Isolation and characterization of an h(2)-oxidizing thermophilic methanogen

The complete genome sequence of Sedimentibacter sp. strain MB35-C1, isolated from the sewage sludge

Here, we report the complete genome sequence of Sedimentibacter sp. strain MB35-C1, which was isolated from sewage sludge at the Wastewater Treatment Plant of Sanming Steel Co. Ltd. in Fujian, China. The resulting genome of strain MB35-C1 is a single contig of 3,621,605 bp.

Enrichment and characterization of human-associated mucin-degrading microbial consortia by sequential passage

Mucin is a glycoprotein secreted throughout the mammalian gastrointestinal tract that can support endogenous microorganisms in the absence of complex polysaccharides. While several mucin-degrading bacteria have been identified, the interindividual differences in microbial communities capable of metabolizing this complex polymer are not well described. To determine whether community assembly on mucin is deterministic across individuals or whether taxonomically distinct but functionally similar mucin-degrading communities are selected across fecal inocula, we used a 10-day in vitro sequential batch culture fermentation from three human donors with mucin as the sole carbon source. For each donor, 16S rRNA gene amplicon sequencing was used to characterize microbial community succession, and the short-chain fatty acid profile was determined from the final community. All three communities reached a steady-state by day 7 in which the community composition stabilized. Taxonomic comparisons amongst communities revealed that one of the final communities had Desulfovibrio, another had Akkermansia, and all three shared other members, such as Bacteroides. Metabolic output differences were most notable for one of the donor's communities, with significantly less production of acetate and propionate than the other two communities. These findings demonstrate the feasibility of developing stable mucin-degrading communities with shared and unique taxa. Furthermore, the mechanisms and efficiencies of mucin degradation across individuals are important for understanding how this community-level process impacts human health.

Methanooceanicella nereidis gen. nov., sp. nov., the first oceanic Methanocellaceae methanogen, isolated from potential methane hydrate bearing area offshore southwestern Taiwan

A novel mesophilic, hydrogenotrophic methanogen, strain CWC-04T, was obtained from a sediment sample extracted from a gravity core retrieved at station 22 within the KP-9 area off the southwestern coast of Taiwan during the ORIII-1368 cruise in 2009. Cells of strain CWC-04T were rod-shaped, 1.4-2.9 µm long by 0.5-0.6 µm wide, and occurred singly. Strain CWC-04Tutilized formate, H2/CO2, 2-propanol/CO2 or 2-butanol/CO2 as catabolic substrates. The optimal growth conditions were 42 °C, 0.17 M NaCl and pH 5.35. The genomic DNA G+C content calculated from the genome sequence of strain CWC-04T was 46.19 mol%. Phylogenetic analysis of 16S rRNA gene revealed that strain CWC-04T is affiliated with the genus Methanocella. The 16S rRNA gene sequences similarities within strains Methanocella arvoryzae MRE50T, Methanocella paludicola SANAET and Methanocella conradii HZ254T were 93.7, 93.0 and 91.3 %, respectively. In addition, the optical density of CWC-04T culture dropped abruptly upon entering the late-log growth phase, with virus-like particles (150 nm in diameter) being observed on and around the cells. This observation suggests that strain CWC-04T harbours a lytic virus. Based on these phenotypic, phylogenetic and genomic results, we propose that strain CWC-04T represents a novel species of a novel genus in the family Methanocellaceae, for which the name Methanooceanicella nereidis gen. nov., sp. nov. is proposed. The type strain is CWC-04T (=BCRC AR10050T=NBRC 113165T).

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).

Co-metabolic Effect of Glucose on Methane Production and Phenanthrene Removal in an Enriched Phenanthrene-Degrading Consortium Under Methanogenesis

Anaerobic digestion is used to treat diverse waste classes, and polycyclic aromatic hydrocarbons (PAHs) are a class of refractory compounds that common in wastes treated using anaerobic digestion. In this study, a microbial consortium with the ability to degrade phenanthrene under methanogenesis was enriched from paddy soil to investigate the cometabolic effect of glucose on methane (CH₄) production and phenanthrene (a representative PAH) degradation under methanogenic conditions. The addition of glucose enhanced the CH₄ production rate (from 0.37 to 2.25mg⋅L^-1⋅d^-1) but had no influence on the degradation rate of phenanthrene. Moreover, glucose addition significantly decreased the microbial α-diversity (from 2.59 to 1.30) of the enriched consortium but showed no significant effect on the microbial community (R ²=0.39, p=0.10), archaeal community (R ²=0.48, p=0.10), or functional profile (R ²=0.48, p=0.10). The relative abundance of genes involved in the degradation of aromatic compounds showed a decreasing tendency with the addition of glucose, whereas that of genes related to CH₄ synthesis was not affected. Additionally, the abundance of genes related to the acetate pathway was the highest among the four types of CH₄ synthesis pathways detected in the enriched consortium, which averagely accounted for 48.24% of the total CH₄ synthesis pathway, indicating that the acetate pathway is dominant in this phenanthrene-degrading system during methanogenesis. Our results reveal that achieving an ideal effect is diffcult via co-metabolism in a single-stage digestion system of PAH under methanogenesis; thus, other anaerobic systems with higher PAH removal efficiency should be combined with methanogenic digestion, assembling a multistage pattern to enhance the PAH removal rate and CH₄ production in anaerobic digestion.

Iron availability is a key factor for freshwater cyanobacterial survival against saline stress

Estuaries are among the most productive ecosystems and dynamic environments on Earth. Varying salinity is the most important challenge for phytoplankton survival in estuaries. In order to investigate the role of iron nutrition on phytoplankton survival under salinity stress, a freshwater cyanobacterial strain was cultivated in media added with different proportions of seawater (measured with siderophore activities), and supplied with gel-immobilized ferrihydrite as iron source. Results showed that the strain grew well in media with 0% seawater supplied with ferrihydrite as iron source. Surprisingly, the biomasses in media with 50% seawater, with more newly excreted siderophore, were similar to those with 0% seawater, but better than those with 6.25%, 12.5% and 25% seawater. Smaller iron isotopic discriminations between the cyanobacterial cells associated iron and dissolved iron were observed in media with 0% and 50% seawater suggested that higher fractions of iron uptake from aqueous dissolved iron reservoir by these comparatively larger biomasses. In summary, this study proved that iron availability plays a key role in cyanobacterial survival under varying salinity stress, and suggested that siderophores introduced by seawater may accelerate iron dissolution, increase iron availability, and make cyanobacterial cells overcome the adverse effects of high-salinity, and indicated that siderophore excretion is a kind of survival strategy for phytoplankton in face of salinity stress.

Methanolobus halotolerans sp. nov., isolated from the saline Lake Tus in Siberia

A halotolerant, psychrotolerant and methylotrophic methanogen, strain SY-01^T, was isolated from the saline Lake Tus in Siberia. Cells of strain SY-01^T were non-motile, cocci and 0.8-1.0 µm in diameter. The only methanogenic substrate utilized by strain SY-01^T was methanol. The temperature range of growth for strain SY-01^T was from 4 to 40 °C and the optimal temperature for growth was 30 °C. The pH range of growth was from pH 7.2 to 9.0, with optimal growth at pH 8.0. The NaCl range of growth was 0-1.55 M with optimal growth at 0.51 M NaCl. The G+C content of the genome of strain SY-01^T was 43.6 mol % as determined by genome sequencing. Phylogenetic analysis revealed that strain SY-01^T was most closely related to Methanolobus zinderi SD1^T (97.3 % 16S rRNA gene sequence similarity), and had 95.5-97.2 % similarities to other Methanolobus species with valid names. Genome relatedness between strain SY-01^T and DSM 21339^T was computed using average nucleotide identity and digital DNA-DNAhybridization, which yielded values of 79.7 and 21.7 %, respectively. Based on morphological, phenotypic, phylogenetic and genomic relatedness data presented here, it is evident that strain SY-01^T represents a novel species of the genus Methanolobus, and the name Methanolobus halotolerans sp. nov. is proposed. The type strain is SY-01^T (=BCRC AR10051^T=NBRC 113166 ^T=DSM 107642^T).

Methanofollis fontis sp. nov., a methanogen isolated from marine sediment near a cold seep at Four-Way Closure Ridge offshore southwestern Taiwan

A mesophilic, hydrogenotrophic methanogen, strain FWC-SCC2^T, was isolated from deep-sea sediments collected by a real-time video multiple-corer at the C5-6 station near a cold seep at Four-Way Closure Ridge region during R/V Ocean Researcher III ORIII-1900 cruise in 2015. The cells were irregular cocci, non-motile and 0.8-1.2 µm in diameter. The methanogenic substrates utilized by strain FWC-SCC2^T were formate or H₂+CO₂, but not acetate, methanol, ethanol or methylamines. Strain FWC-SCC2^T was lysed in SDS (0.01 %, w/v). The M _r of surface-layer protein was 116 400. The optimum growth conditions of strain FWC-SCC2^T were 37 °C, 0.17 M NaCl and pH 6.7-7.0. The genomic DNA G+C content calculated from the genome sequence of strain FWC-SCC2^T was 59.5 mol %. Phylogenetic analysis revealed that strain FWC-SCC2^T was a member of the genus Methanofollis, and was most closely related to Methanofollis tationis Chile 9^T (97.6 % similarity of 16S rRNA gene sequence) and shared 97.4, 95.9, 95.9 and 95.4 % with Methanofollis liminatans GKZPZ^T, Methanofollis formosanus ML15^T, Methanofollis aquaemaris N2F9704^T and Methanofollis ethanolicus HASU^T, respectively. The genome relatedness values between strain FWC-SCC2^T and M. tationis DSM 2702^T were estimated by average nucleotide identity and digital DNA-DNA hybridization analyses and the results were 79.4 and 21.2 %, respectively. Based on the differences in physiological and biochemical properties, 16S rRNA gene phylogeny and genome relatedness presented here, it is suggested that strain FWC-SCC2^T represents a novel species of the genus Methanofollis, and the name Methanofollis fontis sp. nov. is proposed. The type strain is FWC-SCC2^T (=BCRC AR10052^T=DSM 107935^T= NBRC 113164^T).

Comparative Genomics Guides Elucidation of Vitamin B12 Biosynthesis in Novel Human-Associated Akkermansia Strains

There is significant interest in the therapeutic and probiotic potential of the common gut bacterium Akkermansia muciniphila. However, knowledge of both the genomic and physiological diversity of this bacterial lineage is limited. Using a combination of genomic, molecular biological, and traditional microbiological approaches, we identified at least four species-level phylogroups with differing functional potentials that affect how these bacteria interact with both their human host and other members of the human gut microbiome. Specifically, we identified and isolated Akkermansia strains that were able to synthesize vitamin B₁₂. The ability to synthesize this important cofactor broadens the physiological capabilities of human-associated Akkermansia strains, fundamentally altering our understanding of how this important bacterial lineage may affect human health.

Akkermansia muciniphila is a mucin-degrading bacterium found in the gut of most humans and is considered a “next-generation probiotic.” However, knowledge of the genomic and physiological diversity of human-associated Akkermansia sp. strains is limited. Here, we reconstructed 35 metagenome-assembled genomes and combined them with 40 publicly available genomes for comparative genomic analysis. We identified at least four species-level phylogroups (AmI to AmIV), with distinct functional potentials. Most notably, we identified genes for cobalamin (vitamin B₁₂) biosynthesis within the AmII and AmIII phylogroups. To verify these predictions, 10 Akkermansia strains were isolated from adults and screened for vitamin B₁₂ biosynthesis genes via PCR. Two AmII strains were positive for the presence of cobalamin biosynthesis genes, while all 9 AmI strains tested were negative. To demonstrate vitamin B₁₂ biosynthesis, we measured the production of acetate, succinate, and propionate in the presence and absence of vitamin supplementation in representative strains of the AmI and AmII phylogroups, since cobalamin is an essential cofactor in propionate metabolism. Results showed that the AmII strain produced acetate and propionate in the absence of supplementation, which is indicative of vitamin B₁₂ biosynthesis. In contrast, acetate and succinate were the main fermentation products for the AmI strains when vitamin B₁₂ was not supplied in the culture medium. Lastly, two bioassays were used to confirm vitamin B₁₂ production by the AmII phylogroup. This novel physiological trait of human-associated Akkermansia strains may affect how these bacteria interact with the human host and other members of the human gut microbiome.

IMPORTANCE There is significant interest in the therapeutic and probiotic potential of the common gut bacterium Akkermansia muciniphila. However, knowledge of both the genomic and physiological diversity of this bacterial lineage is limited. Using a combination of genomic, molecular biological, and traditional microbiological approaches, we identified at least four species-level phylogroups with differing functional potentials that affect how these bacteria interact with both their human host and other members of the human gut microbiome. Specifically, we identified and isolated Akkermansia strains that were able to synthesize vitamin B₁₂. The ability to synthesize this important cofactor broadens the physiological capabilities of human-associated Akkermansia strains, fundamentally altering our understanding of how this important bacterial lineage may affect human health.

Methanoculleus sediminis sp. nov., a methanogen from sediments near a submarine mud volcano

A mesophilic, hydrogenotrophic methanogen, strain S3Fa(T), was isolated from sediments collected by Ocean Researcher I cruise ORI-934 in 2010 near the submarine mud volcano MV4 located at the upper slope of south-west Taiwan. The methanogenic substrates utilized by strain S3Fa(T) were formate and H2/CO2 but not acetate, secondary alcohols, methylamines, methanol or ethanol. Cells of strain S3Fa(T) were non-motile, irregular cocci, 0.5-1.0 μm in diameter. The surface-layer protein showed an Mr of 128,000.The optimum growth conditions were 37 °C, pH 7.1 and 0.17 M NaCl. The DNA G+C content of the genome of strain S3Fa(T) was 62.3 mol%. Phylogenetic analysis revealed that strain S3Fa(T) was most closely related to Methanoculleus marisnigri JR1(T) (99.3% 16S rRNA gene sequence similarity). Genome relatedness between strain S3Fa(T) and Methanoculleus marisnigri JR1(T) was computed using both genome-to-genome distance analysis (GGDA) and average nucleotide identity (ANI) with values of 46.3-55.5% and 93.08%, respectively. Based on morphological, phenotypic, phylogenetic and genomic relatedness data, it is evident that strain S3Fa(T) represents a novel species of the genus Methanoculleus, for which the name Methanoculleus sediminis sp. nov. is proposed. The type strain is S3Fa(T) ( = BCRC AR10044(T) = DSM 29354(T)).

Methanoculleus taiwanensis sp. nov., a methanogen isolated from deep marine sediment at the deformation front area near Taiwan

A mesophilic, hydrogenotrophic methanogen, strain CYW4T, was isolated from deep-sea sediment obtained by the Ocean Researcher I cruiser, ORI-961, in 2011. The sediment was from the deformation front area offshore of south-western Taiwan. Here, seismic reflections indicated that methane hydrates were abundant. The methanogenic substrates utilized by strain CYW4T were formate and H2/CO2, but not acetate, secondary alcohols, methylamines, methanol and ethanol. Cells of strain CYW4T were non-motile, irregular cocci and 0.6–1.5 µm in diameter. The S-layer protein had an M r of 112 000. The optimum growth conditions were at 37 °C, pH 8.1 and 0.08 M NaCl. Growth of the strain was stimulated by acetate. The G+C content of the chromosomal DNA of strain CYW4T was 61 mol%. Phylogenetic analysis revealed that strain CYW4T was most closely related to Methanoculleus marisnigri JR1T (96.82 % 16S rRNA gene sequence similarity). Based on the morphological, phenotypic and phylogenetic characteristics presented here, it is evident that strain CYW4T represents a novel species of the genus Methanoculleus , and the name Methanoculleus taiwanensis sp. nov. is proposed. The type strain is CYW4T ( = BCRC AR10043T = NBRC 110782T). The optical density of cultures of strain CYW4T dropped abruptly upon entering the stationary growth phase. During this time numerous particles of approximately 50 nm in diameter were observed on and around the cells. This suggests that strain CYW4T harbours a lytic virus that is induced in the stationary phase, which is of interest because only a few lytic viruses have been reported in methanogens.

Artificial symbiosis for acetone-butanol-ethanol (ABE) fermentation from alkali extracted deshelled corn cobs by co-culture of Clostridium beijerinckii and Clostridium cellulovorans

Background

Butanol is an industrial commodity and also considered to be a more promising gasoline substitute compared to ethanol. Renewed attention has been paid to solvents (acetone, butanol and ethanol) production from the renewable and inexpensive substrates, for example, lignocellulose, on account of the depletion of oil resources, increasing gasoline prices and deteriorating environment. Limited to current tools for genetic manipulation, it is difficult to develop a genetically engineered microorganism with combined ability of lignocellulose utilization and solvents production. Mixed culture of cellulolytic microorganisms and solventogenic bacteria provides a more convenient and feasible approach for ABE fermentation due to the potential for synergistic utilization of the metabolic pathways of two organisms. But few bacteria pairs succeeded in producing biobutanol of high titer or high productivity without adding butyrate. The aim of this work was to use Clostridium cellulovorans 743B to saccharify lignocellulose and produce butyric acid, instead of adding cellulase and butyric acid to the medium, so that the soluble sugars and butyric acid generated can be subsequently utilized by Clostridium beijerinckii NCIMB 8052 to produce butanol in one pot reaction.

Results

A stable artificial symbiotic system was constructed by co-culturing a celluloytic, anaerobic, butyrate-producing mesophile (C. cellulovorans 743B) and a non-celluloytic, solventogenic bacterium (C. beijerinckii NCIMB 8052) to produce solvents by consolidated bioprocessing (CBP) with alkali extracted deshelled corn cobs (AECC), a low-cost renewable feedstock, as the sole carbon source. Under optimized conditions, the co-culture degraded 68.6 g/L AECC and produced 11.8 g/L solvents (2.64 g/L acetone, 8.30 g/L butanol and 0.87 g/L ethanol) in less than 80 h. Besides, a real-time PCR assay based on the 16S rRNA gene sequence was performed to study the dynamics of the abundance of each strain during the co-culturing process, which figured out the roles of each strain at different periods in the symbiosis.

Conclusion

Our work illustrated the great potential of artificial symbiosis in biofuel production from lignocellulosic biomass by CBP. The dynamics of the abundance of C. beijerinckii and C. cellulovorans revealed mechanisms of cooperation and competition between the two strains during the co-culture process.

Partaking of Archaea to biogeochemical cycling in oxygen-deficient zones of meromictic saline Lake Faro (Messina, Italy)

We used a combination of molecular and microbiological approaches to determine the activity, abundance and diversity of archaeal populations inhabiting meromictic saline Lake Faro (Messina, Italy). Analysis of archaeal 16S rRNA, amoA, accA and hbd genes and transcripts revealed that sub- and anoxic layers of Lake Faro are primarily inhabited by the organisms related to the clusters of Marine Group I.1a of Thaumarchaeota frequently recovered from oxygen-depleted marine ecosystems. These organisms dominated the metabolically active archaea down to the bottom of the lake, indicating their adaptation to recurrent changes in the levels of water column hypoxia. The upper microaerobic layer of Lake Faro redoxcline has the maximal rates of dark primary production much lower than those of other previously studied pelagic redoxclines, but comparable to the values of meso- and bathypelagic areas of Mediterranean Sea. Application of bacterial inhibitors, especially azide, significantly declined the CO2 fixation rates in the low interface and monimolimnion, whereas archaea-specific inhibitor had effect only in upper part of the redoxcline. Based on these findings, we hypothesize that dark bicarbonate fixation in suboxic zone of Lake Faro results mainly from archaeal activity which is affected by the predicted lack in oxygen in lower layers.

Design and characterization of a microbial fuel cell for the conversion of a lignocellulosic crop residue to electricity

Agricultural crop residues contain high amounts of biochemical energy as cellulose and lignin. A portion of this biomass could be sustainably harvested for conversion to bioenergy to help offset fossil fuel consumption. In this study, the potential for converting lignocellulosic biomass directly to electricity in a microbial fuel cell (MFC) was explored. Design elements of tubular air cathode MFCs and leach-bed bioreactors were integrated to develop a new solid-substrate MFC in which cellulose hydrolysis, fermentation, and anode respiration occurred in a single chamber. Electricity was produced continuously from untreated corncob pellets for >60 d. Addition of rumen fluid increased power production, presumably by providing growth factors to anode-respiring bacteria. Periodic exposure to oxygen also increased power production, presumably by limiting the diversion of electrons to methanogenesis. In the absence of methanogenesis, bioaugmentation with Geobacter metallireducens further improved MFC performance. Under these conditions, the maximum power density was 230 mW/m(3).

Mercury resistance and mercuric reductase activities and expression among chemotrophic thermophilic Aquificae

Mercury (Hg) resistance (mer) by the reduction of mercuric to elemental Hg is broadly distributed among the Bacteria and Archaea and plays an important role in Hg detoxification and biogeochemical cycling. MerA is the protein subunit of the homodimeric mercuric reductase (MR) enzyme, the central function of the mer system. MerA sequences in the phylum Aquificae form the deepest-branching lineage in Bayesian phylogenetic reconstructions of all known MerA homologs. We therefore hypothesized that the merA homologs in two thermophilic Aquificae, Hydrogenobaculum sp. strain Y04AAS1 (AAS1) and Hydrogenivirga sp. strain 128-5-R1-1 (R1-1), specified Hg resistance. Results supported this hypothesis, because strains AAS1 and R1-1 (i) were resistant to >10 μM Hg(II), (ii) transformed Hg(II) to Hg(0) during cellular growth, and (iii) possessed Hg-dependent NAD(P)H oxidation activities in crude cell extracts that were optimal at temperatures corresponding with the strains' optimal growth temperatures, 55°C for AAS1 and 70°C for R1-1. While these characteristics all conformed with the mer system paradigm, expression of the Aquificae mer operons was not induced by exposure to Hg(II) as indicated by unity ratios of merA transcripts, normalized to gyrA transcripts for hydrogen-grown AAS1 cultures, and by similar MR specific activities in thiosulfate-grown cultures with and without Hg(II). The Hg(II)-independent expression of mer in the deepest-branching lineage of MerA from bacteria whose natural habitats are Hg-rich geothermal environments suggests that regulated expression of mer was a later innovation likely in environments where microorganisms were intermittently exposed to toxic concentrations of Hg.

Threshold acetate concentrations for acetate catabolism by aceticlastic methanogenic bacteria

Marked differences were found for minimum threshold concentrations of acetate catabolism by Methanosarcina barkeri 227 (1.180 mM), Methanosarcina mazei S-6 (0.396 mM), and a Methanothrix sp. (0.069 mM). This indicates that the aceticlastic methanogens responsible for the conversion of acetate to methane in various ecosystems might be different, depending on the prevailing in situ acetate concentrations.

Isolation and characterization of a novel thermophilic, freshwater methanogen

A novel thermophilic, coccoid methanogen isolated from nonthermal freshwater sediments is described. Hydrogen plus carbon dioxide and formate were substrates for methanogenesis, and methane production was stimulated by yeast extract, Casamino Acids, and tryptose. Growth also occurred autotrophically. Elevated levels of sodium chloride were not required for maximum growth and were inhibitory above 2%. The minimum doubling time occurred at 57 degrees C, and the upper and lower limits for methane production were 62 and 26 degrees C, respectively. The optimum pH for growth was between 7.0 and 7.5. Inhibitory antibiotics included metronidazole, anisomycin, chloramphenicol, and lasalocid. Colonies were circular, dark yellow, shiny, and convex with entire edges. Cells were 1 to 2.5 mum in diameter, nonmotile, occurring singly or in pairs, and fimbriated. Cells were lysed by pronase or trypsin digestion, glass-distilled water, and 1% sodium dodecyl sulfate. Electron micrographs of thin sections showed a monolayered cell wall ca. 20 nm thick. The DNA base ratio was 49.2 mol% guanine plus cytosine. The whole cell protein pattern differed from that of other named coccoid methanogens.

Effects of Temperature on Methanogenesis in a Thermophilic (58 degrees C) Anaerobic Digestor

The short-term effects of temperature on methanogenesis from acetate or CO(2) in a thermophilic (58 degrees C) anaerobic digestor were studied by incubating digestor sludge at different temperatures with C-labeled methane precursors (CH(3)COO or CO(2)). During a period when Methanosarcina sp. was numerous in the sludge, methanogenesis from acetate was optimal at 55 to 60 degrees C and was completely inhibited at 65 degrees C. A Methanosarcina culture isolated from the digestor grew optimally on acetate at 55 to 58 degrees C and did not grow or produce methane at 65 degrees C. An accidental shift of digestor temperature from 58 to 64 degrees C during this period caused a sharp decrease in gas production and a large increase in acetate concentration within 24 h, indicating that the aceticlastic methanogens in the digestor were the population most susceptible to this temperature increase. During a later period when Methanothrix sp. was numerous in the digestor, methanogenesis from CH(3)COO was optimal at 65 degrees C and completely inhibited at 75 degrees C. A partially purified Methanothrix enrichment culture derived from the digestor had a maximum growth temperature near 70 degrees C. Methanogenesis from CO(2) in the sludge was optimal at 65 degrees C and still proceeded at 75 degrees C. A CO(2)-reducing Methanobacterium sp. isolated from the digestor was capable of methanogenesis at 75 degrees C. During the period when Methanothix sp. was apparently dominant, sludge incubated for 24 h at 65 degrees C produced more methane than sludge incubated at 60 degrees C, and no acetate accumulated at 65 degrees C. Methanogenesis was severely inhibited in sludge incubated at 70 degrees C, but since neither acetate nor H(2) accumulated, production of these methanogenic substrates by fermentative bacteria was probably the most temperature-sensitive process. Thus, there was a correlation between digestor performance at different temperatures and responses to temperature by cultures of methanogens believed to play important roles in the digestor.

Methanogenesis in a Thermophilic (58 degrees C) Anaerobic Digestor: Methanothrix sp. as an Important Aceticlastic Methanogen

Aceticlastic methanogens and other microbial groups were enumerated in a 58 degrees C laboratory-scale (3 liter) anaerobic digestor which was fed air-classified municipal refuse, a lignocellulosic waste (loading rate = 1.8 to 2.7 g of volatile solids per liter per day; retention time = 10 days). Two weeks after start-up, Methanosarcina sp. was present in high numbers (10 to 10 CFU/ml) and autofluorescent Methanosarcina-like clumps were abundant in sludge examined by using epifluorescence microscopy. After about 4 months of digestor operation, numbers of Methanosarcina sp. dropped 2 to 3 orders of magnitude and large numbers (most probable number = 10 to 10/ml) of a thermophilic aceticlastic methanogen morphologically resembing Methanothrix sp. were found. Methanothrix sp. had apparently displaced Methanosarcina sp. as the dominant aceticlastic methanogen in the digestor. During the period when Methanothrix sp. was apparently dominant, acetate concentrations varied between 0.3 and 1.5 mumol/ml during the daily feeding cycle, and acetate was the precursor of 63 to 66% of the methane produced during peak digestor methanogenesis. The apparent K(m) value obtained for methanogenesis from acetate, 0.3 mumol/ml, indicated that the aceticlastic methanogens were nearly saturated for substrate during most of the digestor cycle. CO(2)-reducing methanogens were capable of methanogenesis at rates more than 12 times greater than those usually found in the digestor. Added propionate (4.5 mumol/ml) was metabolized slowly by the digestor populations and slightly inhibited methanogenesis. Added n-butyrate, isobutyrate, or n-valerate (4.5 mumol/ml each) were broken down within 24 h. Isobutyrate was oxidized to acetate, a novel reaction possibly involving isomerization to n-butyrate. The rapid growth rate and versatile metabolism of Methanosarcina sp. make it a likely organism to be involved in start-up, whereas the low K(m) value of Methanothrix sp. for acetate may cause it to be favored in stable digestors operated with long retention times.

Methanosarcina mazei LYC, a New Methanogenic Isolate Which Produces a Disaggregating Enzyme

A methanogenic coccoid organism, Methanosarcina mazei LYC, was isolated from alkaline sediment obtained from an oil exploration drilling site. The isolate resembled M. mazei S-6 by exhibiting different morphophases during its normal growth cycle. It differed from M. mazei S-6 by undergoint a spontaneous shift from large, irregular aggregates of cells to small, individual, irregular, coccoid units. In batch cultures at pH 7.0, M. mazei LYC grew as aggregates during the early growth stage. As the batch culture began exponential growth, the cell aggregates spontaneously dispersed: the culture liquid became turbid, and myriads of tiny (diameter, 1 to 3 mum) coccoid units were observed under phase-contrast microscopy. Disaggregation apparently was accomplished by the production of an enzyme which hydrolyzed the heteropolysaccharide component of the cell wall; the enzyme was active on other Methanosarcina strains as well. Although the enzyme was active when tested at pH 6.0, it apparently was not produced at that pH: when strain LYC was grown at pH 6.0, only cell aggregates were present throughout batch growth. Individual coccoid cells of M. mazei LYC were sensitive to sodium dodecyl sulfate, but the large aggregates of cells were not. Strain LYC rapidly used H(2)-CO(2), in addition to methanol, and mono-, di-, and trimethylamine as methanogenic substrates; acetate was used very slowly. Its optimum growth temperature was 40 degrees C, and its optimum pH was 7.2.

Life Cycles in the Methanogenic Archaebacterium Methanosarcina mazei

Methanosarcina mazei S6 and LYC were used to study the structure and differentiation of the aggregating methanogens. Cultures harvested under various conditions are described at the ultrastructural level. Cells of strain S6 are enclosed by a layer 12 nm thick in contact with the plasma membrane. In sarcinal colonies, cells are held in close association by a fibrous matrix up to 60 nm thick. Colony maturation was examined in strain S6 over a period of 1 year. Changes occurred in the shape and staining of individual cells. Also, various inclusion bodies were observed that either persist throughout colony maturation or are only found at certain growth stages. Two types of cores that are composed of double membranes in M. mazei S6 are described. One has a 90-nm diameter and contains electron-dense granules similar to those found in the cytoplasm. The other core type does not contain granules, is more numerous, and is found in older cultures. Two life cycles are described for M. mazei based on electron microscope examinations. A complex life cycle involving the release of single cells is described with two variations for strains S6 and LYC. When released cells of strain S6 are placed in fresh medium they can repeat the cycle. In addition, a limited cycle is described for both strains of M. mazei. This limited cycle contains the only sarcinal morphotypes observed in M. barkeri. When M. mazei S6 remains in the limited cycle and does not disaggregate in stationary phase, several types of possible resting forms are found.

Isolation and characterization of a moderately halophilic methanogen from a solar saltern

A moderately halophilic methanogenic bacterium was enriched with trimethylamine and isolated from the sediment of a solar salt pond (total dissolved solids of pond water, 250 g/liter; pH 7.5). The isolate (strain SF1, DSM 3243) was an irregular coccus which stained gram negative, with a diameter of 1 mum and a thin monolayered cell wall. The organism grew singly, in pairs, and in irregular clumps. Colonies were tannish yellow, circular, with entire edges, and about 1 mm in diameter within 1 week. Only methylamines or methanol was used for growth and methanogenesis. Most rapid growth (doubling time, 10.2 h) occurred at a temperature of 37 degrees C and a pH of 7.4. The optimum NaCl concentration was 2.1 M. Yeast extract or rumen fluid was required. The isolate was lysed by sodium dodecyl sulfate (0.1 g/liter) and was sensitive to chloramphenicol. The G+C content of the DNA was 41 (+/-1) mol%.

Removal of headspace CO2 increases biological hydrogen production

For biological hydrogen production by fermentation to be a useful method of hydrogen generation, molar yields of hydrogen must be increased. While heat treatment of a soil inoculum increases hydrogen yields by preventing loss of hydrogen to methanogenesis, hydrogen is still lost to acetic acid generation from hydrogen and CO2. To reduce hydrogen losses via acetogenesis, CO2 concentrations in the headspace were substantially reduced during hydrogen production using a chemical scavenger (KOH). CO2 in the headspace was decreased from 24.5% (control) to a maximum of 5.2% during the highest gas production phase, resulting in a hydrogen partial pressure of 87.4%. This reduction in CO2 increased the hydrogen yield by 43% (from 1.4 to 2.0 mol of H2/mol of glucose). The soluble byproducts in all tests consisted primarily of acetate and ethanol. Higher concentrations of ethanol (10.9 mM) remained in solution from bottles with CO2 removal than in the control (1.2 mM), likely as a result of hydrogen inhibition of biological ethanol conversion to acetic acid. These results show that hydrogen production can be increased by removing CO2 in the reactor vessel, likely as a result of suppression of acetogenesis.

Methanocalculus chunghsingensis sp. nov., isolated from an estuary and a marine fishpond in Taiwan

Three novel halotolerant, hydrogenotrophic methanogens, designated strains K1F9705bT, K1F9705c and O1F9704a, were isolated from an estuary in Eriln Shi, Taiwan, and from a nearby marine water aquaculture fishpond. These isolates were irregular cocci that stained Gram-negative. Strains K1F9705bT and K1F9705c were non-motile, but strain O1F9704a was weakly motile with flagella. They were able to use formate and H2/CO2 to form methane, but they could not catabolize acetate, methanol, trimethylamine or secondary alcohols. Acetate was required for cell growth. Tungsten greatly stimulated the growth of strains K1F9705bT and K1F9705c, but did not affect the growth of strain O1F9704a. Optimal pH and temperature for growth of these three isolates were respectively 7.2 and 37 degrees C. Optimal NaCl concentration for growth was 0.5% for strain O1F9704a and 1.0% for strains K1F9705c and K1F9705bT. Moreover, all strains grew well at up to 8-12% NaCl. Analysis of the 16S rRNA gene revealed that these isolates are members of the genus Methanocalculus, but are distinct from Methanocalculus taiwanensis, Methanocalculus pumilus and Methanocalculus halotolerans, with sequence similarities of 98.4, 98.3 and 98.2%, respectively. In addition, strain K1F9705bT possessed 85, 80, 37, 29 and 10% DNA-DNA relatedness to strain K1F9705c, strain O1F9704a, M. pumilus, M. halotolerans and M. taiwanensis, respectively. Analysis of protein profiles and the Mr of surface (S)-layer glycoprotein subunits showed that these three new isolates are closely related to, but distinct from, known Methanocalculus species. A novel species, Methanocalculus chunghsingensis sp. nov., is proposed for strains K1F9705bT, K1F9705c and O1F9704a. The type strain is K1F9705bT (=OCM 772T=DSM 14646T).

Sulfurihydrogenibium azorense, sp. nov., a thermophilic hydrogen-oxidizing microaerophile from terrestrial hot springs in the Azores

Five hydrogen-oxidizing, thermophilic, strictly chemolithoautotrophic, microaerophilic strains, with similar (99–100 %) 16S rRNA gene sequences were isolated from terrestrial hot springs at Furnas, São Miguel Island, Azores, Portugal. The strain, designated Az-Fu1T, was characterized. The motile, 0·9–2·0 μm rods were Gram-negative and non-sporulating. The temperature growth range was from 50 to 73 °C (optimum at 68 °C). The strains grew fastest in 0·1 % (w/v) NaCl and at pH 6, although growth was observed from pH 5·5 to 7·0. Az-Fu1Tcan use elemental sulfur, sulfite, thiosulfate, ferrous iron or hydrogen as electron donors, and oxygen (0·2–9·0 %, v/v) as electron acceptor. Az-Fu1Tis also able to grow anaerobically, with elemental sulfur, arsenate and ferric iron as electron acceptors. The Az-Fu1TG+C content was 33·6 mol%. Maximum-likelihood analysis of the 16S rRNA phylogeny placed the isolate in a distinct lineage within theAquificales, closely related toSulfurihydrogenibium subterraneum(2·0 % distant). The 16S rRNA gene of Az-Fu1Tis 7·7 % different from that ofPersephonella marinaand 6·8 % different fromHydrogenothermus marinus. Based on the phenotypic and phylogenetic characteristics presented here, it is proposed that Az-Fu1Tbelongs to the recently described genusSulfurihydrogenibium. It is further proposed that Az-Fu1Trepresents a new species,Sulfurihydrogenibium azorense.

Bacterial artificial chromosome (BAC) library as a tool for physical mapping of the archaeon Methanosarcina thermophila TM-1

We have used a variety of methods to characterize the genome of the archaeon Methanosarcina thermophila TM-1. Pulsed-field gel analysis indicates a genome size of 2.8 Mb. We have constructed a bacterial artificial chromosome (BAC) library of M. thermophila and have used it to generate physical maps for this organism. The library is made up of 384 clones with an average insert size of 58 kb representing 8.0 genome equivalents. The utility of the library for low-resolution physical mapping was shown by identifying NotI linking clones and using these to order the NotI macrorestriction fragments of M. thermophila into a 2.8 Mb map. Hybridization of nine single copy genes and a 16S rRNA sequence to these macrorestriction fragments forms the basis for the first genetic map in this organism. High-resolution physical maps, consisting of overlapping clones, have been created using HindIII fingerprints of BAC clones. In this way, we identified a minimal path of five clones that span a 270 kb NotI fragment. The ease of manipulating BAC clones makes the BAC system an excellent choice for the construction of low-resolution and high-resolution physical and genetic maps of archaeal genomes. It also provides a substrate for future genome-sequencing efforts.

Enhanced biodegradation of aromatic pollutants in cocultures of anaerobic and aerobic bacterial consortia

Toxic aromatic pollutants, concentrated in industrial wastes and contaminated sites, can potentially be eliminated by low cost bioremediation systems. Most commonly, the goal of these treatment systems is directed at providing optimum environmental conditions for the mineralization of the pollutants by naturally occurring microflora. Electrophilic aromatic pollutants with multiple chloro, nitro and azo groups have proven to be persistent to biodegradation by aerobic bacteria. These compounds are readily reduced by anaerobic consortia to lower chlorinated aromatics or aromatic amines but are not mineralized further. The reduction increases the susceptibility of the aromatic molecule for oxygenolytic attack. Sequencing anaerobic and and aerobic biotreatment steps provide enhanced mineralization of many electrophilic aromatic pollutants. The combined activity of anaerobic and aerobic bacteria can also be obtained in a single treatment step if the bacteria are immobilized in particulate matrices (e.g. biofilm, soil aggregate, etc.). Due to the rapid uptake of oxygen by aerobes and facultative bacteria compared to the slow diffusion of oxygen, oxygen penetration into active biofilms seldom exceeds several hundred micrometers. The anaerobic microniches established inside the biofilms can be applied to the reduction of electron withdrawing functional groups in order to prepare recalcitrant aromatic compounds for further mineralization in the aerobic outer layer of the biofilm. Aside from mineralization, polyhydroxylated and chlorinated phenols as well as nitroaromatics and aromatic amines are susceptible to polymerization in aerobic environments. Consequently an alternative approach for bioremediation systems can be directed towards incorporating these aromatic pollutants into detoxified humic-like substances. The activation of aromatic pollutants for polymerization can potentially be encouraged by an anaerobic pretreatment step prior to oxidation. Anaerobic bacteria can modify aromatic pollutants by demethylating methoxy groups and reducing nitro groups. The resulting phenols and aromatic amines are readily polymerized in a subsequent aerobic step.

Biology, ecology, and biotechnological applications of anaerobic bacteria adapted to environmental stresses in temperature, pH, salinity, or substrates

Anaerobic bacteria include diverse species that can grow at environmental extremes of temperature, pH, salinity, substrate toxicity, or available free energy. The first evolved archaebacterial and eubacterial species appear to have been anaerobes adapted to high temperatures. Thermoanaerobes and their stable enzymes have served as model systems for basic and applied studies of microbial cellulose and starch degradation, methanogenesis, ethanologenesis, acetogenesis, autotrophic CO2 fixation, saccharidases, hydrogenases, and alcohol dehydrogenases. Anaerobes, unlike aerobes, appear to have evolved more energy-conserving mechanisms for physiological adaptation to environmental stresses such as novel enzyme activities and stabilities and novel membrane lipid compositions and functions. Anaerobic syntrophs do not have similar aerobic bacterial counterparts. The metabolic end products of syntrophs are potent thermodynamic inhibitors of energy conservation mechanisms, and they require coordinated consumption by a second partner organism for species growth. Anaerobes adapted to environmental stresses and their enzymes have biotechnological applications in organic waste treatment systems and chemical and fuel production systems based on biomass-derived substrates or syngas. These kinds of anaerobes have only recently been examined by biologists, and considerably more study is required before they are fully appreciated by science and technology.

Glycine betaine and potassium ion are the major compatible solutes in the extremely halophilic methanogen Methanohalophilus strain Z7302

Methanohalophilus strain Z7302 was previously isolated from a hypersaline environment and grows over a range of NaCl concentrations from 1.7 to 4.4 M. We examined the relationships between cell growth rate, cell volume, and intracellular solute concentrations with increasing salinity. This extremely halophilic methanogen synthesized three zwitterionic compounds, beta-glutamine, N epsilon-acetyl-beta-lysine, and glycine betaine, and also accumulated potassium ion as compatible solutes to balance the external and internal osmotic pressures. Potassium and glycine betaine were the predominant compatible solutes when Methanohalophilus strain Z7302 was grown at high external NaCl concentrations and approached intracellular levels of 3 and 4 M, respectively.

Distribution of compatible solutes in the halophilic methanogenic archaebacteria

Accumulation of compatible solutes, by uptake or de novo synthesis, enables bacteria to reduce the difference between osmotic potentials of the cell cytoplasm and the extracellular environment. To examine this process in the halophilic and halotolerant methanogenic archaebacteria, 14 strains were tested for the accumulation of compatible solutes in response to growth in various extracellular concentrations of NaCl. In external NaCl concentrations of 0.7 to 3.4 M, the halophilic methanogens accumulated K+ ion and low-molecular-weight organic compounds. beta-Glutamate was detected in two halotolerant strains that grew below 1.5 M NaCl. Two unusual beta-amino acids, N epsilon-acetyl-beta-lysine and beta-glutamine (3-aminoglutaramic acid), as well as L-alpha-glutamate were compatible solutes among all of these strains. De novo synthesis of glycine betaine was also detected in several strains of moderately and extremely halophilic methanogens. The zwitterionic compounds (beta-glutamine, N epsilon-acetyl-beta-lysine, and glycine betaine) and potassium were the predominant compatible solutes among the moderately and extremely halophilic methanogens. This is the first report of beta-glutamine as a compatible solute and de novo biosynthesis of glycine betaine in the methanogenic archaebacteria.

Methanocorpusculaceae fam. nov., represented by Methanocorpusculum parvum, Methanocorpusculum sinense spec. nov. and Methanocorpusculum bavaricum spec. nov

Two new methanogenic bacteria, Methanocorpusculum sinense spec. nov. strain DSM 4274 from a pilot plant for treatment of distillery wastewater in Chengdu (Province Sichuan, China), and Methanocorpusculum bavaricum spec. nov. strain DSM 4179, from a wastewater pond of the sugar factory in Regensburg (Bavaria, FRG) are described. Methanocorpusculum strains are weakly motile and form irregularly coccoid cells, about 1 micron in diameter. The cell envelope consists of a cytoplasmic membrane and a S-layer, composed of hexagonally arranged glycoprotein subunits with molecular weights of 90,000 (Methanocorpusculum parvum), 92,000 (M. sinense), and 94,000 (M. bavaricum). The center-to-center spacings are 14.3 nm, 15.8 nm and 16.0 nm, respectively. Optimal growth of strains is obtained in the mesophilic temperature range and at a pH around 7. Methane is produced from H2/CO2, formate, 2-propanol/CO2 and 2-butanol/CO2 by M. parvum and M. bavaricum, whereas M. sinense can only utilize H2/CO2 and formate. Growth of M. sinense and M. bavaricum is dependent on the presence of clarified rumen fluid. The G + C content of the DNA of the three strains is ranging from 47.7-53.6 mol% as determined by different methods. A similar, but distinct polar lipid pattern indicates a close relationship between the three Methanocorpusculum species. The polyamine patterns of M. parvum, M. sinense and M. bavaricum are similar, but distinct from those of other methanogens and are characterized by a high concentration of the otherwise rare 1,3-diaminopropane. Quantitative comparison of the antigenic fingerprint of members of Methanocorpusculum revealed no antigenic relationship with any one of the reference methanogens tested. On the basis of the distant phylogenetic position of M. parvum and the data presented in this paper a new family, the Methanocorpusculaceae fam. nov., is defined.

Antigenic mosaic of Methanogenium spp.: analysis with poly- and monoclonal antibody probes

Eight well-characterized Methanogenium strains, including the six described type strains, were analyzed with poly- and monoclonal antibody probes to examine the antigenic mosaic of the genus. The pattern of cross-reactions showed that the mosaic is complex and varies with the strains; thus, these organisms have developed a considerable antigenic diversity, which is expressed in their envelopes. Every strain shared at least one determinant with at least one other strain, demonstrating the antigenic cohesiveness of the group. This finding, together with the fact that most strains displayed a distinctive antigenic fingerprint (notwithstanding the limited number of probes available), emphasizes the potential of antibodies for rapid identification of new isolates and for direct elucidation of Methanogenium strains in microbial mixtures.

Effects of Hydrogen Pressure during Growth and Effects of Pregrowth with Hydrogen on Acetate Degradation by Methanosarcina Species

Methanosarcina barkeri 227 and Methanosarcina mazei S-6 grew with acetate as the substrate; we found little effect of H 2 on the rate of aceticlastic growth in the presence of various H 2 pressures between 2 and 810 Pa. We used physical (H 2 addition or flushing the headspace to remove H 2 ) and biological (H 2 -producing or -utilizing bacteria in cocultures) methods for controlling H 2 pressure in Methanosarcina cultures growing on acetate. Added H 2 (ca. 100 Pa) was removed rapidly (a few hours) by M. barkeri and slowly (within a day) by M. mazei . When the H 2 produced by the aceticlastic methanogens was removed by coculturing with an H 2 -using Desulfovibrio sp., the H 2 pressure was about 2.2 Pa. Under these conditions the stoichiometry of aceticlastic methanogenesis did not change. H 2 -grown inocula of M. barkeri grew with acetate as the sole catabolic substrate if the inoculum culture was transferred during logarithmic growth to acetate-containing medium or if the transfer was accomplished within 1 or 2 days after exhaustion of H 2 . H 2 -grown cultures incubated for 4 or more days after exhaustion of H 2 were able to grow with H 2 but not with acetate as the sole catabolic substrate. Addition of small quantities of H 2 to acetate-containing medium permitted these cultures to initiate growth on acetate.

Antigenic mosaic of Methanosarcinaceae: partial characterization of Methanosarcina barkeri 227 surface antigens by monoclonal antibodies

Hybridomas were constructed with spleen cells from mice immunized against Methanosarcina barkeri 227. The reaction with the resulting monoclonal antibodies identified two antigenic determinants. Determinant 8A is present in M. barkeri 227, where it is accessible to antibody on whole bacterial cells. 8A is undetectable in (or absent from) M. barkeri R1M3, an immunologically closely related strain. Determinant 8C is present in both strains, but with M. barkeri 227 it is found only in extracts and cannot be demonstrated in whole cells. It therefore appears to be hidden. A soluble form of antigen 8A (antigen 227) was obtained treating whole M. barkeri 227 cells with absolute methanol. This antigen was further purified by affinity chromatography with antibody 8A. Chemical and immunochemical analyses of these preparations showed that antigen 227 is a high-molecular-weight (4 X 10(5)) structure composed mainly of one carbohydrate, glucose, and small amounts of amino acids. Its solubility properties suggest that this molecule is associated with a lipid moiety.