information is available, however, on the diversity, abundance and ecological role of Archaea in freshwater sediments. A serious pitfall for the study of Archaea is their low cultivability under laboratory-controlled conditions thus constraining the progress towards the complete understanding of their metabolic capabilities and ecological functions. Most of the work is thus based on molecular techniques that allow the identification and quantification of target microorganisms without their cultivation. In this PhD project, we applied a combination of high-throughput sequencing and quantitative PCR to investigate the distribution, abundance and composition of archaeal communities in sediments from different freshwater systems (lakes, lagoons and reservoirs encompassing a wide range of conditions and typologies). The work has been focused in two archaeal groups consistently found, and especially abundant, in sediments: the phylum Bathyarchaeota and the class Thermoplasmata Els arqueus abunden en ambients extrems però també són un component rellevant dels sòls, del plàncton oceànic i lacustre i dels sediments. Molts estudis han destacat la importància dels arqueus en els cicles de nutrients dels sediments marins tant a escala local com global. En canvi, es disposa de menys informació sobre la diversitat, abundància i paper que juguen els arqueus en sediments d’aigua dolça a excepció dels metanògens. Com a dificultat afegida, la majoria d’arqueus sedimentaris no s’han pogut cultivar encara al laboratori, el que dificulta el seu estudi. La solució a aquests problemes passa per l’aplicació de tècniques moleculars que permeten la identificació i recompte dels microorganismes diana sense necessitat de cultivar-los. En aquesta tesi s’han combinat diferents tècniques moleculars (seqüenciació massiva i PCR quantitativa) per a conèixer la distribució, abundància i composició de les comunitats d’arqueus en sediments de sistemes aquàtics d’aigua dolça (llacs, llacunes i embassaments amb diferents condicions i tipologies). La tesi s’ha centrat en dos grups d’arqueus que són ubics i especialment abundants en sediments: el fílum Bathyarchaeota i la classe Thermoplasmata

The ecological processes underlying the observed patterns in community composition of archaea in swine manure slurry are poorly understood. We studied the archaeal communities from six swine manure slurry storage tanks using paired-end Illumina sequencing of the v3 hypervariable region of 16S rRNA gene. Across all samples, the archaeal community was dominated by methanogens related toThermoplasmata, Methanomicrobia, andMethanobacteriaclasses. At the genus level, the archaeal community was dominated by a single uncultured lineage of archaea,vadinCA11, followed by methanogenic generaMethanobrevibacter,Methanosarcina,Methanosphaera,Methanogenium,Methanocorpusculum,Methanoculleus, andMethanomicrococcus. Significant phylogenetic signals were detected across relatively short phylogenetic distances, indicating that closely related archaeal operational taxonomic units (OTUs) tend to have similar niches. The standardized effect sizes of mean nearest taxon distance (SES.MNTD) showed that archaeal community was phylogenetically clustered, suggesting that environmental filtering deterministically influence the within-community composition of archaea. However, between-community analysis based onβ-nearest taxon index (βNTI) revealed that both deterministic selection and stochastic processes operate simultaneously to govern the assembly of archaeal communities. These findings significantly enhance our understanding of archaeal community assembly and underlying ecological processes is swine manure slurry.

Archaeal communities in mineral soils were compared between a boreal forest in Finland and cold-temperate forest in Japan using 16S rRNA gene-targeted high-throughput sequencing. In boreal soils, Thaumarchaeota Group 1.1c archaea predominated and Thaumarchaeota Group 1.1a-associated and Group 1.1b archaea were also detected. In temperate soils, Thaumarchaeota Group 1.1a-associated and Group 1.1b archaea were dominant members at the subsurface, whereas their dominancy was replaced by Thermoplasmata archaea at the subsoil. An analysis of the ammonia monooxygenase subunit A gene of Archaea also indicated the distribution of Thaumarchaeota Group 1.1a-associated and Group 1.1b archaea in these soils.

Biofilm formation, one of the primary causes of biofouling, results in reduced membrane flux or increased transmembrane pressure and thus represents a major impediment to the wider implementation of membrane bioreactor (MBR) technologies for water purification. Most studies have focused on the role of bacteria in membrane fouling as they are the most dominant and best studied organisms present in the MBR. In contrast, there is limited information on the role of the archaeal community in biofilm formation in MBRs. This study investigated the composition of the archaeal community during the process of biofouling in an MBR. The archaeal community was observed to have lower richness and diversity in the biofilm than the sludge during the establishment of biofilms at low transmembrane pressure (TMP). Clustering of the communities based on the Bray–Curtis similarity matrix indicated that a subset of the sludge archaeal community formed the initial biofilms. The archaeal community in the biofilm was mainly composed of Thermoprotei, Thermoplasmata, Thermococci, Methanopyri, Methanomicrobia and Halobacteria. Among them, the Thermoprotei and Thermoplasmata were present at higher relative proportions in the biofilms than they were in the sludge. Additionally, the Thermoprotei, Thermoplasmata and Thermococci were the dominant organisms detected in the initial biofilms at low TMP, while as the TMP increased, the Methanopyri, Methanomicrobia, Aciduliprofundum and Halobacteria were present at higher abundances in the biofilms at high TMP. Published version

In the present study, benthic microbial communities along the Pearl Estuary, a typical subtropical estuary in China subjected to extensive anthropogenic disturbance, were investigated using 16S rRNA gene-based pyrosequencing. The results showed that microbial communities in freshwater samples were clearly distinct from those in saltwater samples, since the relative sequence abundances of Deltaproteobacteria, Thermoplasmata and Marine Group I (MG-I) were higher in saltwater sediments, whereas Chloroflexi, Spirochaetes, Betaproteobacteria and methanogens were more prevalent in freshwater sediments. In addition, bacterial communities showed vertical stratifications in saltwater sediments, but remained constant with depth in freshwater sediments. The total organic carbon and carbon/nitrogen ratio in sediments correlated significantly with the overall community variations. The predominance of various microorganisms in specific niches led to efforts to identify their functional couplings by exploring their co-occurrence patterns. Using network analysis, strong positive correlations were observed between sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria, and between SRB and nitrite-oxidizing bacteria, indicating the potential interactions of intra-sulfur cycle processes, as well as sulfur and nitrogen cycles, in coastal sediments. Archaeal clades revealed strong and wide correlations between the Miscellaneous Crenarchaeotal Group (MCG) and other groups, suggesting a central role of MCG in the coastal benthic environment. Inversely, MG-I displayed negative correlations with other clades, which might indicate that the lifestyles of heterotrophic and autotrophic clades were mutually exclusive. This study presented a detailed outline of the biogeographic patterns of benthic microbial communities along the Pearl Estuary and provided new information regarding the potential interactions of various biogeochemical cycles in coastal sediments.

A central goal in marine microecology is to understand the ecological factors shaping spatiotemporal microbial patterns and the underlying processes. We hypothesized that abiotic and/or biotic interactions are probably more important for explaining the distribution patterns of marine bacterioplankton than environmental filtering. In this study, surface seawater samples were collected about 7000 miles from the Mediterranean Sea, transecting the North Atlantic Ocean, to the Brazilian marginal sea. In bacterial biosphere, SAR11, SAR86, Rhodobacteraceae, and Rhodospiriaceae were predominant in the Mediterranean Sea; Prochlorococcus was more frequent in Atlantic Ocean; whereas in the Brazilian coastal sea, the main bacterial members were Synechococcus and SAR11. With respect to archaea, Euryarchaeota were predominant in the Atlantic Ocean and Thaumarchaeota in the Mediterranean Sea. With respect to the eukaryotes, Syndiniales, Spumellaria, Cryomonadida, and Chlorodendrales were predominant in the open ocean, while diatoms and microzooplankton were dominant in the coastal sea. Distinct clusters of prokaryotes and eukaryotes displayed clear spatial heterogeneity. Among the environmental parameters measured, temperature and salinity were key factors controlling bacterial and archaeal community structure, respectively, whereas N/P/Si contributed to eukaryotic variation. The relative contribution of environmental parameters to the microbial distribution pattern was 45.2%. Interaction analysis showed that Gammaproteobacteria, Alphaproteobacteria, and Flavobacteriia were the keystone taxa within the positive-correlation network, while Thermoplasmata was the main contributor in the negative-correlation network. Our study demonstrated that microbial communities are co-governed by environmental filtering and biotic interactions, which are the main deterministic driving factors modulating the spatiotemporal patterns of marine plankton synergistically at the regional or global levels.

cited By 0; International audience; Acid mine drainages are characterized by their low pH and the presence of dissolved toxic metallic species. Microorganisms survive in different microhabitats within the ecosystem, namely water, sediments, and biofilms. In this report, we surveyed the microbial diversity within all domains of life in the different microhabitats at Los Rueldos abandoned mercury underground mine (NW Spain), and predicted bacterial function based on community composition. Sediment samples contained higher proportions of soil bacteria (AD3, Acidobacteria), as well as Crenarchaeota and Methanomassiliicoccaceae archaea. Oxic and hypoxic biofilm samples were enriched in bacterial iron oxidizers from the genus Leptospirillum, order Acidithiobacillales, class Betaproteobacteria, and archaea from the class Thermoplasmata. Water samples were enriched in Cyanobacteria and Thermoplasmata archaea at a 3–98% of the sunlight influence, whilst Betaproteobacteria, Thermoplasmata archaea, and Micrarchaea dominated in acid water collected in total darkness. Stalactites hanging from the Ferich mine ceiling were dominated by the neutrophilic iron oxidizer Gallionella and other lineages that were absent in the rest of the microhabitats (e.g., Chlorobi, Chloroflexi). Eukaryotes were detected in biofilms and open-air water samples, and belonged mainly to clades SAR (Alveolata and Stramenopiles), and Opisthokonta (Fungi). Oxic and hypoxic biofilms displayed higher proportions of ciliates (Gonostomum, Oxytricha), whereas water samples were enriched in fungi (Paramicrosporidium and unknown microbial Helotiales). Predicted unction through bacterial community composition suggested adaptive evolutive convergence of function in heterogeneous communities. Our study showcases a broad description of the microbial diversity across different microhabitats in the same environment and expands the knowledge on the diversityof microbial eukaryotes in AMD habitats.

The microbial community in eutrophic freshwater sediment was investigated from a 67-cm-deep sediment core collected from the Daechung Reservoir in South Korea, where cyanobacterial blooms have occurred annually for the past 30 years. The majority of core sediments were characterized by dark-grayish, fine-grained mud with abundant gas-escaped and thinly laminated layers. Intervals of summer and winter seasons were represented by periodic peaks of geochemical profiles of parameters such as grain size and relative carbon mass ratios to various nutrients such as nitrogen, sulfur, and phosphorus. In bacteria, Proteobacteria (66.6%) was the most prevalent phylum, followed by Chloroflexi (8.9%), Bacteroidetes (5.1%), and Spirochaetes (2.6%). Archaea were also abundant, representing approximately half of the total prokaryotes in the sediments. Notably, three Bacteria (Sulfuricurvum, Sideroxydans, and Gallionella) and one Archaea (Thermoplasmata) accounted for 43.4% and 38.4% of the total bacteria and archaea, respectively, implying that iron and sulfur oxidizing microorganisms dominate in this eutrophic freshwater sediment. These results indicate that 1) eutrophic freshwater lakes in monsoon climates undergo a stratified sedimentary process with seasonal and annual variations in geochemical and microbial profiles, and 2) the microbial oxidative metabolism of iron and sulfur is notably active in sediments from a eutrophic lake.