Estimates of biogenic methane production rates in deep marine sediments at Hydrate Ridge, Cascadia margin

Methane hydrate found in marine sediments is thought to contain gigaton quantities of methane and is considered an important potential fuel source and climate-forcing agent. Much of the methane in hydrates is biogenic, so models that predict the presence and distribution of hydrates require accurate rates of in situ methanogenesis. We estimated the in situ methanogenesis rates in Hydrate Ridge (HR) sediments by coupling experimentally derived minimal rates of methanogenesis to methanogen biomass determinations for discrete locations in the sediment column. When starved in a biomass recycle reactor, Methanoculleus submarinus produced ca. 0.017 fmol methane/cell/day. Quantitative PCR (QPCR) directed at the methyl coenzyme M reductase subunit A gene (mcrA) indicated that 75% of the HR sediments analyzed contained <1,000 methanogens/g. The highest numbers of methanogens were found mostly from sediments <10 m below seafloor. By considering methanogenesis rates for starved methanogens (adjusted to account for in situ temperatures) and the numbers of methanogens at selected depths, we derived an upper estimate of <4.25 fmol methane produced/g sediment/day for the samples with fewer methanogens than the QPCR method could detect. The actual rates could vary depending on the real number of methanogens and various seafloor parameters that influence microbial activity. However, our calculated rate is lower than rates previously reported for such sediments and close to the rate derived using geochemical modeling of the sediments. These data will help to improve models that predict microbial gas generation in marine sediments and determine the potential influence of this source of methane on the global carbon cycle.     

Diversity of dimethylsulfide-degrading methanogens and sulfate-reducing bacteria in anoxic sediments along the Medway Estuary,UK

Methane is a powerful greenhouse gas but the microbial diversity mediating methylotrophic methanogenesis is not well-characterized. One overlooked route to methane is via the degradation of dimethylsulfide (DMS), an abundant organosulfur compound in the environment. Methanogens and sulfate-reducing bacteria (SRB) can degrade DMS in anoxic sediments depending on sulfate availability. However, we know little about the underlying microbial community and how sulfate availability affects DMS degradation in anoxic sediments. We studied DMS-dependent methane production along the salinity gradient of the Medway Estuary (UK) and characterized, for the first time, the DMS-degrading methanogens and SRB using cultivation-independent tools. DMS metabolism resulted in high methane yield (39%–42% of the theoretical methane yield) in anoxic sediments regardless of their sulfate content. Methanomethylovorans, Methanolobus and Methanococcoides were dominant methanogens in freshwater, brackish and marine incubations respectively, suggesting niche-partitioning of the methanogens likely driven by DMS amendment and sulfate concentrations. Adding DMS also led to significant changes in SRB composition and abundance in the sediments. Increases in the abundance of Sulfurimonas and SRB suggest cryptic sulfur cycling coupled to DMS degradation. Our study highlights a potentially important pathway to methane production in sediments with contrasting sulfate content and sheds light on the diversity of DMS degraders.     

Microbial diversity and community structure of a highly active anaerobic methane‐oxidizing sulfate‐reducing enrichment

Anaerobic oxidation of methane (AOM) is an important methane sink in the ocean but the microbes responsible for AOM are as yet resilient to cultivation. Here we describe the microbial analysis of an enrichment obtained in a novel submerged‐membrane bioreactor system and capable of high‐rate AOM (286 μmol g_{dry weight}^?1 day^?1) coupled to sulfate reduction. By constructing a clone library with subsequent sequencing and fluorescent in situ hybridization, we showed that the responsible methanotrophs belong to the ANME‐2a subgroup of anaerobic methanotrophic archaea, and that sulfate reduction is most likely performed by sulfate‐reducing bacteria commonly found in association with other ANME‐related archaea in marine sediments. Another relevant portion of the bacterial sequences can be clustered within the order of Flavobacteriales but their role remains to be elucidated. Fluorescent in situ hybridization analyses showed that the ANME‐2a cells occur as single cells without close contact to the bacterial syntrophic partner. Incubation with ¹³C‐labelled methane showed substantial incorporation of ¹³C label in the bacterial C₁₆ fatty acids (bacterial; 20%, 44% and 49%) and in archaeal lipids, archaeol and hydroxyl‐archaeol (21% and 20% respectively). The obtained data confirm that both archaea and bacteria are responsible for the anaerobic methane oxidation in a bioreactor enrichment inoculated with Eckernförde bay sediment.     

Microbial methane cycling in sediments of Arctic thermokarst lagoons

Thermokarst lagoons represent the transition state from a freshwater lacustrine to a marine environment, and receive little attention regarding their role for greenhouse gas production and release in Arctic permafrost landscapes. We studied the fate of methane (CH₄) in sediments of a thermokarst lagoon in comparison to two thermokarst lakes on the Bykovsky Peninsula in northeastern Siberia through the analysis of sediment CH₄ concentrations and isotopic signature, methane-cycling microbial taxa, sediment geochemistry, lipid biomarkers, and network analysis. We assessed how differences in geochemistry between thermokarst lakes and thermokarst lagoons, caused by the infiltration of sulfate-rich marine water, altered the microbial methane-cycling community. Anaerobic sulfate-reducing ANME-2a/2b methanotrophs dominated the sulfate-rich sediments of the lagoon despite its known seasonal alternation between brackish and freshwater inflow and low sulfate concentrations compared to the usual marine ANME habitat. Non-competitive methylotrophic methanogens dominated the methanogenic community of the lakes and the lagoon, independent of differences in porewater chemistry and depth. This potentially contributed to the high CH₄ concentrations observed in all sulfate-poor sediments. CH₄ concentrations in the freshwater-influenced sediments averaged 1.34 ± 0.98 μmol g⁻¹, with highly depleted δ¹³C-CH₄ values ranging from −89‰ to −70‰. In contrast, the sulfate-affected upper 300 cm of the lagoon exhibited low average CH₄ concentrations of 0.011 ± 0.005 μmol g⁻¹ with comparatively enriched δ¹³C-CH₄ values of −54‰ to −37‰ pointing to substantial methane oxidation. Our study shows that lagoon formation specifically supports methane oxidizers and methane oxidation through changes in pore water chemistry, especially sulfate, while methanogens are similar to lake conditions.     

Detection Methanogens in Newly Settled Sediments from Xuanwu Lake in Nanjing, China

Sediments from Xuanwu Lake have been dredged in the past 3 years to improve the water quality, but methanogenesis should still exist in the newly settled sediment. Methane production, methanogens, and physiochemical parameters were detected in the surface sediments (0–5 cm) and/or vertical sediments (0–21 cm, segmented at interval of 3 cm). Methane flux at water–air interface varied among five detected sites. Principal component analysis showed that CH₄ flux, content of water and the concentration of total nitrogen (TN), CH₄ and organic matters (OM) weighed most heavily on the component I in surface sediments while different patterns were observed for vertical sediments. The copy number of the 16S rRNA gene for bacteria was lower in the surface sediment (0–6 cm) than that in deeper sediments (12–21 cm), while 16S rRNA genes of Archaea were almost evenly distributed in the vertical sediments. Representatives belonging to the orders Methanobacteriales, Methanomicrobiales, and Methanosarcinales were detected in all samples of the vertical sediments, except that no members of the Methanococcales were detected in the samples at 0–6 cm. The level of Methanobacteriales reached a highest density at 18.1 × 10⁴ copies g⁻¹ dry weight (dw) at 6–9 cm; for Methanosarcinales (76.89 × 10⁶ copies g⁻¹ dw) and Methanococcales (82.70 × 10³ copies g⁻¹ dw) at 12–15 cm, whereas for Methanomicrobiales (43.37 × 10⁶ copies g⁻¹ dw) at 9–12 cm. Methanosarcinaceae and Methanosaetaceae reached to their highest densities at 6–9 and 9–12 cm, respectively. These data provided useful information for better understanding the methanogenesis in the newly settled sediments of a recently dredged lake.     

Inhibitory effects of 2-bromoethanesulfonate and protection by addition of coenzyme M in hydrogen-oxidizing marine enrichment cultures

Abstract Since bromoethanesulfonate (BES) is an inhibitor of methane production (competitive with methyl-coenzyme M), cells able to accumulate large internal pools of methyl-coenzyme M via uptake of its precursor, HS-CoM, should be protected from BES by addition of HS-CoM to the growth medium. Hydrogen-oxidizing marine methanogen enrichments were prepared from anaerobic sediment samples collected at Sippewisset Salt Marsh and Oyster Bay Inlet near Woods Hole, MA. The three enrichments studied were a mixture of cell types with at least 50% of the culture comprised of methanogens. Methane production was found to be sensitive to BES with half maximal inhibition occurring at 5–20 μM BES depending on the enrichment. For each, half maximal protection against 40 μM BES occurred at a HS-CoM: BES molar ratio of 20: 1 to 40: 1. Since the protected enrichments exhibited normal sensitivity toward BES after removal of HS-CoM, it was concluded that methane production in the presence of both BES and HS-CoM resulted from true protection and not growth of BES-resistant mutants. These results suggest that uptake of HS-CoM may be a general property of methanogens occupying anaerobic marine sediments. It is possible that uptake of this coenzyme is an important nutritional feature of methanogens in their natural habitat.     

Methane formation and release in a small Wisconsin lake

Abstract

Tharae rate of methane released from the sediment‐water interface and from the surface of the water of Lake Wingra, Madison, Wisconsin, was measured during the summer months for 2 years. The amount of methane escaping the lake is estimated to be an important factor in the carbon budget of the lake. Most rapid methanogenesis was in shallow water (less than 1 m deep) and in the uppermost 5 cm of sediment. The numbers of methanogenic bacteria were estimated by a most probable number technique to vary from approximately 10² to 3 × 10⁴ methanogens per gram of dry weight sediment during winter and summer, respectively.     

Relationship between δ13C of chironomid remains and methane flux in Swedish lakes

1. Methanogenic carbon can be incorporated by methane‐oxidising bacteria, leading to a ¹³C‐depleted stable carbon isotopic composition (δ¹³C) of chironomids that feed on these microorganisms. This has been shown for the chironomid tribe Chironomini, but very little information is available about the δ¹³C of other abundant chironomid groups and the relationship between chironomid δ¹³C and methane production in lakes. 2. Methane flux was measured at the water surface of seven lakes in Sweden. Furthermore, fluxes from the sediments to the water column were measured in transects in two of the lakes. Methane fluxes were then compared with δ¹³C of chitinous chironomid remains isolated from the lake surface sediments. Several different chironomid groups were examined (Chironomini, Orthocladiinae, Tanypodinae and Tanytarsini). 3. Remains of Orthocladiinae in the seven study lakes had the highest δ¹³C values (?31.3 to ?27.0‰), most likely reflecting δ¹³C of algae and other plant‐derived organic matter. Remains of Chironomini and Tanypodinae had lower δ¹³C values (?33.2 to ?27.6‰ and ?33.6 to ?28.0‰, respectively). A significant negative correlation was observed between methane fluxes at the lake surface and δ¹³C of Chironomini (r = ?0.90, P = 0.006). Methane release from the sediments was also negatively correlated with δ¹³C of Chironomini (r = ?0.67, P = 0.025) in the transect samples obtained from two of the lakes. The remains of other chironomid taxa were only weakly or not correlated with methane fluxes measured in our study lakes (P > 0.05). 4. Selective incorporation of methane‐derived carbon can explain the observed correlations between methane fluxes and δ¹³C values of Chironomini. Remains of this group might therefore have the potential to provide information about past changes in methane availability in lakes using sediment records. However, differences in productivity, algal δ¹³C composition and the importance of allochthonous organic matter input between the studied lakes may also have influenced Chironomini δ¹³C. More detailed studies with a higher number of analysed samples and detailed measurement of δ¹³C of different ecosystem components (e.g. methane, dissolved inorganic carbon) will be necessary to further resolve the relative contribution of different carbon sources to δ¹³C of chironomid remains.     

Stratified Communities of Methanogens in the Jiulong River Estuarine Sediments, Southern China

Methane is a potent greenhouse gas and produced mainly by methanogens. Few studies have specifically dealt so far with methanogens in estuarine environments. In this study, diversity and distribution of methanogens were investigated by clone library and T-RFLP analysis in a Jiulong River estuarine sediment core which contained clear sulfate–methane-transition zone. The majority of obtained sequences in clone libraries and T-RF peaks from T-RFLP analysis were assigned mainly to Methanosaeta, Methanomicrobiales and Methanosarcinales/ANME. The fragments of Methanosarcinales/ANME were most dominant group (mean 51 %) and composed largely of ANME-2a. In addition, Methanosaeta and Methanomicrobiales accounted for 21 and 28 % of all fragments. Therefore, the presence of Methanomicrobiales, Methanosaeta and ANME-2a was indicative of acetoclastic methanogenesis, hydrogenotrophic methanogenesis, and anaerobic methane oxidation in Jiulong River estuarine sediments. This study provided the important knowledge towards understanding methane cycling association of representative of methanogens involved in estuarine environments.     

Methanogenic activity and diversity in the centre of the Amsterdam Mud Volcano, Eastern Mediterranean Sea

Marine mud volcanoes are geological structures emitting large amounts of methane from their active centres. The Amsterdam mud volcano (AMV), located in the Anaximander Mountains south of Turkey, is characterized by intense active methane seepage produced in part by methanogens. To date, information about the diversity or the metabolic pathways used by the methanogens in active centres of marine mud volcanoes is limited. (14)C-radiotracer measurements showed that methylamines/methanol, H(2)/CO(2) and acetate were used for methanogenesis in the AMV. Methylotrophic methanogenesis was measured all along the sediment core, Methanosarcinales affiliated sequences were detected using archaeal 16S PCR-DGGE and mcrA gene libraries, and enrichments of methanogens showed the presence of Methanococcoides in the shallow sediment layers. Overall acetoclastic methanogenesis was higher than hydrogenotrophic methanogenesis, which is unusual for cold seep sediments. Interestingly, acetate porewater concentrations were extremely high in the AMV sediments. This might be the result of organic matter cracking in deeper hotter sediment layers. Methane was also produced from hexadecanes. For the most part, the methanogenic community diversity was in accordance with the depth distribution of the H(2)/CO(2) and acetate methanogenesis. These results demonstrate the importance of methanogenic communities in the centres of marine mud volcanoes.     

Methyl-compounds driven benthic carbon cycling in the sulfate-reducing sediments of South China Sea

Methane is a potent greenhouse gas; methane production and consumption within seafloor sediments has generated intense interest. Anaerobic oxidation of methane (AOM) and methanogenesis (MOG) primarily occur at the depth of the sulfate–methane transition zone or underlying sediment respectively. Methanogenesis can also occur in the sulfate-reducing sediments through the utilization of non-competitive methylated compounds; however, the occurrence and importance of this process are not fully understood. Here, we combined a variety of data, including geochemical measurements, rate measurements and molecular analyses to demonstrate the presence of a cryptic methane cycle in sulfate-reducing sediments from the continental shelf of the northern South China Sea. The abundance of methanogenic substrates as well as the high MOG rates from methylated compounds indicated that methylotrophic methanogenesis was the dominant methanogenic pathway; this conclusion was further supported by the presence of the methylotrophic genus Methanococcoides. High potential rates of AOM were observed in the sediments, indicating that methane produced in situ could be oxidized simultaneously by AOM, presumably by ANME-2a/b as indicated by 16S rRNA gene analysis. A significant correlation between the relative abundance of methanogens and methanotrophs was observed over sediment depth, indicating that methylotrophic methanogenesis could potentially fuel AOM in this environment. In addition, higher potential rates of AOM than sulfate reduction rates at in situ methane conditions were observed, making alternative electron acceptors important to support AOM in sulfate-reducing sediment. AOM rates were stimulated by the addition of Fe/Mn oxides, suggesting AOM could be partially coupled to metal oxide reduction. These results suggest that methyl-compounds driven methane production drives a cryptic methane cycling and fuels AOM coupled to the reduction of sulfate and other electron acceptors.     

Carbon isotopic heterogeneity of coenzyme F430 and membrane lipids in methane‐oxidizing archaea

Archaeal ANaerobic MEthanotrophs (ANME) facilitate the anaerobic oxidation of methane (AOM), a process that is believed to proceed via the reversal of the methanogenesis pathway. Carbon isotopic composition studies indicate that ANME are metabolically diverse and able to assimilate metabolites including methane, methanol, acetate, and dissolved inorganic carbon (DIC). Our data support the interpretation that ANME in marine sediments at methane seeps assimilate both methane and DIC, and the carbon isotopic compositions of the tetrapyrrole coenzyme F430 and the membrane lipids archaeol and hydroxy‐archaeol reflect their relative proportions of carbon from these substrates. Methane is assimilated via the methyl group of CH₃‐tetrahydromethanopterin (H₄MPT) and DIC from carboxylation reactions that incorporate free intracellular DIC. F430 was enriched in ¹³C (mean δ¹³C = ?27‰ for Hydrate Ridge and ?80‰ for the Santa Monica Basin) compared to the archaeal lipids (mean δ¹³C = ?97‰ for Hydrate Ridge and ?122‰ for the Santa Monica Basin). We propose that depending on the side of the tricarboxylic acid (TCA) cycle used to synthesize F430, its carbon was derived from 76% DIC and 24% methane via the reductive side or 57% DIC and 43% methane via the oxidative side. ANME lipids are predicted to contain 42% DIC and 58% methane, reflecting the amount of each assimilated into acetyl‐CoA. With isotope models that include variable fractionation during biosynthesis for different carbon substrates, we show the estimated amounts of DIC and methane can result in carbon isotopic compositions of ? 73‰ to ? 77‰ for F430 and ? 105‰ for archaeal lipids, values close to those for Santa Monica Basin. The F430 δ¹³C value for Hydrate Ridge was ¹³C‐enriched compared with the modeled value, suggesting there is divergence from the predicted two carbon source models.     

Sediment Distribution of Methanogenic Bacteria in Lake Erie and Cleveland Harbor

The direct fluorescent-antibody technique was employed to determine the distribution patterns of four species of methanogens in the sediments of Lake Erie and Cleveland Harbor. Methanobacterium ruminantium was the most numerous methanogen found in regions of high-organic-silt sediments. The population of this species ranged from 10⁶ to 10⁹ cells/g of dry sediment. Methanobacterium strain MoH and Methanosarcina barkeri were identified in sand-silt, clay, or sand sediments. These methanogens ranged in density from 10⁶ to 10⁷ cells/g of dry sediment. Methanospirillum hungatii was observed only after an organic enrichment was performed on Cleveland Harbor sediments. The seasonal and selective sediment distribution of these methanogens appears to be related to the type and concentration of carbon as substrate as well as to the activities of heterotrophic and sulfate-reducing bacteria.     

Enrichment of syngas‐converting communities from a multi‐orifice baffled bioreactor

The substitution of natural gas by renewable biomethane is an interesting option to reduce global carbon footprint. Syngas fermentation has potential in this context, as a diverse range of low‐biodegradable materials that can be used. In this study, anaerobic sludge acclimatized to syngas in a multi‐orifice baffled bioreactor (MOBB) was used to start enrichments with CO. The main goals were to identify the key players in CO conversion and evaluate potential interspecies metabolic interactions conferring robustness to the process. Anaerobic sludge incubated with 0.7 × 10⁵ Pa CO produced methane and acetate. When the antibiotics vancomycin and/or erythromycin were added, no methane was produced, indicating that direct methanogenesis from CO did not occur. Acetobacterium and Sporomusa were the predominant bacterial species in CO‐converting enrichments, together with methanogens from the genera Methanobacterium and Methanospirillum. Subsequently, a highly enriched culture mainly composed of a Sporomusa sp. was obtained that could convert up to 1.7 × 10⁵ Pa CO to hydrogen and acetate. These results attest the role of Sporomusa species in the enrichment as primary CO utilizers and show their importance for methane production as conveyers of hydrogen to methanogens present in the culture.     

Biogeochemistry of billabong sediments. II. Seasonal variations in methane production

1. We examined the temporal (seasonal and diel) and spatial variation in methane flux from sediments of a billabong in south-eastern Australia, and related it to variations in the rate of organic matter decay, concentration of interstitial metabolites, and sediment redox. 2. Total gas ebullition ranged from <2 to >59mlm^?2h^?1, and was highest in the summer months when water temperatures were >25°C. These rates are equivalent to carbon fluxes of about 16–30gC—CH₄m^?2yr^?1. Ebullition was greater from unvegetated sediments than from sediments colonized by the emergent macrophyte Eleockaris sphacelata, R, Br. or the submerged macrophyte Vallisneria gigantea Graeb. There were no consistent differences in the rate of ebullition over the day and the night. 3. Methane accounted for about 42–45% of total sediment gas in the vegetated sediments, but about 60% in the unvegetated sediments. These ratios did not vary greatly throughout the year. Carbon dioxide was a minor component of sediment gas, usually comprising <5% of the total. Carbon dioxide contents were highest in summer, especially in unvegetated and E. sphacelata beds. 4. In vitro methanogenesis ranged from 3 ± 0.9 to 106 ± 30 nmol g(dry weight)^?1 h^?1, being highest in summer and lowest in winter. Added acetate (5mM) increased the rate of methanogenesis by up to 10-fold, with the effect being greater in summer than winter. Generally, added acetate had least effect in E. sphacelata sediments. The maximum rate of in vitro methanogenesis with added acetate was 243 ± 57 nmolg(dry weight)^?1 h^?1. 5. Ebullition was highly correlated with the rate of in vitro methanogenesis, with a rime lag of about 4 weeks. About 35–60% of benthic in vitro methanogenesis could be accounted for by ebullitive loss: the remainder was presumably lost via diffusion, flux through emergent plants or by oxidation. The rate of organic-matter degradation, assessed with amylopectin azure, varied throughout the year, but there was no clear relationship between ebullition and organic-matter decay. 6. Concentrations of interstitial ammonium, which also varied seasonally, ranged from 1 ± 0.2 to 13 ± 1 mgNl^?1. There was no clear relationship between ebullition rates and ammonium concentrations, Redox potential was most positive in the E. sphacelata sediments, but there was little consistent difference in the redox potential of V. gigantea and unvegetated sediments. Redox potential appeared not to be a controlling factor in methane release.     

Major substrates for microbial sulfate reduction in the sediments of Ise Bay, Japan

To clarify the anaerobic microbial interactions in the process of carbon mineralization in marine eutrophic environments, the microbial sulfate reduction and methane production rates were examined in coastal marine sediments of Ise Bay, Japan, in autumn 1990. Sulfate reduction rates (51–210 nmol ml⁻¹ day⁻¹ at 24°C) were much higher than the methane production ones (<1.78 nmol ml⁻¹ day⁻¹) in the surface sediments (top 2 cm) at the six stations surveyed (water depth: 10.7–23.3 m). Substrates for sulfate-reducing bacteria (SRB) were estimated after the addition of a specific inhibitor for SRB (20 mmol l⁻¹ molybdate) into the sediment slurry, from the substrate accumulation rates. In the presence of the inhibitor, sulfate reduction was completely stopped and volatile fatty acids (mainly acetate) were accumulated, although hydrogen was not. Methane production occurred markedly accompanied by consumption of the accumulated acetate from the third day after the addition of molybdate. The maximum rate of methane production was 1.2–1.9 μmol ml⁻¹ day⁻¹, which was similar to those in highly polluted freshwater sediments such as the Tama River, Tokyo, Japan. These results show that acetate is a common major substrate for sulfate reduction and methane production, and SRB competitively inhibit potential acetoclastic methanogenesis in coastal sediments. Methanogens may potentially inhabit the sediments at low levels of population density and activity.     

Effect of biostimulation on the microbial community in PCB-contaminated sediments through periodic amendment of sediment with iron

Reductive dehalogenation of polychlorinated biphenyls (PCBs) by indigenous dehalorespiring microorganisms in contaminated sediments may be enhanced via biostimulation by supplying hydrogen generated through the anaerobic corrosion of elemental iron added to the sediment. In this study, the effect of periodic amendment of sediment with various dosages of iron on the microbial community present in sediment was investigated using phospholipid fatty acid analysis (PLFA) over a period of 18 months. Three PCB-contaminated sediments (two freshwater lake sediments and one marine sediment) were used. Signature biomarker analysis of the microbial community present in all three sediments revealed the enrichment of Dehalococcoides species, the population of which was sustained for a longer period of time when the sediment microcosms were amended with the lower dosage of iron (0.01 g iron per g dry sediment) every 6 months as compared to the blank system (without iron). Lower microbial stress levels were reported for the system periodically amended with 0.01 g of iron per g dry sediment every 6 months, thus reducing the competition from other hydrogen-utilizing microorganisms like methanogens, iron reducers, and sulfate reducers. The concentration of hydrogen in the system was found to be an important factor influencing the shift in microbial communities in all sediments with time. Periodic amendment of sediment with larger dosages of iron every 3 months resulted in the early prevalence of Geobacteraceae and sulfate-reducing bacteria followed by methanogens. An average pH of 8.4 (range of 8.2–8.6) and an average hydrogen concentration of 0.75% (range of 0.3–1.2%) observed between 6 and 15 months of the study were found to be conducive to sustaining the population of Dehalococcoides species in the three sediments amended with 0.01 g iron per g dry sediment. Biostimulation of indigenous PCB dechlorinators by the periodic amendment of contaminated sediments with low dosages of iron metal may therefore be an effective technology for remediation of PCB-contaminated sediments.     

Methyl Coenzyme M Reductase A (mcrA) Gene-Based Investigation of Methanogens in the Mudflat Sediments of Yangtze River Estuary, China

Methanogen populations of an intertidal mudflat in the Yangtze River estuary of China were investigated based on the methyl coenzyme M reductase A (mcrA) gene using 454-pyrosequencing and quantitative real-time polymerase chain reaction (qPCR). Samples were collected at six depths from three locations. In the qPCR analyses, a mean depth-wise change of mcrA gene abundance was observed from (1.23?±?0.13)×10⁷ to (1.16?±?0.29)×10⁸ per g dried soil, which was inversely correlated with the depletion of sulfate (R ²?=0.74; α?=?0.05) and salinity (R ²?=?0.66; α?=?0.05). The copy numbers of mcrA was at least 1 order of magnitude higher than dissimilatory sulfate reductase B (dsrB) genes, likely indicating the importance of methanogenesis at the mudflat. Sequences related to the orders Methanomicrobiales, Methanosarcinales, Methanobacteriales, Methanococcales and the uncultured methanogens; Rice Cluster I (RC-I), Zoige cluster I (ZC-I) and anaerobic methane oxidizing archaeal lineage-1 (ANME-1) were detected. Methanomicrobiales and Methanosarcinales dominated the entire sediment layers, but detectable changes of proportions were observed with depth. The hydrogenotrophic methanogens Methanomicrobiales slightly increased with depth while Methanosarcinales showed the reverse. Chao1 and ACE richness estimators revealed higher diversity of methanogens near the surface (0–10 cm) when compared with the bottom sediments. The near-surface sediments were mainly dominated by the family Methanosarcinaceae (45 %), which has members that can utilize substrates that cannot be used by sulfate-reducing bacteria. Overall, current data indicate that Methanosarcinales and Methanomicrobiales are the most dominant methanogens within the entire depth profile down to 100 cm, with higher abundance and diversity of methanogens in the deeper and upper sediment layers, respectively.     

Biomass measurement of methane forming bacteria in environmental samples

Methane-forming bacteria contain unusual phytanylglycerol ether phospholipids which can be extracted from the bacteria in sediments and assayed quantitatively by high performance liquid chromatography (HPLC). In this procedure the lipids were extracted, the phospholipids recovered, hydrolyzed, purified by thin layer chromatography, derivatized and assayed by HPLC. Ether lipids were recovered quantitatively from Methanobacterium thermoautotrophicum and sediments at levels as low as 8 × 10^?14 moles. In freshwater and marine sediments the flux of methane to the atmosphere and the methane levels in the pore water reflects the recovery of the phytanyl glycerol ether lipid ‘signature’. The proportion of the ether phospholipid to the total recoverable phospholipid was highest in anaerobic digester sewage sludge and deeper subsurface freshwater sediment horizons.     

Molecular Existence and Diversity of Nitrite-Dependent Anaerobic Methane Oxidizing (n-Damo) Bacteria in the Lakes of Badain of the Gobi Desert

Nitrite-dependent anaerobic methane oxidation (n-damo) process, mediated by Candidatus Methylomirabilis oxyfera of the candidate phylum NC10, was discovered recently which plays an important role in coupling the global nitrogen and carbon cycles. However, the distribution and diversity of this new anaerobic methane-oxidizing microorganism have not been investigated in desert lakes yet. The present study successfully retrieved n-damo bacterial 16S rRNA and pmoA gene sequences using PCR technique from lakes in Badain Jaran Desert of China. Phylogenetic analyses showed that n-damo bacteria widely occurred in brine and freshwater lakes on the desert with high diversity, including both sediment and water samples. The results of quantitative PCR indicated that the abundance of the 16S rRNA gene in lake sediments varied from 1.12?±?0.68?×?10⁵ to 1.64?±?0.70?×?10⁵ copies g^?1 (dry weight), while that in water samples per milliliter was generally one order of magnitude lower than sediments. Correlation analyses suggested that n-damo bacterial abundance and diversity strongly depended on salinity. In lake sediments, the distribution, abundance, and diversity of n-damo bacteria were significantly associated with depth due to the concentration gradient of the NO_x^- and ammonium. This study provided new insights into both the n-damo community patterns and its interaction with ambient environmental factors in the desert lake ecosystem.