Proposed minimal standards for description of methanogenic archaea

Methanogenic archaea are a diverse, polyphyletic group of strictly anaerobic prokaryotes capable of producing methane as their primary metabolic product. It has been over three decades since minimal standards for their taxonomic description have been proposed. In light of advancements in technology and amendments in systematic microbiology, revision of the older criteria for taxonomic description is essential. Most of the previously recommended minimum standards regarding phenotypic characterization of pure cultures are maintained. Electron microscopy and chemotaxonomic methods like whole-cell protein and lipid analysis are desirable but not required. Because of advancements in DNA sequencing technologies, obtaining a complete or draft whole genome sequence for type strains and its deposition in a public database are now mandatory. Genomic data should be used for rigorous comparison to close relatives using overall genome related indices such as average nucleotide identity and digital DNA-DNA hybridization. Phylogenetic analysis of the 16S rRNA gene is also required and can be supplemented by phylogenies of the mcrA gene and phylogenomic analysis using multiple conserved, single-copy marker genes. Additionally, it is now established that culture purity is not essential for studying prokaryotes, and description of Candidatus methanogenic taxa using single-cell or metagenomics along with other appropriate criteria is a viable alternative. The revisions to the minimal criteria proposed here by the members of the Subcommittee on the Taxonomy of Methanogenic Archaea of the International Committee on Systematics of Prokaryotes should allow for rigorous yet practical taxonomic description of these important and diverse microbes.

Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species

Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed from the atmosphere for ~5 million years, has several aqueous chambers, some with low atmospheric O₂ (~7%). The cave's surface-water microbial community is dominated by bacteria we identified as Thiovulum. We show that this strain, and others from subsurface environments, are phylogenetically distinct from marine Thiovulum. We assembled a closed genome of the Movile strain and confirmed its metabolism using RNAseq. We compared the genome of this strain and one we assembled from public data from the sulfidic Frasassi caves to four marine genomes, including Candidatus Thiovulum karukerense and Ca. T. imperiosus, whose genomes we sequenced. Despite great spatial and temporal separation, the genomes of the Movile and Frasassi Thiovulum were highly similar, differing greatly from the very diverse marine strains. We concluded that cave Thiovulum represent a new species, named here Candidatus Thiovulum stygium. Based on their genomes, cave Thiovulum can switch between aerobic and anaerobic sulfide oxidation using O₂ and NO₃^- as electron acceptors, the latter likely via dissimilatory nitrate reduction to ammonia. Thus, Thiovulum is likely important to both S and N cycles in sulfidic caves. Electron microscopy analysis suggests that at least some of the short peritrichous structures typical of Thiovulum are type IV pili, for which genes were found in all strains. These pili may play a role in veil formation, by connecting adjacent cells, and in the motility of these exceptionally fast swimmers.

Carbon metabolism and adaptation of hyperalkaliphilic microbes in serpentinizing spring of Manleluag, the Philippines

Reduced substrates produced by the serpentinization reaction under hydration of olivine may have fuelled biological processes on early Earth. To understand the adaptive strategies and carbon metabolism of the microbes in the serpentinizing ecosystems, we reconstructed 18 draft genomes representing dominant species of Omnitrophicaeota, Gammaproteobacteria and Methanobacteria from the Manleluag serpentinizing spring in Zambales, Philippines (hyperalkaline and rich in methane and hydrogen). Phylogenomics revealed that two genomes were affiliated with a candidate phylum NPL-UPA2 and the references of all our genomes were derived from ground waters, hot springs and the deep biosphere. C1 metabolism appears to be widespread as most of the genomes code for methanogenesis, CO oxidation and CO₂ fixation. However, likely due to the low CO₂ concentration and election acceptors, the biomass in the spring was extremely low (<10³  cell/ml). Various Na⁺ and K⁺ transporters and Na⁺ -driving ATPases appear to be encoded by these genomes, suggesting that nutrient acquisition, bioenergetics and normal cytoplasmic pH were dependent on Na⁺ and K⁺ pumps. Our results advance our understanding of the metabolic potentials and bioenergetics of serpentinizing springs and provide a framework of the ecology of early Earth.

Quantitative assessment of exposure to fecal contamination in urban environment across nine cities in low-income and lower-middle-income countries and a city in the United States

BACKGROUND

During 2014 to 2019, the SaniPath Exposure Assessment Tool, a standardized set of methods to evaluate risk of exposure to fecal contamination in the urban environment through multiple exposure pathways, was deployed in 45 neighborhoods in ten cities, including Accra and Kumasi, Ghana; Vellore, India; Maputo, Mozambique; Siem Reap, Cambodia; Atlanta, United States; Dhaka, Bangladesh; Lusaka, Zambia; Kampala, Uganda; Dakar, Senegal.

OBJECTIVE

Assess and compare risk of exposure to fecal contamination via multiple pathways in ten cities.

METHODS

In total, 4053 environmental samples, 4586 household surveys, 128 community surveys, and 124 school surveys were collected. E. coli concentrations were measured in environmental samples as an indicator of fecal contamination magnitude. Bayesian methods were used to estimate the distributions of fecal contamination concentration and contact frequency. Exposure to fecal contamination was estimated by the Monte Carlo method. The contamination levels of ten environmental compartments, frequency of contact with those compartments for adults and children, and estimated exposure to fecal contamination through any of the surveyed environmental pathways were compared across cities and neighborhoods.

RESULTS

Distribution of fecal contamination in the environment and human contact behavior varied by city. Universally, food pathways were the most common dominant route of exposure to fecal contamination across cities in low-income and lower-middle-income countries. Risks of fecal exposure via water pathways, such as open drains, flood water, and municipal drinking water, were site-specific and often limited to smaller geographic areas (i.e., neighborhoods) instead of larger areas (i.e., cities).

CONCLUSIONS

Knowledge of the relative contribution to fecal exposure from multiple pathways, and the environmental contamination level and frequency of contact for those "dominant pathways" could provide guidance for Water, Sanitation, and Hygiene (WASH) programming and investments and enable local governments and municipalities to improve intervention strategies to reduce the risk of exposure to fecal contamination.

The Chemoautotrophically Based Movile Cave Groundwater Ecosystem, a Hotspot of Subterranean Biodiversity

Movile Cave hosts one of the world’s most diverse subsurface invertebrate communities. In the absence of matter and energy input from the surface, this ecosystem relies entirely on in situ primary productivity by chemoautotrophic microorganisms. The energy source for these microorganisms is the oxidation of hydrogen sulfide provided continuously from the deep thermomineral aquifer, alongside methane, and ammonium. The microbial biofilms that cover the water surface, the cave walls, and the sediments, along with the free-swimming microorganisms, represent the food that protists, rotifers, nematodes, gastropods, and crustacean rely on. Voracious water-scorpions, leeches, and planarians form the peak of the aquatic food web in Movile Cave. The terrestrial community is even more diverse. It is composed of various species of worms, isopods, pseudoscorpions, spiders, centipedes, millipedes, springtails, diplurans, and beetles. An updated list of invertebrate species thriving in Movile Cave is provided herein. With 52 invertebrate species (21 aquatic and 31 terrestrial), of which 37 are endemic for this unusual, but fascinating environment, Movile Cave is the first known chemosynthesis-based groundwater ecosystem. Therefore, Movile Cave deserves stringent attention and protection.

Microbial properties of the granular sludge in a psychrophilic UASB reactor fed with electronics industry wastewater containing organic chemicals

In this study, a lab-scale upflow anaerobic sludge blanket (UASB) reactor was applied to the treatment of artificial electronics industry wastewater containing tetramethylammonium-hydroxide (TMAH), monoethanolamine (MEA), and isopropyl-alcohol (IPA) in order to evaluate process performance and degradation properties. During 800 days of operation, 96% efficiency of chemical oxygen demand (COD) removal was stably achieved at an organic loading rate of 8.5 kgCOD/m³/day at 18-19 °C. MEA degradation, carried out by acid-forming eubacteria, was confirmed within a week. The physical properties of the retained granular sludge were degraded by feeding with TMAH wastewater, but maintained by feeding with MEA wastewater due to an accumulation of species from the genus Methanosaeta and family Geobacteraceae. Analysis of the microbial community structure via SEM and 16S rRNA genes showed a proliferation of Methanomethylovorans-like cells and Methanosaeta-like cells at the surface and in the core of the granular sludge with TMAH, MEA and IPA acclimation. Furthermore, a batch degradation experiment confirmed that process inhibition due to increasing chemical concentration was relatively stronger for TMAH than for MEA or IPA. Thus, controlling the TMAH concentration of the influent to below 1 gCOD/L will be important for the stable treatment of electronics industry wastewater by UASB technology.

Spatial and seasonal variation of methanogenic community in a river-bay system in South China

River-bay system is a transitional zone connecting land and ocean and an important natural source for methane emission. Methanogens play important roles in the global greenhouse gas budget and carbon cycle since they produce methane. The abundance and community assemblage of methanogens in such a dynamic system are not well understood. Here, we used quantitative PCR and high-throughput sequencing of the mcrA gene to investigate the abundance and community composition of methanogens in the Shenzhen River-Bay system, a typical subtropical river-bay system in Southern of China, during the wet and dry seasons. Results showed that mcrA gene abundance was significantly higher in the sediments of river than those of estuary, and was higher in wet season than dry season. Sequences of mcrA gene were mostly assigned to three orders, including Methanosarcinales, Methanomicrobiales, and Methanobacteriales. Specifically, Methanosarcina, Methanosaeta, and Methanobacterium were the most abundant and ubiquitous genera. Methanogenic communities generally clustered according to habitat (river vs. estuary), and salinity was the major factor driving the methanogenic community assemblage. Furthermore, the indicator groups for two habitats were identified. For example, Methanococcoides, Methanoculleus, and Methanogenium preferentially existed in estuarine sediments, whereas Methanomethylovorans, Methanolinea, Methanoregula, and Methanomassiliicoccales were more abundant in riverine sediments, indicating distinct ecological niches. Overall, these findings reveal the distribution patterns of methanogens and expand our understanding of methanogenic community assemblage in the river-bay system. Key Points • Abundance of methanogens was relatively higher in riverine sediments. • Methanogenic community in estuarine habitat separated from that in riverine habitat. • Salinity played a vital role in regulating methanogenic community assemblage.

Methanogenic Archaea Can Produce Methane in Deliquescence-Driven Mars Analog Environments

The current understanding of the Martian surface indicates that briny environments at the near-surface are temporarily possible, e.g. in the case of the presumably deliquescence-driven Recurring Slope Lineae (RSL). However, whether such dynamic environments are habitable for terrestrial organisms remains poorly understood. This hypothesis was tested by developing a Closed Deliquescence System (CDS) consisting of a mixture of desiccated Martian Regolith Analog (MRA) substrate, salts, and microbial cells, which over the course of days became wetted through deliquescence. The methane produced via metabolic activity for three methanogenic archaea: Methanosarcina mazei, M. barkeri and M. soligelidi, was measured after exposing them to three different MRA substrates using either NaCl or NaClO₄ as a hygroscopic salt. Our experiments showed that (1) M. soligelidi rapidly produced methane at 4 °C, (2) M. barkeri produced methane at 28 °C though not at 4 °C, (3) M. mazei was not metabolically reactivated through deliquescence, (4) none of the species produced methane in the presence of perchlorate, and (5) all species were metabolically most active in the phyllosilicate-containing MRA. These results emphasize the importance of the substrate, microbial species, salt, and temperature used in the experiments. Furthermore, we show here for the first time that water provided by deliquescence alone is sufficient to rehydrate methanogenic archaea and to reactivate their metabolism under conditions roughly analogous to the near-subsurface Martian environment.

Microbial eukaryotes in the suboxic chemosynthetic ecosystem of Movile Cave, Romania

Movile Cave is a small system of partially inundated galleries in limestone settings close to the Black Sea in Southeast Romania. Isolated from the surface for 6 million years, its sulfidic, methane and ammonia-rich waters harbour unique chemosynthetic prokaryotic communities that include sulphur and ammonium-metabolizing chemolithotrophs, methanogens, methanotrophs and methylotrophs. The cave also harbours cave-dwelling invertebrates and fungi, but the diversity of other microbial eukaryotes remained completely unknown. Here, we apply an 18S rRNA gene-based metabarcoding approach to study the composition of protist communities in floating microbial mats and plankton from a well-preserved oxygen-depleted cave chamber. Our results reveal a wide protist diversity with, as dominant groups, ciliates (Alveolata), Stramenopiles, especially bicosoecids, and jakobids (Excavata). Ciliate sequences dominated both, microbial mats and plankton, followed by either Stramenopiles or excavates. Stramenopiles were more prominent in microbial mats, whereas jakobids dominated the plankton fraction of the oxygen-depleted water column. Mats cultured in the laboratory were enriched in Cercozoa. Consistent with local low oxygen levels, Movile Cave protists are most likely anaerobic or microaerophilic. Several newly detected OTU clades were very divergent from cultured species or environmental sequences in databases and represent phylogenetic novelty, notably within jakobids. Movile Cave protists likely cover a variety of ecological roles in this ecosystem including predation, parasitism, saprotrophy and possibly diverse prokaryote-protist syntrophies.

Evaluation of process performance and retained sludge properties of a psychrophilic UASB reactor for treatment of iso-plophyl alcohol (2-propanol)-containing wastewater

In this study, a continuous feeding experiment was conducted with synthetic iso-plophyl alcohol (2-propanol)-containing wastewater using a lab-scale psychrophilic UASB reactor to evaluate process performance and retained sludge properties. For smooth acclimation, methanogenic granular sludge was seeded and a proportion of 2-propanol in the synthetic wastewater containing sucrose and volatile fatty acids was increased stepwise from 0% to 30%, 60% and then 90% of COD (chemical oxygen demand). As a result, after a 4-week period for acclimation to 2-propanol degradation, a COD removal rate of 95% was achieved at an organic loading rate (OLR) of 8.4 kg COD/m³/day. Additionally, the physical properties of the retained granular sludge were maintained even when the reactor was supplied with 2-propanol-rich wastewater for more than 200 days. From the batch assays using serum bottles, methanogenic degradation of 2-propanol was observed with acetone accumulation. By comparison, 2-propanol degradation was clearly inhibited in the presence of chloroform as a specific inhibitor of methanogen. A domain archaeal community structure analysis targeting 16S rRNA genes showed the relative abundance of the genus Methanospillium was increased in the 2-propanol acclimated sludge. These results suggested Methanospillium related species in the granular sludge appreciably contributed to the direct degradation of 2-proapanol into acetone under an anaerobic condition.

Non-Psychrophilic Methanogens Capable of Growth Following Long-Term Extreme Temperature Changes, with Application to Mars

Although the martian environment is currently cold and dry, geomorphological features on the surface of the planet indicate relatively recent (<4 My) freeze/thaw episodes. Additionally, the recent detections of near-subsurface ice as well as hydrated salts within recurring slope lineae suggest potentially habitable micro-environments within the martian subsurface. On Earth, microbial communities are often active at sub-freezing temperatures within permafrost, especially within the active layer, which experiences large ranges in temperature. With warming global temperatures, the effect of thawing permafrost communities on the release of greenhouse gases such as carbon dioxide and methane becomes increasingly important. Studies examining the community structure and activity of microbial permafrost communities on Earth can also be related to martian permafrost environments, should life have developed on the planet. Here, two non-psychrophilic methanogens, Methanobacterium formicicum and Methanothermobacter wolfeii, were tested for their ability to survive long-term (~4 year) exposure to freeze/thaw cycles varying in both temperature and duration, with implications both for climate change on Earth and possible life on Mars.

Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses

BACKGROUND

Movile Cave (Mangalia, Romania) is a unique ecosystem where the food web is sustained by microbial primary production, analogous to deep-sea hydrothermal vents. Specifically, chemoautotrophic microbes deriving energy from the oxidation of hydrogen sulphide and methane form the basis of the food web.

RESULTS

Here, we report the isolation of the first methane-oxidizing bacterium from the Movile Cave ecosystem, Candidatus Methylomonas sp. LWB, a new species and representative of Movile Cave microbial mat samples. While previous research has suggested a prevalence of anoxic conditions in deeper lake water and sediment, using small-scale shotgun metagenome sequencing, we show that metabolic genes encoding enzymes for aerobic methylotrophy are prevalent in sediment metagenomes possibly indicating the presence of microoxic conditions. Moreover, this study also indicates that members within the family Gallionellaceae (Sideroxydans and Gallionella) were the dominant taxa within the sediment microbial community, thus suggesting a major role for microaerophilic iron-oxidising bacteria in nutrient cycling within the Movile Cave sediments.

CONCLUSIONS

In this study, based on phylogenetic and metabolic gene surveys of metagenome sequences, the possibility of aerobic microbial processes (i.e., methylotrophy and iron oxidation) within the sediment is indicated. We also highlight significant gaps in our knowledge on biogeochemical cycles within the Movile Cave ecosystem, and the need to further investigate potential feedback mechanisms between microbial communities in both lake sediment and lake water.

Geochemical Influence on Microbial Communities at CO2-Leakage Analog Sites

Microorganisms influence the chemical and physical properties of subsurface environments and thus represent an important control on the fate and environmental impact of CO₂ that leaks into aquifers from deep storage reservoirs. How leakage will influence microbial populations over long time scales is largely unknown. This study uses natural analog sites to investigate the long-term impact of CO₂ leakage from underground storage sites on subsurface biogeochemistry. We considered two sites with elevated CO₂ levels (sample groups I and II) and one control site with low CO₂ content (group III). Samples from sites with elevated CO₂ had pH ranging from 6.2 to 4.5 and samples from the low-CO₂ control group had pH ranging from 7.3 to 6.2. Solute concentrations were relatively low for samples from the control group and group I but high for samples from group II, reflecting varying degrees of water-rock interaction. Microbial communities were analyzed through clone library and MiSeq sequencing. Each 16S rRNA analysis identified various bacteria, methane-producing archaea, and ammonia-oxidizing archaea. Both bacterial and archaeal diversities were low in groundwater with high CO₂ content and community compositions between the groups were also clearly different. In group II samples, sequences classified in groups capable of methanogenesis, metal reduction, and nitrate reduction had higher relative abundance in samples with relative high methane, iron, and manganese concentrations and low nitrate levels. Sequences close to Comamonadaceae were abundant in group I, while the taxa related to methanogens, Nitrospirae, and Anaerolineaceae were predominant in group II. Our findings provide insight into subsurface biogeochemical reactions that influence the carbon budget of the system including carbon fixation, carbon trapping, and CO₂ conversion to methane. The results also suggest that monitoring groundwater microbial community can be a potential tool for tracking CO₂ leakage from geologic storage sites.

Method for Indirect Quantification of CH4 Production via H2O Production Using Hydrogenotrophic Methanogens

Hydrogenotrophic methanogens are an intriguing group of microorganisms from the domain Archaea. Methanogens exhibit extraordinary ecological, biochemical, and physiological characteristics and possess a huge biotechnological potential. Yet, the only possibility to assess the methane (CH₄) production potential of hydrogenotrophic methanogens is to apply gas chromatographic quantification of CH₄. In order to be able to effectively screen pure cultures of hydrogenotrophic methanogens regarding their CH₄ production potential we developed a novel method for indirect quantification of the volumetric CH₄ production rate by measuring the volumetric water production rate. This method was established in serum bottles for cultivation of methanogens in closed batch cultivation mode. Water production was estimated by determining the difference in mass increase in a quasi-isobaric setting. This novel CH₄ quantification method is an accurate and precise analytical technique, which can be used to rapidly screen pure cultures of methanogens regarding their volumetric CH₄ evolution rate. It is a cost effective alternative determining CH₄ production of methanogens over CH₄ quantification by using gas chromatography, especially if applied as a high throughput quantification method. Eventually, the method can be universally applied for quantification of CH₄ production from psychrophilic, thermophilic and hyperthermophilic hydrogenotrophic methanogens.

Biologically Produced Methane as a Renewable Energy Source

Methanogens are a unique group of strictly anaerobic archaea that are more metabolically diverse than previously thought. Traditionally, it was thought that methanogens could only generate methane by coupling the oxidation of products formed by fermentative bacteria with the reduction of CO₂. However, it has recently been observed that many methanogens can also use electrons extruded from metal-respiring bacteria, biocathodes, or insoluble electron shuttles as energy sources. Methanogens are found in both human-made and natural environments and are responsible for the production of ∼71% of the global atmospheric methane. Their habitats range from the human digestive tract to hydrothermal vents. Although biologically produced methane can negatively impact the environment if released into the atmosphere, when captured, it can serve as a potent fuel source. The anaerobic digestion of wastes such as animal manure, human sewage, or food waste produces biogas which is composed of ∼60% methane. Methane from biogas can be cleaned to yield purified methane (biomethane) that can be readily incorporated into natural gas pipelines making it a promising renewable energy source. Conventional anaerobic digestion is limited by long retention times, low organics removal efficiencies, and low biogas production rates. Therefore, many studies are being conducted to improve the anaerobic digestion process. Researchers have found that addition of conductive materials and/or electrically active cathodes to anaerobic digesters can stimulate the digestion process and increase methane content of biogas. It is hoped that optimization of anaerobic digesters will make biogas more readily accessible to the average person.

Propidium monoazide treatment to distinguish between live and dead methanogens in pure cultures and environmental samples

In clinical trials investigating human health and in the analysis of microbial communities in cultures and natural environments, it is a substantial challenge to differentiate between living, potentially active communities and dead cells. The DNA-intercalating dye propidium monoazide (PMA) enables the selective masking of DNA from dead, membrane-compromised cells immediately before DNA extraction. In the present study, we evaluated for the first time a PMA treatment for methanogenic archaea in cultures and particle-rich environmental samples. Using microscopic analyses, we confirmed the applicability of the LIVE/DEAD(®) BacLight™ kit to methanogenic archaea and demonstrated the maintenance of intact cell membranes of methanogens in the presence of PMA. Although strain-specific differences in the efficiency of PMA treatment to methanogenic archaea were observed, we developed an optimal procedure using 130 μM PMA and 5min of photo-activation with blue LED light. The results showed that the effectiveness of the PMA treatment strongly depends on the texture of the sediment/soil: silt and clay-rich sediments represent a challenge at all concentrations, whereas successful suppression of DNA from dead cells with compromised membranes was possible for low particle loads of sandy soil (total suspended solids (TSS)≤200 mg mL(-1)). Conclusively, we present two strategies to overcome the problem of insufficient light activation of PMA caused by the turbidity effect (shielding) in particle-rich environmental samples by (i) dilution of the particle-rich sample and (ii) detachment of the cells and the free DNA from the sediment prior to a PMA treatment. Both strategies promise to be usable options for distinguishing living cells and free DNA in complex environmental samples.

Assessing the Ecophysiology of Methanogens in the Context of Recent Astrobiological and Planetological Studies

Among all known microbes capable of thriving under extreme and, therefore, potentially extraterrestrial environmental conditions, methanogens from the domain Archaea are intriguing organisms. This is due to their broad metabolic versatility, enormous diversity, and ability to grow under extreme environmental conditions. Several studies revealed that growth conditions of methanogens are compatible with environmental conditions on extraterrestrial bodies throughout the Solar System. Hence, life in the Solar System might not be limited to the classical habitable zone. In this contribution we assess the main ecophysiological characteristics of methanogens and compare these to the environmental conditions of putative habitats in the Solar System, in particular Mars and icy moons. Eventually, we give an outlook on the feasibility and the necessity of future astrobiological studies concerning methanogens.

Influence of Martian regolith analogs on the activity and growth of methanogenic archaea, with special regard to long-term desiccation

Methanogenic archaea have been studied as model organisms for possible life on Mars for several reasons: they can grow lithoautotrophically by using hydrogen and carbon dioxide as energy and carbon sources, respectively; they are anaerobes; and they evolved at a time when conditions on early Earth are believed to have looked similar to those of early Mars. As Mars is currently dry and cold and as water might be available only at certain time intervals, any organism living on this planet would need to cope with desiccation. On Earth there are several regions with low water availability as well, e.g., permafrost environments, desert soils, and salt pans. Here, we present the results of a set of experiments investigating the influence of different Martian regolith analogs (MRAs) on the metabolic activity and growth of three methanogenic strains exposed to culture conditions as well as long-term desiccation. In most cases, concentrations below 1 wt% of regolith in the media resulted in an increase of methane production rates, whereas higher concentrations decreased the rates, thus prolonging the lag phase. Further experiments showed that methanogenic archaea are capable of producing methane when incubated on a water-saturated sedimentary matrix of regolith lacking nutrients. Survival of methanogens under these conditions was analyzed with a 400 day desiccation experiment in the presence of regolith analogs. All tested strains of methanogens survived the desiccation period as it was determined through reincubation on fresh medium and via qPCR following propidium monoazide treatment to identify viable cells. The survival of long-term desiccation and the ability of active metabolism on water-saturated MRAs strengthens the possibility of methanogenic archaea or physiologically similar organisms to exist in environmental niches on Mars. The best results were achieved in presence of a phyllosilicate, which provides insights of possible positive effects in habitats on Earth as well.

Methanobacterium aggregans sp. nov., a hydrogenotrophic methanogenic archaeon isolated from an anaerobic digester

A novel, strictly anaerobic, hydrogenotrophic methanogen, strain E09F.3T, was isolated from a commercial biogas plant in Germany. Cells of E09F.3T were Gram-stain-negative, non-motile, slightly curved rods, long chains of which formed large aggregates consisting of intertwined bundles of chains. Cells utilized H2+CO2 and, to a lesser extent, formate as substrates for growth and methanogenesis. The optimal growth temperature was around 40 °C; maximum growth rate was obtained at pH around 7.0 with approximately 6.8 mM NaCl. The DNA G+C content of strain E09F.3T was 39.1 mol%. Phylogenetic analyses based on 16S rRNA and mcrA gene sequences placed strain E09F.3T within the genus Methanobacterium. On the basis of 16S rRNA gene sequence similarity, strain E09F.3T was closely related to Methanobacterium congolense CT but morphological, physiological and genomic characteristics indicated that strain E09F.3T represents a novel species. The name Methanobacterium aggregans sp. nov. is proposed for this novel species, with strain E09F.3T ( = DSM 29428T = JCM 30569T) as the type strain.

Genetic resources for methane production from biomass described with the Gene Ontology

Methane (CH₄) is a valuable fuel, constituting 70–95% of natural gas, and a potent greenhouse gas. Release of CH₄ into the atmosphere contributes to climate change. Biological CH₄ production or methanogenesis is mostly performed by methanogens, a group of strictly anaerobic archaea. The direct substrates for methanogenesis are H₂ plus CO₂, acetate, formate, methylamines, methanol, methyl sulfides, and ethanol or a secondary alcohol plus CO₂. In numerous anaerobic niches in nature, methanogenesis facilitates mineralization of complex biopolymers such as carbohydrates, lipids and proteins generated by primary producers. Thus, methanogens are critical players in the global carbon cycle. The same process is used in anaerobic treatment of municipal, industrial and agricultural wastes, reducing the biological pollutants in the wastes and generating methane. It also holds potential for commercial production of natural gas from renewable resources. This process operates in digestive systems of many animals, including cattle, and humans. In contrast, in deep-sea hydrothermal vents methanogenesis is a primary production process, allowing chemosynthesis of biomaterials from H₂ plus CO₂. In this report we present Gene Ontology (GO) terms that can be used to describe processes, functions and cellular components involved in methanogenic biodegradation and biosynthesis of specialized coenzymes that methanogens use. Some of these GO terms were previously available and the rest were generated in our Microbial Energy Gene Ontology (MENGO) project. A recently discovered non-canonical CH₄ production process is also described. We have performed manual GO annotation of selected methanogenesis genes, based on experimental evidence, providing “gold standards” for machine annotation and automated discovery of methanogenesis genes or systems in diverse genomes. Most of the GO-related information presented in this report is available at the MENGO website (http://www.mengo.biochem.vt.edu/).

Methanosarcina spelaei sp. nov., a methanogenic archaeon isolated from a floating biofilm of a subsurface sulphurous lake

A novel methanogenic archaeon, strain MC-15(T), was isolated from a floating biofilm on a sulphurous subsurface lake in Movile Cave (Mangalia, Romania). Cells were non-motile sarcina-like cocci with a diameter of 2-4 µm, occurring in aggregates. The strain was able to grow autotrophically on H2/CO2. Additionally, acetate, methanol, monomethylamine, dimethylamine and trimethylamine were utilized, but not formate or dimethyl sulfide. Trypticase peptone and yeast extract were not required for growth. Optimal growth was observed at 33 °C, pH 6.5 and a salt concentration of 0.05 M NaCl. The predominant membrane lipids of MC-15(T) were archaeol and hydroxyarchaeol phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylinositol as well as hydroxyarchaeol phosphatidylserine and archaeol glycosaminyl phosphatidylinositol. The closely related species, Methanosarcina vacuolata and Methanosarcina horonobensis, had a similar composition of major membrane lipids to strain MC-15(T). The 16S rRNA gene sequence of strain MC-15(T) was similar to those of Methanosarcina vacuolata DSM 1232(T) (sequence similarity 99.3%), Methanosarcina horonobensis HB-1(T) (98.8%), Methanosarcina barkeri DSM 800(T) (98.7%) and Methanosarcina siciliae T4/M(T) (98.4%). DNA-DNA hybridization revealed 43.3% relatedness between strain MC-15(T) and Methanosarcina vacuolata DSM 1232(T). The G+C content of the genomic DNA was 39.0 mol%. Based on physiological, phenotypic and genotypic differences, strain MC-15(T) represents a novel species of the genus Methanosarcina, for which the name Methanosarcina spelaei sp. nov. is proposed. The type strain is MC-15(T) ( = DSM 26047(T) = JCM 18469(T)).