Methanogenium frigidum sp. nov., a psychrophilic, H2-using methanogen from Ace Lake, Antarctica

Methanovulcanius yangii gen. nov., sp. nov., a hydrogenotrophic methanogen, isolated from a submarine mud volcano in the offshore area of southwestern Taiwan

A novel mesophilic, hydrogenotrophic methanogen, strain CYW5T, was isolated from a sediment sample of a piston core collected from submarine mud volcano MV5 located in the offshore area of southwestern Taiwan. Cells of strain CYW5T were irregular coccids, 0.5-1.0 µm in diameter and lysed easily by 0.01 % sodium dodecyl sulphate (SDS) treatment. Strain CYW5Tutilized formate or hydrogen plus carbon dioxide as catabolic substrates for methanogenesis. The optimal growth conditions were 37 °C, 0.043-0.085 M NaCl and pH 6.02-7.32. The genomic DNA G+C content calculated from the genome sequence of strain CYW5T was 56.2 mol%. The results of phylogenetic analysis of 16S rRNA gene sequences indicated that strain CYW5T represented a member of the family Methanomicrobiaceae in the order Methanomicrobiales, and was closely related to the members of the genus Methanogenium. The most closely related species was Methanogenium cariaci JR1T (94.9 % of 16S rRNA gene sequence identity). The average nucleotide identity and average amino acid identity values between strain CYW5T and members of the family Methanomicrobiaceae were 74.7-78.5 % and 49.1-64.9%, respectively. Although many of the morphological and physiological characteristics of strain CYW5T and the species of the genus Methanogenium were similar, they were distinguishable by the differences in genomic G+C content and temperature, NaCl and pH ranges for growth. Based on these phenotypic, phylogenetic and genomic results, we propose that strain CYW5T represents a novel species, of a novel genus, named Methanovulcanius yangii gen. nov., sp. nov. The type strain is CYW5T (=BCRC AR10048T=DSM 100756T=NBRC 111404T).

Phylogenetically and physiologically diverse methanogenic archaea inhabit the Indian hot spring environments

Mesophilic and thermophilic methanogens belonging to the hydrogenotrophic, methylotrophic, and acetotrophic groups were isolated from Indian hot spring environments using BY and BCYT growth media. Following initial Hinf I-based PCR-RFLP screening, 70 methanogens were sequenced to ascertain their identity. These methanogens were phylogenetically and physiologically diverse and represented different taxa distributed across three physiological groups, i.e., hydrogenotrophs (53), methylotrophs (14) and acetotrophs (3). Overall, methanogens representing three families, five genera, and ten species, including two putative novel species, were recognized. The highest number and diversity of methanogens was observed at 40 ℃, dominated by Methanobacterium (10; 3 species), Methanosarcina (9; 3 species), Methanothermobacter (7; 2 species), Methanomethylovorans (5; 1 species) and Methanoculleus (3; 1 species). Both putative novel methanogen species were isolated at 40 ℃ and belonged to the genera Methanosarcina and Methanobacterium. At 55 ℃, limited diversity was observed, and resulted in the isolation of only two genera of methanogens, i.e., Methanothermobacter (28; 2 species) and Methanosarcina (4; 1 species). At 70 ℃, only members of the genus Methanothermobacter (5; 2 species) were isolated, whereas no methanogen could be cultured at 85 ℃. Ours is the first study that documents the extensive range of cultivable methanogenic archaea inhabiting hot springs across various geothermal provinces of India.

Complexity of temperature dependence in methanogenic microbial environments

There is virtually no environmental process that is not dependent on temperature. This includes the microbial processes that result in the production of CH₄, an important greenhouse gas. Microbial CH₄ production is the result of a combination of many different microorganisms and microbial processes, which together achieve the mineralization of organic matter to CO₂ and CH₄. Temperature dependence applies to each individual step and each individual microbe. This review will discuss the different aspects of temperature dependence including temperature affecting the kinetics and thermodynamics of the various microbial processes, affecting the pathways of organic matter degradation and CH₄ production, and affecting the composition of the microbial communities involved. For example, it was found that increasing temperature results in a change of the methanogenic pathway with increasing contribution from mainly acetate to mainly H₂/CO₂ as immediate CH₄ precursor, and with replacement of aceticlastic methanogenic archaea by thermophilic syntrophic acetate-oxidizing bacteria plus thermophilic hydrogenotrophic methanogenic archaea. This shift is consistent with reaction energetics, but it is not obligatory, since high temperature environments exist in which acetate is consumed by thermophilic aceticlastic archaea. Many studies have shown that CH₄ production rates increase with temperature displaying a temperature optimum and a characteristic apparent activation energy (E_a). Interestingly, CH₄ release from defined microbial cultures, from environmental samples and from wetland field sites all show similar E_a values around 100 kJ mol^-1 indicating that CH₄ production rates are limited by the methanogenic archaea rather than by hydrolysis of organic matter. Hence, the final rather than the initial step controls the methanogenic degradation of organic matter, which apparently is rarely in steady state.

Archaeal lipids

The major archaeal membrane glycerolipids are distinguished from those of bacteria and eukaryotes by the contrasting stereochemistry of their glycerol backbones, and by the use of ether-linked isoprenoid-based alkyl chains rather than ester-linked fatty acyl chains for their hydrophobic moieties. These fascinating compounds play important roles in the extremophile lifestyles of many species, but are also present in the growing numbers of recently discovered mesophilic archaea. The past decade has witnessed significant advances in our understanding of archaea in general and their lipids in particular. Much of the new information has come from the ability to screen large microbial populations via environmental metagenomics, which has revolutionised our understanding of the extent of archaeal biodiversity that is coupled with a strict conservation of their membrane lipid compositions. Significant additional progress has come from new culturing and analytical techniques that are gradually enabling archaeal physiology and biochemistry to be studied in real time. These studies are beginning to shed light on the much-discussed and still-controversial process of eukaryogenesis, which probably involved both bacterial and archaeal progenitors. Puzzlingly, although eukaryotes retain many attributes of their putative archaeal ancestors, their lipid compositions only reflect their bacterial progenitors. Finally, elucidation of archaeal lipids and their metabolic pathways have revealed potentially interesting applications that have opened up new frontiers for biotechnological exploitation of these organisms. This review is concerned with the analysis, structure, function, evolution and biotechnology of archaeal lipids and their associated metabolic pathways.

Efficiency of sweet whey fermentation with psychrophilic methanogens

Sweet whey is a waste product from the dairy industry that is difficult to manage. High hopes are fostered regarding its neutralization in the methane fermentation. An economically viable alternative to a typical mesophilic fermentation seems to be the process involving psychrophilic bacteria isolated from the natural environment. This study aimed to determine the feasibility of exploiting psychrophilic microorganisms in methane fermentation of sweet whey. The experiments were carried out under dynamic conditions using Bio Flo 310 type flow-through anaerobic bioreactors. The temperature inside the reactors was 10 ± 1 °C. The HRT was 20 days and the OLR was 0.2 g COD/dm³/day. The study yielded 132.7 ± 13.8 mL biogas/g_CODremoved. The CH₄ concentration in the biogas was 32.7 ± 1.6%, that of H₂ was 8.7 ± 4.7%, whereas that of CO₂ reached 58.42 ± 2.47%. Other gases were also determined, though in lower concentrations. The COD and BOD₅ removal efficiency reached 21.4 ± 0.6% and 17.6 ± 1.0%, respectively.

Critical insights into psychrophilic anaerobic digestion: Novel strategies for improving biogas production

Anaerobic digestion (AD) under psychrophilic temperature has only recently garnered deserved attention. In major parts of Europe, USA, Canada and Australia, climatic conditions are more suited for psychrophilic (<20 ℃) rather than mesophilic (35 - 37 ℃) and thermophilic (55 - 60 ℃) AD. Low temperature has adverse effects on important cellular processes which may render the cell biology inactive. Moreover, cold climate can also alter the physical and chemical properties of wastewater, thereby reducing the availability of substrate to microbes. Hence, the use of low temperature acclimated microbial biomass could overcome thermodynamic constraints and carry out flexible structural and conformational changes to proteins, membrane lipid composition, expression of cold-adapted enzymes through genotypic and phenotypic variations. Reduction in organic loading rate is beneficial to methane production under low temperatures. Moreover, modification in the design of existing reactors and the use of hybrid reactors have already demonstrated improved methane generation in the lab-scale. This review also discusses some novel strategies such as direct interspecies electron transfer (DIET), co-digestion of substrate, bioaugmentation, and bioelectrochemical system assisted AD which present promising prospects. While DIET can facilitate syntrophic electron exchange in diverse microbes, the addition of organic-rich co-substrate can help in maintaining suitable C/N ratio in the anaerobic digester which subsequently can enhance methane generation. Bioaugmentation with psychrophilic strains could reduce start-up time and ensure daily stable performance for wastewater treatment facilities at low temperatures. In addition to the technical discussion, the economic assessment and future outlook on psychrophilic AD are also highlighted.

The effect of temperature fluctuation on the microbial diversity and community structure of rural household biogas digesters at Qinghai Plateau

Seasonal temperature-fluctuation has been regarded as a key environmental factor affecting rural biogas fermentation yields. The present study investigated the impact of seasonal temperature-fluctuation on operating-temperatures and biogas production in rural household digesters at Qinghai Plateau and revealed the related changes in microbial diversity and community structure by 16S rRNA gene high-throughput sequencing (HTS) analysis. Our results showed closely positive correlation between operating-temperatures and biogas production. HTS analysis indicated the highest diversity for bacteria community in autumn (at highest operating-temperatures) and late winter (at lowest operating-temperatures) and for archaea community only in autumn. HTS analysis classified bacteria into 21 phyla and 346 genera with the most predominant phyla Firmicutes, Bacteroidetes and Proteobacteria (> 72.4% in total) and the most predominant genera Proteiniphilum, Clostridium sensustricto 1, Petrimonas, Pseudomonas and Fastidiosipila (37.09-38.61% in total). HTS analysis also revealed two main archaea orders (Methanomicrobiales and Methanobacteriales) and one predominant genus Methanogenium to support plateau biogas fermentation. Especially, a remarkable impact of temperature on the community abundances of bacteria phyla Synergistetes and archaea genera Methanogenium and Thermogymnomonas was observed, and such microbial community structure changes were positively consistent with the biogas production. The present work provided the first set of evidences to link temperature-controlled modulation of microbial community structure with rural household biogas production at Qinghai Plateau.

Exploring Marine Environments for the Identification of Extremophiles and Their Enzymes for Sustainable and Green Bioprocesses

Sea environments harbor a wide variety of life forms that have adapted to live in hard and sometimes extreme conditions. Among the marine living organisms, extremophiles represent a group of microorganisms that attract increasing interest in relation to their ability to produce an array of molecules that enable them to thrive in almost every marine environment. Extremophiles can be found in virtually every extreme environment on Earth, since they can tolerate very harsh environmental conditions in terms of temperature, pH, pressure, radiation, etc. Marine extremophiles are the focus of growing interest in relation to their ability to produce biotechnologically useful enzymes, the so-called extremozymes. Thanks to their resistance to temperature, pH, salt, and pollutants, marine extremozymes are promising biocatalysts for new and sustainable industrial processes, thus representing an opportunity for several biotechnological applications. Since the marine microbioma, i.e., the complex of microorganisms living in sea environments, is still largely unexplored finding new species is a central issue for green biotechnology. Here we described the main marine environments where extremophiles can be found, some existing or potential biotechnological applications of marine extremozymes for biofuels production and bioremediation, and some possible approaches for the search of new biotechnologically useful species from marine environments.

Temperature Controls Crystalline Iron Oxide Utilization by Microbial Communities in Methanic Ferruginous Marine Sediment Incubations

Microorganisms can use crystalline iron minerals for iron reduction linked to organic matter degradation or as conduits for direct interspecies electron transfer (mDIET) to syntrophic partners, e.g., methanogens. The environmental conditions that lead either to reduction or conduit use are so far unknown. We investigated microbial community shifts and interactions with crystalline iron minerals (hematite and magnetite) in methanic ferruginous marine sediment incubations during organic matter (glucose) degradation at varying temperatures. Iron reduction rates increased with decreasing temperature from 30°C to 4°C. Both hematite and magnetite facilitated iron reduction at 4°C, demonstrating that microorganisms in the methanic zone of marine sediments can reduce crystalline iron oxides under psychrophilic conditions. Methanogenesis occurred, however, at higher rates with increasing temperature. At 30°C, both hematite and magnetite accelerated methanogenesis onset and maximum process rates. At lower temperatures (10°C and 4°C), hematite could still facilitate methanogenesis but magnetite served more as an electron acceptor for iron reduction than as a conduit. Different temperatures selected for different key microorganisms: at 30°C, members of genus Orenia, Halobacteroidaceae, at 10°C, Photobacterium and the order Clostridiales, and at 4°C Photobacterium and Psychromonas were enriched. Members of the order Desulfuromonadales harboring known dissimilatory iron reducers were also enriched at all temperatures. Our results show that crystalline iron oxides predominant in some natural environments can facilitate electron transfer between microbial communities at psychrophilic temperatures. Furthermore, temperature has a critical role in determining the pathway of crystalline iron oxide utilization in marine sediment shifting from conduction at 30°C to predominantly iron reduction at lower temperatures.

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.

Archaeal S-Layers: Overview and Current State of the Art

In contrast to bacteria, all archaea possess cell walls lacking peptidoglycan and a number of different cell envelope components have also been described. A paracrystalline protein surface layer, commonly referred to as S-layer, is present in nearly all archaea described to date. S-layers are composed of only one or two proteins and form different lattice structures. In this review, we summarize current understanding of archaeal S-layer proteins, discussing topics such as structure, lattice type distribution among archaeal phyla and glycosylation. The hexagonal lattice type is dominant within the phylum Euryarchaeota, while in the Crenarchaeota this feature is mainly associated with specific orders. S-layers exclusive to the Crenarchaeota have also been described, which are composed of two proteins. Information regarding S-layers in the remaining archaeal phyla is limited, mainly due to organism description through only culture-independent methods. Despite the numerous applied studies using bacterial S-layers, few reports have employed archaea as a study model. As such, archaeal S-layers represent an area for exploration in both basic and applied research.

PCR-DGGE Analysis on Microbial Community Structure of Rural Household Biogas Digesters in Qinghai Plateau

To investigate contribution of environmental factor(s) to microbial community structure(s) involved in rural household biogas fermentation at Qinghai Plateau, we collected slurry samples from 15 digesters, with low-temperature working conditions (11.1-15.7 °C) and evenly distributed at three counties (Datong, Huangyuan, and Ledu) with cold plateau climate, to perform polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and further sequencing. The bacterial communities in the total 15 digesters were classified into 38 genera with Mangroviflexus (12.1%) as the first dominant, and the archaeal communities into ten genera with Methanogenium (38.5%) as the most dominant. For each county, the digesters with higher biogas production, designated as HP digesters, exclusively had 1.6-3.1 °C higher fermentation temperature and the unique bacterial structure composition related, i.e., unclassified Clostridiales for all the HP digesters and unclassified Marinilabiliaceae and Proteiniclasticum for Ledu HP digesters. Regarding archaeal structure composition, Methanogenium exhibited significantly higher abundances at all the HP digesters and Thermogymnomonas was the unique species only identified at Ledu HP digesters with higher-temperature conditions. Redundancy analysis also confirmed the most important contribution of temperature to the microbial community structures investigated. This report emphasized the correlation between temperature and specific microbial community structure(s) that would benefit biogas production of rural household digesters at Qinghai Plateau.

Prokaryotic assemblages in the maritime Antarctic Lake Limnopolar (Byers Peninsula, South Shetland Islands)

The potentially metabolically active components within the prokaryotic assemblages inhabiting the Antarctic Lake Limnopolar (Byers Peninsula, Maritime Antarctica) were investigated by a polyphasic approach which included culture-dependent and culture-independent methods (based on RNA molecules). Results support previous observations on the Proteobacteria and Bacteroidetes dominance, followed by Actinobacteria, in Antarctic lakes. In particular, Alpha-, Betaproteobacteria and Bacteroidetes were mainly detected by CARD-FISH and cDNA cloning, whereas Gammaproteobacteria and Actinobacteria dominated within the cultivable fraction. Overall, this study demonstrates the survival potential and physiological heterogeneity of the prokaryotic community in the Lake Limnopolar. The microbial community composition in the lake is affected by external influences (such as marine environment by sea spray and seabird dropping, and microbial mats and mosses of the catchment). However, most external bacteria would be inactive, whereas typical polar taxa dominate the potentially active fraction and are subsidized by external nutrient sources, thus assuming the main biogeochemical roles within the lake.

Microbial Diversity in Extreme Marine Habitats and Their Biomolecules

Extreme marine environments have been the subject of many studies and scientific publications. For many years, these environmental niches, which are characterized by high or low temperatures, high-pressure, low pH, high salt concentrations and also two or more extreme parameters in combination, have been thought to be incompatible to any life forms. Thanks to new technologies such as metagenomics, it is now possible to detect life in most extreme environments. Starting from the discovery of deep sea hydrothermal vents up to the study of marine biodiversity, new microorganisms have been identified, and their potential uses in several applied fields have been outlined. Thermophile, halophile, alkalophile, psychrophile, piezophile and polyextremophile microorganisms have been isolated from these marine environments; they proliferate thanks to adaptation strategies involving diverse cellular metabolic mechanisms. Therefore, a vast number of new biomolecules such as enzymes, polymers and osmolytes from the inhabitant microbial community of the sea have been studied, and there is a growing interest in the potential returns of several industrial production processes concerning the pharmaceutical, medical, environmental and food fields.

Adaptations of archaeal and bacterial membranes to variations in temperature, pH and pressure

The cytoplasmic membrane of a prokaryotic cell consists of a lipid bilayer or a monolayer that shields the cellular content from the environment. In addition, the membrane contains proteins that are responsible for transport of proteins and metabolites as well as for signalling and energy transduction. Maintenance of the functionality of the membrane during changing environmental conditions relies on the cell's potential to rapidly adjust the lipid composition of its membrane. Despite the fundamental chemical differences between bacterial ester lipids and archaeal ether lipids, both types are functional under a wide range of environmental conditions. We here provide an overview of archaeal and bacterial strategies of changing the lipid compositions of their membranes. Some molecular adjustments are unique for archaea or bacteria, whereas others are shared between the two domains. Strikingly, shared adjustments were predominantly observed near the growth boundaries of bacteria. Here, we demonstrate that the presence of membrane spanning ether-lipids and methyl branches shows a striking relationship with the growth boundaries of archaea and bacteria.

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.

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.

The seasonal variation of emission of greenhouse gases from a full-scale sewage treatment plant

The seasonal variety of greenhouse gas (GHGs) emissions and the main emission source in a sewage treatment plant were investigated. The emission coefficient to treated wastewater was 291gCO2m(-3). The main source of GHGs was CO2 from the consumption of electricity, nitrous oxide from the sludge incineration process, and methane from the water treatment process. They accounted for 43.4%, 41.7% and 8.3% of the total amount of GHGs emissions, respectively. The amount of methane was plotted as a function of water temperature ranging between 13.3 and 27.3°C. An aeration tank was the main source of methane emission from all the units. Almost all the methane was emitted from the aeration tank, which accounted for 86.4% of the total gaseous methane emission. However, 18.4% of the methane was produced in sewage lines, 15.4% in the primary sedimentation tank, and 60.0% in the aeration tank.

Response of Methanogens in Arctic Sediments to Temperature and Methanogenic Substrate Availability

Although cold environments are major contributors to global biogeochemical cycles, comparatively little is known about their microbial community function, structure, and limits of activity. In this study a microcosm based approach was used to investigate the effects of temperature, and methanogenic substrate amendment, (acetate, methanol and H2/CO2) on methanogen activity and methanogen community structure in high Arctic wetlands (Solvatnet and Stuphallet, Svalbard). Methane production was not detected in Stuphallet sediment microcosms (over a 150 day period) and occurred within Solvatnet sediments microcosms (within 24 hours) at temperatures from 5 to 40°C, the maximum temperature being at far higher than in situ maximum temperatures (which range from air temperatures of -1.4 to 14.1°C during summer months). Distinct responses were observed in the Solvatnet methanogen community under different short term incubation conditions. Specifically, different communities were selected at higher and lower temperatures. At lower temperatures (5°C) addition of exogenous substrates (acetate, methanol or H2/CO2) had no stimulatory effect on the rate of methanogenesis or on methanogen community structure. The community in these incubations was dominated by members of the Methanoregulaceae/WCHA2-08 family-level group, which were most similar to the psychrotolerant hydrogenotrophic methanogen Methanosphaerula palustris strain E1-9c. In contrast, at higher temperatures, substrate amendment enhanced methane production in H2/CO2 amended microcosms, and played a clear role in structuring methanogen communities. Specifically, at 30°C members of the Methanoregulaceae/WCHA2-08 predominated following incubation with H2/CO2, and Methanosarcinaceaeand Methanosaetaceae were enriched in response to acetate addition. These results may indicate that in transiently cold environments, methanogen communities can rapidly respond to moderate short term increases in temperature, but not necessarily to the seasonal release of previously frozen organic carbon from thawing permafrost soils. However, as temperatures increase such inputs of carbon will likely have a greater influence on methane production and methanogen community structure. Understanding the action and limitations of anaerobic microorganisms within cold environments may provide information which can be used in defining region-specific differences in the microbial processes; which ultimately control methane flux to the atmosphere.

Methanogenic archaea database containing physiological and biochemical characteristics

The methanogenic archaea are a group of micro-organisms that have developed a unique metabolic pathway for obtaining energy. There are 150 characterized species in this group; however, novel species continue to be discovered. Since methanogens are considered a crucial part of the carbon cycle in the anaerobic ecosystem, characterization of these micro-organisms is important for understanding anaerobic ecology. A methanogens database (MDB; http://metanogen.biotech.uni.wroc.pl/), including physiological and biochemical characteristics of methanogens, was constructed based on the descriptions of isolated type strains. Analysis of the data revealed that methanogens are able to grow from 0 to 122 °C. Methanogens growing at the same temperature may have very different growth rates. There is no clear correlation between the optimal growth temperature and the DNA G+C content. The following substrate preferences are observed in the database: 74.5% of archaea species utilize H2+CO2, 33% utilize methyl compounds and 8.5% utilize acetate. Utilization of methyl compounds (mainly micro-organisms belonging to the genera Methanosarcina and Methanolobus ) is seldom accompanied by an ability to utilize H2+CO2. Very often, data for described species are incomplete, especially substrate preferences. Additional research leading to completion of missing information and development of standards, especially for substrate utilization, would be very helpful.

Geosphere-biosphere interactions in bio-activity volcanic lakes: evidences from Hule and Rìo Cuarto (Costa Rica)

Hule and Río Cuarto are maar lakes located 11 and 18 km N of Poás volcano along a 27 km long fracture zone, in the Central Volcanic Range of Costa Rica. Both lakes are characterized by a stable thermic and chemical stratification and recently they were affected by fish killing events likely related to the uprising of deep anoxic waters to the surface caused by rollover phenomena. The vertical profiles of temperature, pH, redox potential, chemical and isotopic compositions of water and dissolved gases, as well as prokaryotic diversity estimated by DNA fingerprinting and massive 16S rRNA pyrosequencing along the water column of the two lakes, have highlighted that different bio-geochemical processes occur in these meromictic lakes. Although the two lakes host different bacterial and archaeal phylogenetic groups, water and gas chemistry in both lakes is controlled by the same prokaryotic functions, especially regarding the CO2-CH4 cycle. Addition of hydrothermal CO2 through the bottom of the lakes plays a fundamental priming role in developing a stable water stratification and fuelling anoxic bacterial and archaeal populations. Methanogens and methane oxidizers as well as autotrophic and heterotrophic aerobic bacteria responsible of organic carbon recycling resulted to be stratified with depth and strictly related to the chemical-physical conditions and availability of free oxygen, affecting both the CO2 and CH4 chemical concentrations and their isotopic compositions along the water column. Hule and Río Cuarto lakes were demonstrated to contain a CO2 (CH4, N2)-rich gas reservoir mainly controlled by the interactions occurring between geosphere and biosphere. Thus, we introduced the term of bio-activity volcanic lakes to distinguish these lakes, which have analogues worldwide (e.g. Kivu: D.R.C.-Rwanda; Albano, Monticchio and Averno: Italy; Pavin: France) from volcanic lakes only characterized by geogenic CO2 reservoir such as Nyos and Monoun (Cameroon).

Methanospirillum stamsii sp. nov., a psychrotolerant, hydrogenotrophic, methanogenic archaeon isolated from an anaerobic expanded granular sludge bed bioreactor operated at low temperature

A psychrotolerant hydrogenotrophic methanogen, strain Pt1, was isolated from a syntrophic propionate-oxidizing methanogenic consortium obtained from granulated biomass of a two-stage low-temperature (3–8 °C) anaerobic expanded granular sludge bed (EGSB) bioreactor, fed with a mixture of volatile fatty acids (VFAs) (acetate, propionate and butyrate). The strain was strictly anaerobic, and cells were curved rods, 0.4–0.5×7.5–25 µm, that sometimes formed wavy filaments from 25 to several hundred micrometres in length. Cells stained Gram-negative and were non-sporulating. They were gently motile by means of tufted flagella. The strain grew at 5–37 °C (optimum at 20–30 °C), at pH 6.0–10 (optimum 7.0–7.5) and with 0–0.3 M NaCl (optimum 0 M NaCl). Growth and methane production was found with H2/CO2 and very weak growth with formate. Acetate and yeast extract stimulated growth, but were not essential. The G+C content of the DNA of strain Pt1 was 40 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Pt1 was a member of the genus Methanospirillum and showed 97.5 % sequence similarity to Methanospirillum hungatei JF1T and 94 % sequence similarity to Methanospirillum lacunae Ki8-1T. DNA–DNA hybridization of strain Pt1 with Methanospirillum hungatei JF1T revealed 39 % relatedness. On the basis of its phenotypic characteristics and phylogenetic position, strain Pt1 is a representative of a novel species of the genus Methanospirillum , for which the name Methanospirillum stamsii sp. nov. is proposed. The type strain is Pt1T ( = DSM 26304T = VKM B-2808T).

Diversity and ecology of psychrophilic microorganisms

Cold environments represent the majority of the biosphere on Earth and have been successfully colonized by psychrophilic microorganisms that are able to thrive at low temperatures and to survive and even maintain metabolic activity at subzero temperatures. These microorganisms play key ecological roles in their habitats and include a wide diversity of representatives of all three domains (Bacteria, Archaea, Eukarya). In this review, we summarize recent knowledge on the abundance, on the taxonomic and functional biodiversity, on low temperature adaptation and on the biogeography of microbial communities in a range of aquatic and terrestrial cold environments.

Biomethanation under psychrophilic conditions

The biomethanation of organic matter represents a long-standing, well-established technology. Although at mesophilic and thermophilic temperatures the process is well understood, current knowledge on psychrophilic biomethanation is somewhat scarce. Methanogenesis is particularly sensitive to temperature, which not only affects the activity and structure of the microbial community, but also results in a change in the degradation pathway of organic matter. There is evidence of psychrophilic methanogenesis in natural environments, and a number of methanogenic archaea have been isolated with optimum growth temperatures of 15-25 °C. At psychrophilic temperatures, large amounts of heat are needed to operate reactors, thus resulting in a marginal or negative overall energy yield. Biomethanation at ambient temperature can alleviate this requirement, but for stable biogas production, a microbial consortium adapted to low temperatures or a psychrophilic consortium is required. Single-step or two-step high rate anaerobic reactors [expanded granular sludge bed (EGSB) and up flow anaerobic sludge bed (UASB)] have been used for the treatment of low strength wastewater. Simplified versions of these reactors, such as anaerobic sequencing batch reactors (ASBR) and anaerobic migrating blanket reactor (AMBR) have also been developed with the aim of reducing volume and cost. This technology has been further simplified and extended for the disposal of night soil in high altitude, low temperature areas of the Himalayas, where the hilly terrain, non-availability of conventional energy, harsh climate and space constraints limit the application of complicated reactors. Biomethanation at psychrophilic temperatures and the contribution made to night-soil degradation in the Himalayas are reviewed in this article.

Temperature-dependent global gene expression in the Antarctic archaeon Methanococcoides burtonii

Methanococcoides burtonii is a member of the Archaea that was isolated from Ace Lake in Antarctica and is a valuable model for studying cold adaptation. Low temperature transcriptional regulation of global gene expression, and the arrangement of transcriptional units in cold-adapted archaea has not been studied. We developed a microarray for determining which genes are expressed in operons, and which are differentially expressed at low (4°C) or high (23°C) temperature. Approximately 55% of genes were found to be arranged in operons that range in length from 2 to 23 genes, and mRNA abundance tended to increase with operon length. Analysing microarray data previously obtained by others for Halobacterium salinarum revealed a similar correlation between operon length and mRNA abundance, suggesting that operons may play a similar role more broadly in the Archaea. More than 500 genes were differentially expressed at levels up to ≈ 24-fold. A notable feature was the upregulation of genes involved in maintaining RNA in a state suitable for translation in the cold. Comparison between microarray experiments and results previously obtained using proteomics indicates that transcriptional regulation (rather than translation) is primarily responsible for controlling gene expression in M. burtonii. In addition, certain genes (e.g. involved in ribosome structure and methanogenesis) appear to be regulated post-transcriptionally. This is one of few experimental studies describing the genome-wide distribution and regulation of operons in archaea.

Approaching Mars-like geochemical conditions in the laboratory: omission of artificial buffers and reductants in a study of biogenic methane production on a smectite clay

Methanogens have not been shown to metabolize in conditions exactly analogous to those present in Mars' subsurface. In typical studies of methanogenic metabolism, nutrient-rich buffered media and reducing agents are added to the cultures in an attempt to optimize the environment for methanogen survival and growth. To study methanogens in more Mars-relevant laboratory conditions, efforts should be made to eliminate artificial media, buffers, and reducing agents from investigations of methanogenic metabolism. After preliminary work to compare methanogen viability on montmorillonite clay and JSC Mars-1 regolith simulant, a study was conducted to determine whether biological methanogenesis could occur in non-reduced, non-buffered environments containing only H(2), CO(2), montmorillonite, and the liquid fraction extracted from a montmorillonite/deionized water suspension. Biogenic methane was observed in the microenvironments despite the omission of traditional media, buffers, and reducing agents. Mean headspace methane concentration after 96 days of observation was 10.23% ± 0.64% (% vol ± SEM, n = 4). However, methane production was severely decreased with respect to reduced, buffered microenvironments (Day 28: 31.98% ± 0.19%, n = 3). Analysis of results and comparison to previous work indicate that montmorillonite clay has a strong ability to supply micronutrients necessary for methanogenic metabolism, and the liquid fraction from a montmorillonite/deionized water slurry can successfully be used as an alternative to reduced and buffered nutritive media in Mars-relevant studies of methanogenic metabolism.

Extremophiles in biofuel synthesis

The current global energy situation has demonstrated an urgent need for the development of alternative fuel sources to the continually diminishing fossil fuel reserves. Much research to address this issue focuses on the development of financially viable technologies for the production of biofuels. The current market for biofuels, defined as fuel products obtained from organic substrates, is dominated by bioethanol, biodiesel, biobutanol and biogas, relying on the use of substrates such as sugars, starch and oil crops, agricultural and animal wastes, and lignocellulosic biomass. This conversion from biomass to biofuel through microbial catalysis has gained much momentum as biotechnology has evolved to its current status. Extremophiles are a robust group of organisms producing stable enzymes, which are often capable of tolerating changes in environmental conditions such as pH and temperature. The potential application of such organisms and their enzymes in biotechnology is enormous, and a particular application is in biofuel production. In this review an overview of the different biofuels is given, covering those already produced commercially as well as those under development. The past and present trends in biofuel production are discussed, and future prospects for the industry are highlighted. The focus is on the current and future application of extremophilic organisms and enzymes in technologies to develop and improve the biotechnological production of biofuels.

Methanoregula boonei gen. nov., sp. nov., an acidiphilic methanogen isolated from an acidic peat bog

A novel acidiphilic, hydrogenotrophic methanogen, designated strain 6A8(T), was isolated from an acidic (pH 4.0-4.5) and ombrotrophic (rain-fed) bog located near Ithaca, NY, USA. Cultures were dimorphic, containing thin rods (0.2-0.3 μm in diameter and 0.8-3.0 μm long) and irregular cocci (0.2-0.8 μm in diameter). The culture utilized H(2)/CO(2) to produce methane but did not utilize formate, acetate, methanol, ethanol, 2-propanol, butanol or trimethylamine. Optimal growth conditions were near pH 5.1 and 35 °C. The culture grew in basal medium containing as little as 0.43 mM Na(+) and growth was inhibited completely by 50 mM NaCl. To our knowledge, strain 6A8(T) is one of the most acidiphilic (lowest pH optimum) and salt-sensitive methanogens in pure culture. Acetate, coenzyme M, vitamins and yeast extract were required for growth. It is proposed that a new genus and species be established for this organism, Methanoregula boonei gen. nov., sp. nov. The type strain of Methanoregula boonei is 6A8(T) (=DSM 21154(T) =JCM 14090(T)).

Methanobacterium veterum sp. nov., from ancient Siberian permafrost

A methanogenic archaeon, strain MK4(T), was isolated from ancient permafrost after long-term selective anaerobic cultivation. The cells were rods, 2.0-8.0 microm long and 0.40-0.45 microm wide, and stained Gram-negative. Optimal growth was observed at 28 degrees C and pH 7.0-7.2 and in 0.05 M NaCl. The isolate used H(2) plus CO(2), methylamine plus H(2) and methanol plus H(2) as sources for growth and methanogenesis. Phylogenetic analysis of the 16S rRNA gene sequence of the strain showed close affinity with Methanobacterium bryantii (similarity >99 % to the type strain). On the basis of the level of DNA-DNA hybridization (62 %) between strain MK4(T) and Methanobacterium bryantii VKM B-1629(T) and phenotypic and phylogenetic differences, strain MK4(T) was assigned to a novel species of the genus Methanobacterium, Methanobacterium veterum sp. nov., with the type strain MK4(T) (=DSM 19849(T) =VKM B-2440(T)).

Sequence-based analysis of protein energy landscapes reveals nonuniform thermal adaptation within the proteome

Thermal adaptation of individual proteins is often achieved through modulating protein stability, with proteins that are adapted to extreme cold environments having increased conformational flexibility when brought to mesophilic conditions. Conversely, proteins adapted to higher temperatures appear less dynamic and are found to be much more stable against thermal denaturation than their mesophilic counterparts. According to the current paradigm, the adaptation of an organism for survival at higher or lower temperatures is facilitated by the adaptation of the component proteins. We note, however, that these observations have been carried out on relatively few proteins. The extent to which the conformational stabilities of all members of the proteome have been modulated for thermal adaptation remains unclear, with no direct experimental strategies to address this issue. Adapted extremophilies are likely to use a multitude of molecular and biophysical strategies for survival and, therefore, evolution of specific biophysical properties of proteins for optimal function may not be necessary for all proteins in the proteome. Using a sequence-based predictor of protein stability, eScape, an in silico examination of several extremophilic proteomes shows a correlation between the collective stability of the proteins and the thermal range of survival for the organism as expected. Unexpectedly, however, the analysis shows that protein thermostability is modified to different extents across the proteome and depends on the functional role for which the protein is involved. Identification of these differences provides unique opportunities to study interdependence within the proteome as well as the role that the proteome plays in the process of evolutionary thermal adaptation.

Long-term (1,243 days), low-temperature (4-15 degrees C), anaerobic biotreatment of acidified wastewaters: bioprocess performance and physiological characteristics

The feasibility of long-term (>3 years), low-temperature (4-15 degrees C) and anaerobic bioreactor operation, for the treatment of acidified wastewater, was investigated. A hybrid, expanded granular sludge bed-anaerobic filter bioreactor was seeded with a mesophilic inoculum and employed for the mineralization of moderate-strength (3.75-10 kg chemical oxygen demand (COD)m(-3)) volatile fatty acid-based wastewaters at 4-15 degrees C. Bioprocess performance was assessed in terms of COD removal efficiency (CODRE), methane biogas concentration, and yield, and biomass retention. Batch specific methanogenic activity assays were performed to physiologically characterise reactor biomass. Despite transient disimprovements, CODRE and methane biogas concentrations exceeded 80% and 65%, respectively, at an applied organic loading rate (OLR) of 10 kgCODm(-3)d(-1) between 9.5 and 15 degrees C (sludge loading rate (SLR), 0.6 kgCOD kg[VSS](-1)d(-1)). Over 50% of the granular sludge bed was lost to disintegration during operation at 9.5 degrees C, warranting a reduction in the applied OLR to 3.75-5 kgCODm(-3)d(-1) (SLR, c. 0.4-0.5kgCOD kg[VSS](-1)d(-1)). From that point forward, remarkably stable and efficient performance was observed during operation at 4-10 degrees C, with respect to CODRE (>or=82%), methane biogas concentration (>70%) and methane yields (>4l(Methane)d(-1)), suggesting the adaptation of our mesophilic inoculum to psychrophilic operating conditions. Physiological activity assays indicated the development of psychroactive syntrophic and methanogenic populations, including the emergence of putatively psychrophilic propionate-oxidising and hydrogenotrophic methanogenic activity. The data suggest that mesophilic inocula can physiologically adapt to sub-optimal operational temperatures: treatment efficiencies and sludge loading rates at 4 degrees C (day, 1243) were comparable to those achieved at 15 degrees C (day 0). Furthermore, long-term, low-temperature bioreactor operation may act as a selective enrichment for psychrophilic methanogenic activity from mesophilic inocula. The observed efficient and stable bioprocess performance highlights the potential for long-term, low-temperature bioreactor operation.

The possible origin and persistence of life on Enceladus and detection of biomarkers in the plume

The jets of icy particles and water vapor issuing from the south pole of Enceladus are evidence for activity driven by some geophysical energy source. The vapor has also been shown to contain simple organic compounds, and the south polar terrain is bathed in excess heat coming from below. The source of the ice and vapor, and the mechanisms that accelerate the material into space, remain obscure. However, it is possible that a liquid water environment exists beneath the south polar cap, which may be conducive to life. Several theories for the origin of life on Earth would apply to Enceladus. These are (1) origin in an organic-rich mixture, (2) origin in the redox gradient of a submarine vent, and (3) panspermia. There are three microbial ecosystems on Earth that do not rely on sunlight, oxygen, or organics produced at the surface and, thus, provide analogues for possible ecologies on Enceladus. Two of these ecosystems are found deep in volcanic rock, and the primary productivity is based on the consumption by methanogens of hydrogen produced by rock reactions with water. The third ecosystem is found deep below the surface in South Africa and is based on sulfur-reducing bacteria consuming hydrogen and sulfate, both of which are ultimately produced by radioactive decay. Methane has been detected in the plume of Enceladus and may be biological in origin. An indicator of biological origin may be the ratio of non-methane hydrocarbons to methane, which is very low (0.001) for biological sources but is higher (0.1-0.01) for nonbiological sources. Thus, Cassini's instruments may detect plausible evidence for life by analysis of hydrocarbons in the plume during close encounters.