Bathyarchaeota, formerly known as the Miscellaneous Crenarchaeotal Group, is a phylum of global generalists that are widespread in anoxic sediments, which host relatively high abundance archaeal communities. Until now, 25 subgroups have been identified in the Bathyarchaeota. The distinct bathyarchaeotal subgroups diverged to adapt to marine and freshwater environments. Based on the physiological and genomic evidence, acetyl-coenzyme A-centralized heterotrophic pathways of energy conservation have been proposed to function in Bathyarchaeota; these microbes are able to anaerobically utilize (i) detrital proteins, (ii) polymeric carbohydrates, (iii) fatty acids/aromatic compounds, (iv) methane (or short chain alkane) and methylated compounds, and/or (v) potentially other organic matter. Furthermore, bathyarchaeotal members have wide metabolic capabilities, including acetogenesis, methane metabolism, and dissimilatory nitrogen and sulfur reduction, and they also have potential interactions with anaerobic methane-oxidizing archaea, acetoclastic methanogens and heterotrophic bacteria. These results have not only demonstrated multiple and important ecological functions of this archaeal phylum, but also paved the way for a detailed understanding of the evolution and metabolism of archaea as such. This review summarizes the recent findings pertaining to the ecological, physiological and genomic aspects of Bathyarchaeota, highlighting the vital role of this phylum in global carbon cycling.

Published polymerase chain reaction primer sets for detecting the genes encoding 16S rRNA gene and hydrazine oxidoreductase (hzo) in anammox bacteria were compared by using the same coastal marine sediment samples. While four previously reported primer sets developed to detect the 16S rRNA gene showed varying specificities between 12% and 77%, an optimized primer combination resulted in up to 98% specificity, and the recovered anammox 16S rRNA gene sequences were >95% sequence identical to published sequences from anammox bacteria in the Candidatus "Scalindua" group. Furthermore, four primer sets used in detecting the hzo gene of anammox bacteria were highly specific (up to 92%) and efficient, and the newly designed primer set in this study amplified longer hzo gene segments suitable for phylogenetic analysis. The optimized primer set for the 16S rRNA gene and the newly designed primer set for the hzo gene were successfully applied to identify anammox bacteria from marine sediments of aquaculture zone, coastal wetland, and deep ocean where the three ecosystems form a gradient of anthropogenic impact. Results indicated a broad distribution of anammox bacteria with high niche-specific community structure within each marine ecosystem.

The methanogenic alkanes-degrading enrichment culture which had been incubated for over 1,300 days amended with n-alkanes (C15–C20) was investigated through clone libraries of bacteria, archaea and assA, mcrA functional genes. These enrichment cultures were obtained from oily sludge after an initial incubation of the oily sludge without any carbon source and then an enrichment transfer with n-alkanes (C15–C20) for acclimation. Activation of alkanes, methane precursor generation and methanogenic pathways are considered as three pivotal stages for the continuous methanogenesis from degradation of alkanes. The presence of functional genes encoding the alkylsuccinate synthase α-subunit indicated that fumarate addition is most likely the one of initial activation step for degradation of n-alkanes. Degradation intermediates of n-alkanes were octadecanoate, hexadecanoate, butyrate, isobutyrate, acetate and propionate, which could provide the appropriate substrates for acetate formation. Both methyl coenzyme M reductase gene and 16S rRNA gene analysis showed that microorganisms of Methanoseata were the most dominant methanogens, capable of using acetate as the electron donor to produce methane. Bacterial clone libraries showed organisms of Anaerolineaceae (within the phylum of Chloroflexi) were predominant (45.5%), indicating syntrophically cooperation with Methanosaeta archaea was likely involved in the process of methanogenic degradation of alkanes. Alkanes may initially be activated via fumarate addition and degraded to fatty acids, then converted to acetate, which was further converted to methane and carbon dioxide by methanogens.Electronic supplementary materialThe online version of this article (doi:10.1186/s13568-015-0117-4) contains supplementary material, which is available to authorized users.

Thorarchaeota are a new archaeal phylum within the Asgard superphylum, whose ancestors have been proposed to play possible ecological roles in cellular evolution. However, little is known about the lifestyles of these uncultured archaea. To provide a better resolution of the ecological roles and metabolic capacity of Thorarchaeota, we obtained Thorarchaeota genomes reconstructed from metagenomes of different depth layers in mangrove and mudflat sediments. These genomes from deep anoxic layers suggest the presence of Thorarchaeota with the potential to degrade organic matter, fix inorganic carbon, reduce sulfur/sulfate and produce acetate. In particular, Thorarchaeota may be involved in ethanol production, nitrogen fixation, nitrite reduction, and arsenic detoxification. Interestingly, these Thorarchaeotal genomes are inferred to contain the tetrahydromethanopterin and tetrahydrofolate Wood-Ljungdahl (WL) pathways for CO reduction, and the latter WL pathway appears to have originated from bacteria. These archaea are predicted to be able to use various inorganic and organic carbon sources, possessing genes inferred to encode ribulose bisphosphate carboxylase-like proteins (normally without RuBisCO activity) and a near-complete Calvin-Benson-Bassham cycle. The existence of eukaryotic selenocysteine insertion sequences and many genes for proteins previously considered eukaryote-specific in Thorarchaeota genomes provide new insights into their evolutionary roles in the origin of eukaryotic cellular complexity. Resolving the metabolic capacities of these enigmatic archaea and their origins will enhance our understanding of the origins of eukaryotes and their roles in ecosystems.

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An increase in the frequency of seafood-borne gastroenteritis in humans and Vibrio-related disease of fish and invertebrates has generated interest in the ecology of disease-causing Vibrios and the mechanisms driving their evolution. Genome sequencing studies have indicated a substantial contribution of horizontal gene transfer (HGT) to the evolution of Vibrios. Of particular interest is the contribution of HGT to the evolution of Vibrios pathogens and the adaptation of disease-causing Vibrios for survival in diverse environments. In this review, we discuss the diversity and distribution of mobile genetic elements (MGEs) isolated from Vibrios and the contribution of these elements to the expansion of the ecological and pathogenic niches of the host strain. Much of the research on Vibrio MGEs has focused on understanding phages and plasmids and we will primarily discuss the evolution of these elements and also briefly highlight the other diverse elements characterized from Vibrios, which includes genomic islands and conjugative elements.

Microbial assemblage in an n-alkanes-dependent thermophilic methanogenic enrichment cultures derived from production waters of a high-temperature petroleum reservoir was investigated in this study. Substantially higher amounts of methane were generated from the enrichment cultures incubated at 55 °C for 528 days with a mixture of long-chain n-alkanes (C(15)-C(20)). Stoichiometric estimation showed that alkanes-dependent methanogenesis accounted for about 19.8% of the total amount of methane expected. Hydrogen was occasionally detected together with methane in the gas phase of the cultures. Chemical analysis of the liquid cultures resulted only in low concentrations of acetate and formate. Phylogenetic analysis of the enrichment revealed the presence of several bacterial taxa related to Firmicutes, Thermodesulfobiaceae, Thermotogaceae, Nitrospiraceae, Dictyoglomaceae, Candidate division OP8 and others without close cultured representatives, and Archaea predominantly related to uncultured members in the order Archaeoglobales and CO(2)-reducing methanogens. Screening of genomic DNA retrieved from the alkanes-amended enrichment cultures also suggested the presence of new alkylsuccinate synthase alpha-subunit (assA) homologues. These findings suggest the presence of poorly characterized (putative) anaerobic n-alkanes degraders in the thermophilic methanogenic enrichment cultures. Our results indicate that methanogenesis of alkanes under thermophilic condition is likely to proceed via syntrophic acetate and/or formate oxidation linked with hydrogenotrophic methanogenesis.

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