Methanogen activity and microbial diversity in Gulf of Cádiz mud volcano sediments

The Gulf of Cádiz is a tectonically active continental margin with over sixty mud volcanoes (MV) documented, some associated with active methane (CH4) seepage. However, the role of prokaryotes in influencing this CH4 release is largely unknown. In two expeditions (MSM1-3 and JC10) seven Gulf of Cádiz MVs (Porto, Bonjardim, Carlos Ribeiro, Captain Arutyunov, Darwin, Meknes, and Mercator) were analyzed for microbial diversity, geochemistry, and methanogenic activity, plus substrate amended slurries also measured potential methanogenesis and anaerobic oxidation of methane (AOM). Prokaryotic populations and activities were variable in these MV sediments reflecting the geochemical heterogeneity within and between them. There were also marked differences between many MV and their reference sites. Overall direct cell numbers below the SMTZ (0.2–0.5 mbsf) were much lower than the general global depth distribution and equivalent to cell numbers from below 100 mbsf. Methanogenesis from methyl compounds, especially methylamine, were much higher than the usually dominant substrates H2/CO2 or acetate. Also, CH4 production occurred in 50% of methylated substrate slurries and only methylotrophic CH4 production occurred at all seven MV sites. These slurries were dominated by Methanococcoides methanogens (resulting in pure cultures), and prokaryotes found in other MV sediments. AOM occurred in some slurries, particularly, those from Captain Arutyunov, Mercator and Carlos Ribeiro MVs. Archaeal diversity at MV sites showed the presence of both methanogens and ANME (Methanosarcinales, Methanococcoides, and ANME-1) related sequences, and bacterial diversity was higher than archaeal diversity, dominated by members of the Atribacterota, Chloroflexota, Pseudomonadota, Planctomycetota, Bacillota, and Ca. “Aminicenantes.” Further work is essential to determine the full contribution of Gulf of Cádiz mud volcanoes to the global methane and carbon cycles

Methanogen activity and microbial diversity in Gulf of Cádiz mud volcano sediments

The Gulf of Cádiz is a tectonically active continental margin with over sixty mud volcanoes (MV) documented, some associated with active methane (CH4) seepage. However, the role of prokaryotes in influencing this CH4 release is largely unknown. In two expeditions (MSM1-3 and JC10) seven Gulf of Cádiz MVs (Porto, Bonjardim, Carlos Ribeiro, Captain Arutyunov, Darwin, Meknes, and Mercator) were analyzed for microbial diversity, geochemistry, and methanogenic activity, plus substrate amended slurries also measured potential methanogenesis and anaerobic oxidation of methane (AOM). Prokaryotic populations and activities were variable in these MV sediments reflecting the geochemical heterogeneity within and between them. There were also marked differences between many MV and their reference sites. Overall direct cell numbers below the SMTZ (0.2–0.5 mbsf) were much lower than the general global depth distribution and equivalent to cell numbers from below 100 mbsf. Methanogenesis from methyl compounds, especially methylamine, were much higher than the usually dominant substrates H2/CO2 or acetate. Also, CH4 production occurred in 50% of methylated substrate slurries and only methylotrophic CH4 production occurred at all seven MV sites. These slurries were dominated by Methanococcoides methanogens (resulting in pure cultures), and prokaryotes found in other MV sediments. AOM occurred in some slurries, particularly, those from Captain Arutyunov, Mercator and Carlos Ribeiro MVs. Archaeal diversity at MV sites showed the presence of both methanogens and ANME (Methanosarcinales, Methanococcoides, and ANME-1) related sequences, and bacterial diversity was higher than archaeal diversity, dominated by members of the Atribacterota, Chloroflexota, Pseudomonadota, Planctomycetota, Bacillota, and Ca. “Aminicenantes.” Further work is essential to determine the full contribution of Gulf of Cádiz mud volcanoes to the global methane and carbon cycles

Subsurface microbiology and biogeochemistry of a deep, cold-water carbonate mound from the Porcupine Seabight (IODP Expedition 307)

The Porcupine Seabight Challenger Mound is the first carbonate mound to be drilled (∼270 m) and analyzed in detail microbiologically and biogeochemically. Two mound sites and a non-mound Reference site were analyzed with a range of molecular techniques [catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH), quantitative PCR (16S rRNA and functional genes, dsrA and mcrA), and 16S rRNA gene PCR-DGGE] to assess prokaryotic diversity, and this was compared with the distribution of total and culturable cell counts, radiotracer activity measurements and geochemistry. There was a significant and active prokaryotic community both within and beneath the carbonate mound. Although total cell numbers at certain depths were lower than the global average for other subseafloor sediments and prokaryotic activities were relatively low (iron and sulfate reduction, acetate oxidation, methanogenesis) they were significantly enhanced compared with the Reference site. In addition, there was some stimulation of prokaryotic activity in the deepest sediments (Miocene, > 10 Ma) including potential for anaerobic oxidation of methane activity below the mound base. Both Bacteria and Archaea were present, with neither dominant, and these were related to sequences commonly found in other subseafloor sediments. With an estimate of some 1600 mounds in the Porcupine Basin alone, carbonate mounds may represent a significant prokaryotic subseafloor habitat

Fluviicola taffensis gen. nov., sp. nov., a novel freshwater bacterium of the family Cryomorphaceae in the phylum 'Bacteroidetes'

A novel, strictly aerobic, Gram-negative, yellow–orange-pigmented, motile, catalase-positive, oxidase-negative bacterium, RW262T, was isolated from water of the River Taff, Cardiff, UK, during January 2000. Phylogenetic analysis of the 16S rRNA gene indicated that strain RW262T was a member of the family Cryomorphaceae within the phylum ‘Bacteroidetes’. The DNA G+C content of strain RW262T was 37·2 mol%. The predominant fatty acid was the branched-chain saturated fatty acid i15 : 0 (44·2 %). On the basis of polyphasic analysis of phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, it is proposed that this freshwater bacterium represents a novel genus and species within the family Cryomorphaceae, Fluviicola taffensis gen. nov., sp. nov. The type strain is RW262T (=NCIMB 13979T=DSM 16823T)

Culturable phylogenetic diversity of the phylum 'Bacteroidetes' from river epilithon and coastal water and description of novel members of the family Flavobacteriaceae: Epilithonimonas tenax gen. nov., sp. nov. and Persicivirga xylanidelens gen. nov., sp. nov

Members of the phylum ‘Bacteroidetes’ are important heterotrophs involved in cycling organic carbon in aquatic habitats. Their diversity has been studied by molecular methods in both freshwater and marine habitats and many novel genera and species within this phylum have been characterized in recent years. In this study, we examined the diversity of members of the ‘Bacteroidetes’ that could be readily isolated on solid media from river epilithon and coastal sea water. Most (93 %) of the 55 isolates confirmed as members of the ‘Bacteroidetes’ and examined by phylogenetic analysis of 16S rRNA gene sequences belonged to the Flavobacteriaceae. Furthermore, most (62 %) of these were almost certainly members of the genus Flavobacterium and all but one were from river epilithon. Conversely, the sea-water isolates were more widely distributed in clades containing other genera. Some of the isolates were deep-branching within phylogenetic trees and so could not be assigned to putative genera. Two of these deep-branching isolates were characterized by polyphasic taxonomy and are proposed as novel species within two new genera of the family Flavobacteriaceae. These are Epilithonimonas tenax gen. nov., sp. nov. (type strain EP105T=NCIMB 14026T=DSM 16811T) and Persicivirga xylanidelens gen. nov., sp. nov. (type strain SW256T=NCIMB 14027T=DSM 16809T)

Prokaryotic functional diversity in di¡erent biogeochemical depth zones in tidal sediments of the SevernEstuary,UK, revealed by stable-isotope probing

International audienceStable isotope probing of prokaryotic DNA was used to determine activeprokaryotes using 13C-labelled substrates (glucose, acetate, CO2) in sedimentslurries from different biogeochemical zones of the Severn Estuary, UK. Multiple,low concentrations (5100 mM) of 13C-substrate additions and short-termincubations (7 days) were used to minimize changes in the prokaryotic community,while achieving significant 13C-incorporation. Analysis demonstrated clearmetabolic activity within all slurries, although neither the net sulphate removal norCH4 production occurred in the anaerobic sulphate reduction and methanogenesiszone slurries. Some similarities occurred in the prokaryotic populations thatdeveloped in different sediment slurries, particularly in the aerobic and dysaerobiczone slurries with 13C-glucose, which were dominated by Gammaproteobacteriaand Marine Group 1 Archaea, whereas both anaerobic sediment slurries incubatedwith 13C-acetate showed incorporation into Epsilonproteobacteria and otherbacteria, with the sulphate reduction zone slurry also showing 13C-acetateutilization by Miscellaneous Crenarchaeotic Group Archaea. The lower potentialenergy methanogenesis zone slurries were the only conditions where no 13Cincorporationinto Archaea occurred, despite Bacteria being labelled; this wassurprising because Archaea have been suggested to be adapted to low-energyconditions. Overall, our results highlight that uncultured prokaryotes playimportant ecological roles in tidal sediments of the Severn Estuary, providingnew metabolic information for novel groups of Archaea and suggesting broadermetabolisms for largely uncultivated Bacteria

Microbial activities along a 20 million-year-old pristine oil reservoir

Studies on oil reservoir microbiology typically take samples from producing reservoirs and sample fluids that have been pumped to the surface. This comes with problems since producing oil reservoirs are affected by production processes leading to changes in environmental conditions and the natural microbiome. Hence, pumped samples do not display an unaltered picture of the spatial distribution and composition of the microorganisms in the reservoir.We took 13 samples from a freshly drilled sediment core of a pristine, heavily biodegraded oil reservoir in the North Sea. Core samples originated from above, within, and below the reservoir.16S rRNA gene amplicon sequencing of the microbiome revealed distinct differences between sediments and formation water, indicating that studies on microbiomes from formation water alone are not necessarily representative for the microbial processes in an oil reservoir. Fluorescence microscopy showed that microorganisms live in small microcolonies on the sediment surface. CT-scanning with image analysis visualized the water phase distribution inside the reservoir sediments and clearly indicated water-filled voids that might be habitable for microorganisms, enlarging the surface for potential biodegradation. Employing microcosm experiments and reverse isotope labelling, we were able to determine the first degradation rates measured from cores above, within, and below a reservoir ranging from no activity up to 1 mM CO2/(gsediment x year), Results indicate significant degradation potential from autochthonous microorganisms in the reservoir above the water-contact-zone.Evading the general issues of produced oil samples for studying microbiomes results in a more realistic picture of an oil reservoir unaffected by production artefacts

Prokaryotic populations and activities in an interbedded coal deposit, including a previously deeply buried section (1.6–2.3 km) above ∼ 150 Ma basement rock

A largely terrestrial, lignite/coal-bearing, 148 m core from the Waikato Basin, New Zealand, was studied, with a multidisciplinary approach, for subsurface microbiology. The top ≈76 m was Latest Miocene-Late Pleistocene (≈0.4–5.5 Ma) sediments, which overlay an unconformity and a previously deeply buried (1,600–2,300 m, × 55–75°C) ≈69 m section of moderately indurated, Late Eocene-Early Oligocene (≈32–35 Ma) deposits. Below this is weathered, Late Jurassic metasedimentary basement rock (145.5–157.0 Ma). Similar cell numbers (mean 1.2 × 106 cm −3 ), high viability (4–32%), intact phospholipids (biomarkers for living Bacteria) and activity (sulphate reduction, DNA replication) occurred heterogeneously throughout the core, including the weathered basement rock. Substantial numbers of viable anaerobic heterotrophic and lignite-utilizing bacteria (means 3.4 × 10 4 , 3.0 × 10 3 cm −3 ) were present throughout the core. This is similar to some deep terrestrial formations but contrasts with the generally exponentially decreasing prokaryotic populations in sub-seafloor sediments. For Bacteria, ≈76% of the 16S rRNA gene phylotypes were similar above (31.98 m) and below (133.55 m) the 76 m unconformity, which together with similar cell numbers indicates limited deep burial impact/palaeosterilization, or effective re-colonisation. Archaeal populations were not dominant being only detected with general primers at 31.98 m and those detected with methanogen functional primers were different above and below the ≈76 m unconformity. Both dominant bacterial (Proteobacteria, Actinobacteria, Firmicutes, Chloroflexi) and archaeal (Miscellaneous Crenarchaeotic Group, Methanosarcinales and Methanobacteriales) sequences were similar to those previously detected in both marine and terrestrial subsurface environments, reflecting the changing depositional conditions of the formation. However, the presence of ANME sequences had not been previously found in the terrestrial subsurface. A large proportion of the bacterial 16S rDNA diversity was cultured (43% of commonest genera). Prokaryotic populations and activity changed with lithology and depth and substrates (formate, acetate, oxalate) may diffuse from high-carbon, lignite/coaly layers to support bacterial populations in adjacent sandy or clay-silt layers