Anaerobic methane oxidation

To clarify the biological mechanism of anaerobic methane oxidation, experiments were performed with samples of the Black Sea anaerobic sediments and with the aerobic methane-oxidizing bacterium Methylomonas methanica strain 12. The inhibition-stimulation analysis did not allow an unambiguous conclusion to be made about direct and independent role of either methanogenic or sulfate-reducing microorganisms in the biogeochemical process of anaerobic methane oxidation. Enrichment cultures obtained from samples of water and reduced sediments oxidized methane under anaerobic conditions, primarily in the presence of acetate or formate or of a mixture of acetate, formate, and lactate. However, this ability was retained by the cultures for no more than two transfers on corresponding media. Experiments showed that the aerobic methanotroph Mm. methanica strain 12 is incapable of anaerobic methane oxidation at the expense of the reduction of amorphous FeOOH.     

[1-14C] Acetate assimilation by obligate methylotrophs,Pseudomonas methanica and Methylosinus trichosporium

The oxidation of one carbon compounds (methane, methanol, formaldehyde, formate) and primary alcohols (ethanol, propanol, butanol) supported the assimilation of [1-¹⁴C]acetate by cell suspensions of type I obligate methylotroph; Pseudomonas methanica, Texas strain, and type II obligate methylotroph, Methylosinus trichosporium, strain PG. The amount of oxygen consumed and substrate oxidized correlated with the amount of [1-¹⁴C]acetate assimilated during oxidation of C-1 compounds and primary alcohols.Oxidation of methanol, formaldehyde, and primary alcohols in extracts of Pseudomonas methanica, Texas strain, and Methylosinus trichosporium, strain PG, was catalyzed by a phenazine methosulfate linked, ammonium ion dependent methanol dehydrogenase. The oxidation of aldehydes was catalyzed by a phenazine methosulfate linked, ammonium ion independent aldehyde dehydrogenase. Formate was oxidized by a NAD⁺ linked formate dehydrogenase.Deceased.This work was supported by Grant GB 8173 from the National Science Foundation and by a grant from the Robert A. Welch Foundation.     

Oxygen metabolism in Pseudomonas methanica

Three sites of oxygen metabolism in Pseudomonas methanica have been identified on the basis of studies of methane, ethanol and formate oxidation. The three oxidations exhibit different affinities for oxygen and sensitivities to inhibition by cyanide. The results obtained are consistent with the presence of a methane oxygenase and at least two terminal oxidases in Pseudomonas methanica.     

Methane formation and oxidation in the meromictic oligotrophic Lake Gek-Gel (Azerbaijan)

The production and oxidation of methane and diversity of culturable aerobic methanotrophic bacteria in the water column and upper sediments of the meromictic oligotrophic Lake Gek-Gel (Azerbaijan) were studied by radioisotope, molecular, and microbiological techniques. The rate of methane oxidation was low in the aerobic mixolimnion, increased in the chemocline, and peaked at the depth where oxygen was detected in the water column. Aerobic methanotrophic bacteria of type II belonging to the genus Methylocystis were identified in enrichment cultures obtained from the chemocline. Methane oxidation in the anaerobic water of the monimolimnion was much more intense than in the aerobic zone. However, below 29–30 m methane concentration increased and reached 68 μM at the bottom. The highest rate of methane oxidation under anaerobic conditions was revealed in the upper layer of bottom sediments. The rate of methane oxidation significantly exceeding that of methane production suggests a deep source of methane in this lake.     

Occurrence of Methanogenic Archaea in Highly Polluted Sediments of Tropical Santos–São Vicente Estuary (São Paulo, Brazil)

Little is known about the ability of methanogens to grow and produce methane in estuarine environments. In this study, traditional methods for cultivating strictly anaerobic microorganisms were combined with Fluorescence in situ hybridization (FISH) technique to enrich and identify methanogenic Archaea cultures occurring in highly polluted sediments of tropical Santos–São Vicente Estuary (São Paulo, Brazil). Sediment samples were enriched at 30°C under strict anaerobic and halophilic conditions, using a basal medium containing 2% of sodium chloride and amended with glucose, methanol, and sodium salts of acetate, formate and lactate. High methanogenic activity was detected, as evidenced by the biogas containing 11.5 mmol of methane at 20 days of incubation time and methane yield of 0.138-mmol CH₄/g organic matter/g volatile suspense solids. Cells of methanogenic Archaea were selected by serial dilution in medium amended separately with sodium acetate, sodium formate, or methanol. FISH analysis revealed the presence of Methanobacteriaceae and Methanosarcina sp. cells.     

Cultivation of methanogens from shallow marine sediments at Hydrate Ridge, Oregon

Little is known about the methanogenic degradation of acetate, the fate of molecular hydrogen and formate or the ability of methanogens to grow and produce methane in cold, anoxic marine sediments. The microbes that produce methane were examined in permanently cold, anoxic marine sediments at Hydrate Ridge (44 degrees 35' N, 125 degrees 10' W, depth 800 m). Sediment samples (15 to 35 cm deep) were collected from areas of active methane ebullition or areas where methane hydrates occurred. The samples were diluted into enrichment medium with formate, acetate or trimethylamine as catabolic substrate. After 2 years of incubation at 4 degrees C to 15 degrees C, enrichment cultures produced methane. PCR amplification and sequencing of the rRNA genes from the highest dilutions with growth suggested that each enrichment culture contained a single strain of methanogen. The level of sequence similarity (91 to 98%) to previously characterized prokaryotes suggested that these methanogens belonged to novel genera or species within the orders Methanomicrobiales and Methanosarcinales. Analysis of the 16S rRNA gene libraries from DNA extracted directly from the sediment samples revealed phylotypes that were either distantly related to cultivated methanogens or possible anaerobic methane oxidizers related to the ANME-1 and ANME-2 groups of the Archaea. However, no methanogenic sequences were detected, suggesting that methanogens represented only a small proportion of the archaeal community.     

Anaerobic and aerobic oxidation of ferrous iron at neutral pH by chemoheterotrophic nitrate-reducing bacteria

Nine out of ten anaerobic enrichment cultures inoculated with sediment samples from various freshwater, brackish-water, and marine sediments exhibited ferrous iron oxidation in mineral media with nitrate and an organic cosubstrate at pH 7.2 and 30° C. Anaerobic nitrate-dependent ferrous iron oxidation was a biological process. One strain isolated from brackish-water sediment (strain HidR2, a motile, nonsporeforming, gram-negative rod) was chosen for further investigation of ferrous iron oxidation in the presence of acetate as cosubstrate. Strain HidR2 oxidized between 0.7 and 4.9 mM ferrous iron aerobically and anaerobically at pH 7.2 and 30° C in the presence of small amounts of acetate (between 0.2 and 1.1 mM). The strain gained energy for growth from anaerobic ferrous iron oxidation with nitrate, and the ratio of iron oxidized to acetate provided was constant at limiting acetate supply. The ability to oxidize ferrous iron anaerobically with nitrate at approximately pH 7 appears to be a widespread capacity among mesophilic denitrifying bacteria. Since nitrate-dependent iron oxidation closes the iron cycle within the anoxic zone of sediments and aerobic iron oxidation enhances the reoxidation of ferrous to ferric iron in the oxic zone, both processes increase the importance of iron as a transient electron carrier in the turnover of organic matter in natural sediments. Received: 24 April 1997 / Accepted: 22 September 1997     

Variability in fermentation patterns of sugar-utilizing bacteria isolated from anaerobic,intertidal sediments

Three dominant types of sugar-fermenting bacteria were isolated from the anaerobic, intertidal sediments of the Eems-Dollard estuary by applying techniques involving anaerobic agar shake tubes. One of the isolated types was tentatively identified as aStreptococcus species, the other two asBacteroides species. All types were versatile with respect to the utilization of sugars. The fermentation patterns of two types were dependent upon conditions of cultivation. In glucose-limited cultures ofStreptococcus strain NS.G52, the production of lactate was suppressed in favor of formate, acetate, and ethanol. In glucose-limited syntrophic cultures withMethanospirillum hungatei, Bacteroides strain NS.G42 was forced to produce acetate and hydrogen at the expense of ethanol. The fermentation pattern ofBacteroides strain NS.S42, which consisted of acetate, propionate, and succinate, was not affected by conditions of cultivation.     

Aerobic and anaerobic microbial activity in deep subsurface sediments from the savannah river plant

Methanogenesis, sulfate reduction, and rates of carbon mineralization were determined for samples derived at different depths from four cores drilled at the Savannah River Plant, Aiken South Carolina. Three‐gram subsamples of the sediments were dispensed to 10‐mL serum bottles under 5% H₂/95% N₂ and amended with 0.5 mL degassed distilled water with or without the following solutes: formate plus acetate, bicarbonate, lactate, and radiolabeled sulfate, glucose, and Índole. After incubating 1 to 5 days, the sediments were assayed for methane, H₂, ³⁵S, and ^I4CO₂. No methanogenesis was detected at any depth in any core and sulfate was rarely reduced. Evolution of ¹⁴CO₂ from glucose and indole was detected in sediments as deep as 262 and 259 m, respectively. At some depths the ¹⁴CO₂ evolution rate was comparable to that of surface soils; however, at other depths no ¹⁴CO₂ evolution could be detected. Injection of sterile air into anaerobic incubations increased rates of carbon mineralization at all depths that had demonstrated anaerobic activity and stimulated mineralization activity in sediments that were inactive anaerobically, suggesting a predominance of aerobic metabolism. Increasing the concentration of added glucose and indole often increased the resulting rates of ¹⁴CO₂ evolved from these substrates. Our data indicate that both aerobic and anaerobic microorganisms are present and metabolically active in samples from deep subsurface environments.     

土壤中甲烷厌氧氧化菌多样性的分子检测

甲烷厌氧氧化作用是减少海洋底泥甲烷释放的重要生物地球化学过程,然而在陆地生态系统中甲烷厌氧氧化作用及其功能菌群的生态功能仍然不确定。对甲烷厌氧氧化菌多样性的研究可为减少甲烷排放提供重要科学依据。与传统的分离培养方法比较,分子检测方法是一种更为快速和高效的研究手段,可直接和全面的反映参与甲烷厌氧氧化作用的功能微生物。以DNA分子标记物为研究对象,重点探讨三类主要的分子标记基因,即16S rRNA,mcr A和pmo A,所采用的相关探针和引物信息,同时从定性和定量两个角度综述土壤甲烷厌氧氧化菌的多样性研究的主要进展,最后提出厌氧甲烷氧化菌多样性研究中存在的一些问题和相应的解决思路。     

Analysis of alkane-dependent methanogenic community derived from production water of a high-temperature petroleum reservoir

Microbial assemblage in an n-alkanes-dependent thermophilic methanogenic enrichment cultures derived from production waters of a high-temperature petroleum reservoir was investigated in this study. Substantially higher amounts of methane were generated from the enrichment cultures incubated at 55 °C for 528 days with a mixture of long-chain n-alkanes (C₁₅–C₂₀). Stoichiometric estimation showed that alkanes-dependent methanogenesis accounted for about 19.8% of the total amount of methane expected. Hydrogen was occasionally detected together with methane in the gas phase of the cultures. Chemical analysis of the liquid cultures resulted only in low concentrations of acetate and formate. Phylogenetic analysis of the enrichment revealed the presence of several bacterial taxa related to Firmicutes, Thermodesulfobiaceae, Thermotogaceae, Nitrospiraceae, Dictyoglomaceae, Candidate division OP8 and others without close cultured representatives, and Archaea predominantly related to uncultured members in the order Archaeoglobales and CO₂-reducing methanogens. Screening of genomic DNA retrieved from the alkanes-amended enrichment cultures also suggested the presence of new alkylsuccinate synthase alpha-subunit (assA) homologues. These findings suggest the presence of poorly characterized (putative) anaerobic n-alkanes degraders in the thermophilic methanogenic enrichment cultures. Our results indicate that methanogenesis of alkanes under thermophilic condition is likely to proceed via syntrophic acetate and/or formate oxidation linked with hydrogenotrophic methanogenesis.     

Psychromonas antarcticus gen. nov., sp. nov., a new aerotolerant anaerobic, halophilic psychrophile isolated from pond sediment of the McMurdo Ice Shelf, Antarctica

A gram-negative, rod- to oval-shaped, aerotolerant anaerobic bacterium was isolated from an anaerobic enrichment inoculated with sediment taken from below the cyanobacterial mat of a high-salinity pond near Bratina Island on the McMurdo Ice Shelf, Antarctica. The organism was positive for terminal oxidase and catalase and was motile by means of a polar flagellum. Optimal growth of anaerobic cultures occurred at 12° C, at pH 6.5, and at an NaCl concentration of 3% (w/v). Of a variety of polysaccharides tested, only starch and glycogen supported growth. No growth was observed on cellulosic substrates and xylan, and the organism was unable to attack esculin. Monosaccharides and disaccharides, including the cyanobacterial cell-wall constituent N-acetyl glucosamine, were fermented. Per 100 mol of hexose, the following products (in mol) were formed: acetate, 60; formate, 130; ethanol, 56; lactate, 73; CO₂, 15; and butyrate, 2. Propionate, ethanol, n-propanol, n-butanol and succinate were not detectable in the culture medium (< 1 mol per 100 mol of monomer). Hydrogen was not detected in the head space (detection limit < 10^–5 atm). Growth yields in aerobic static liquid cultures were slightly higher than those in anaerobic culture, and fermentation favoured acetate at the expense of electron sink products. Growth was inhibited in aerobic shaking cultures, and the organism did not utilize nitrate or sulfate as electron acceptors. The G+C content of the DNA from the bacterium was 42.8 mol%. A phylogenetic analysis indicated that the organism is a member of the γ-subgroup of Proteobacteria, but that it is distinct from other members of this group based on the sequence of its 16S rRNA gene, mol% G+C, morphology, and physiological and biochemical characteristics. It is designated as a new genus and species; the type strain is star-1 (DSM 10704). Received: 17 June 1996 / Accepted: 13 October 1997     

Chemolithotrophic sulfur bacteria in sediments,mats, and stromatolites of western Australian saline lakes

Samples of stromatolites, microbial mats, and sediments from four saline lakes (approximate seasonal salinity ranges 20–220%o) in Western Australia were used to establish enrichments for elective cultures of aerobic and anaerobic denitrifying chemolithoautotrophs that could grow with thiosulfate as sole energy source. Organisms of these types were obtained from all sources tested. Twenty‐four pure cultures were isolated, all of which were gram‐negative, rod‐shaped bacteria exhibiting a considerable diversity of metabolic capability. Isolation of these obligate and facultative sulfur‐oxidizing chemolithotrophs from the stromatolite and mat habitats indicates the possibility that these rod‐shaped bacteria contribute to the oxidative phase of the sulfur cycle in these habitats, in addition to oxidation by phototrophs or Beggiatoa. Only four of the pure cultures could grow without salt, but all 24 showed significant halophily, some tolerating 3 M NaCl. Three novel isolates of NaCl‐dependent, thiosulfate‐oxidizing, aerobic and denitrifying obligate chemolithotrophs are described. In addition, a facultatively heterotrophic halophilic strain growing either methylotrophically on methylamine or chemolithotrophically on thiosulfate aerobically or with anaerobic denitrification was found.     

Acetate oxidation to CO2 in anaerobic bacteria via a novel pathway not involving reactions of the citric acid cycle

In several sulfate-reducing bacteria capable of complete oxidation of acetate (or acetyl CoA), the citric acid cycle is not operative. No 2-oxoglutarate dehydrogenase activity was found in these organisms, and the labelling pattern of oxaloacetate excludes its synthesis via 2-oxo-glutarate. These sulfate-reducers contained, however, high activities of the enzymes carbon monoxide dehydrogenase and formate dehydrogenase and catalyzed an isotope exchange between CO₂ and the carboxyl group of acetate (or acetyl CoA), showing a direct C-C-cleavage of activated acetic acid. These findings suggest that in the investigated sulfate-reducers acetate is oxidized to CO₂ via C₁ intermediates. The proposed pathway provides a possible explanation for the reported different fluoroacetate sensitivity of acetate oxidation by anaerobic bacteria, for mini-methane formation, as well as for the postulated anaerobic methane oxidation by special sulfate-reducers.     

Studies on an acetate-fermenting strain of Methanosarcina.

An acetate-fermenting strain of Methanosarcina was isolated from an acetate enrichment culture inoculated with anaerobic sludge from a waste treatment digestor. In pure culture, this organism fermented acetate in the absence of added hydrogen at rates comparable in magnitude to those found in digestor systems. This rate was significantly higher than previously obtained for pure cultures of this genus. Mineral components of yeast extract were highly stimulatory for cultures growing on methanol. Comparable stimulation was not observed for cultures growing on acetate. Labeling studies indicated that acetate was converted to methane and CO2 as predicted by previous studies on mixed cultures. Total oxidation or reduction of acetate was not the mechanism of conversion of acetate to methane by the pure culture. The ability of this strain to form colonies or to produce methane from acetate was apparently influenced by the choice of substrate and conditions used for growing the inoculum.     

Oxidation of short-chain fatty acids by sulfate-reducing bacteria in freshwater and in marine sediments

Colony counts of acetate-, propionate- and l-lactate-oxidizing sulfate-reducing bacteria in marine sediments were made. The vertical distribution of these organisms were equal for the three types considered. The highest numbers were found just beneath the border of aerobic and anaerobic layers.Anaerobic mineralization of acetate, propionate and l-lactate was studied in the presence and in the absence of sulfate. In freshwater and in marine sediments, acetate and propionate were oxidized completely with concomitant reduction of sulfate. l-Lactate was always fermented. Lactate-oxidizing, sulfate-reducing bacteria, belonging to the species Desulfovibrio desulfuricans, and lactate-fermenting bacteria were found in approximately equal amounts in the sediments. Acetate-oxidizing, sulfate-reducing bacteria could only be isolated from marine sediments, they belonged to the genus Desulfobacter and oxidized only acetate and ethanol by sulfate reduction. Propionate-oxidizing, sulfate-reducing bacteria belonged to the genus Desulfobulbus. They were isolated from freshwater as well as from marine sediments and showed a relatively large range of usable substrates: hydrogen, formate, propionate, l-lactate and ethanol were oxidized with concomitant sulfate reduction. l-Lactate and pyruvate could be fermented by most of the isolated strains.     

Microbial growth on C1 compounds: Uptake of [14C]formaldehyde and [14C]formate by methane-grown Pseudomonas methanica and determination of the hexose labelling pattern after brief incubation with [14C]methanol

1. A study has been made of the incorporation of carbon from [¹⁴C]formaldehyde and [¹⁴C]formate by cultures of Pseudomonas methanica growing on methane. 2. The distribution of radioactivity within the non-volatile constituents of the ethanol-soluble fractions of the cells, after incubation with labelled compounds for periods of up to 1min., has been analysed by chromatography and radioautography. 3. Radioactivity was fixed from [¹⁴C]formaldehyde mainly into the phosphates of the sugars, glucose, fructose, sedoheptulose and allulose. 4. Very little radioactivity was fixed from [¹⁴C]formate; after 1min. the only products identified were serine and malate. 5. The distribution of radioactivity within the carbon skeleton of glucose, obtained from short-term incubations with [¹⁴C]methanol of Pseudomonas methanica growing on methane, has been investigated. At the earliest time of sampling over 70% of the radioactivity was located in C-1; as the time increased the radioactivity spread throughout the molecule. 6. The results have been interpreted in terms of a variant of the pentose phosphate cycle, involving the condensation of formaldehyde with C-1 of ribose 5-phosphate to give allulose phosphate.     

Influence of pH on Terminal Carbon Metabolism in Anoxic Sediments from a Mildly Acidic Lake

The carbon and electron flow pathways and the bacterial populations responsible for transformation of H₂-CO₂, formate, methanol, methylamine, acetate, glycine, ethanol, and lactate were examined in sediments collected from Knaack Lake, Wis. The sediments were 60% organic matter (pH 6.2) and did not display detectable sulfate-reducing activity, but they contained the following average concentration (in micromoles per liter of sediment) of metabolites and end products: sulfide, 10; methane, 1,540; CO₂, 3,950; formate, 25; acetate, 157; ethanol, 174; and lactate, 138. Methane was produced predominately from acetate, and only 4% of the total CH₄ was derived from CO₂. Methanogenesis was limited by low environmental temperature and sulfide levels and more importantly by low pH. Increasing in vitro pH to neutral values enhanced total methane production rates and the percentage of CO₂ transformed to methane but did not alter the amount of ¹⁴CO₂ produced from [2-¹⁴C]acetate (~24%). Analysis of both carbon transformation parameters with ¹⁴C-labeled tracers and bacterial trophic group enumerations indicated that methanogenesis from acetate and both heterolactic- and acetic acid-producing fermentations were important to the anaerobic digestion process.     

Microbial Diversity of Hydrothermal Sediments in the Guaymas Basin: Evidence for Anaerobic Methanotrophic Communities

Microbial communities in hydrothermally active sediments of the Guaymas Basin (Gulf of California, Mexico) were studied by using 16S rRNA sequencing and carbon isotopic analysis of archaeal and bacterial lipids. The Guaymas sediments harbored uncultured euryarchaeota of two distinct phylogenetic lineages within the anaerobic methane oxidation 1 (ANME-1) group, ANME-1a and ANME-1b, and of the ANME-2c lineage within the Methanosarcinales, both previously assigned to the methanotrophic archaea. The archaeal lipids in the Guaymas Basin sediments included archaeol, diagnostic for nonthermophilic euryarchaeota, and sn-2-hydroxyarchaeol, with the latter compound being particularly abundant in cultured members of the Methanosarcinales. The concentrations of these compounds were among the highest observed so far in studies of methane seep environments. The δ-¹³C values of these lipids (δ-¹³C = −89 to −58‰) indicate an origin from anaerobic methanotrophic archaea. This molecular-isotopic signature was found not only in samples that yielded predominantly ANME-2 clones but also in samples that yielded exclusively ANME-1 clones. ANME-1 archaea therefore remain strong candidates for mediation of the anaerobic oxidation of methane. Based on 16S rRNA data, the Guaymas sediments harbor phylogenetically diverse bacterial populations, which show considerable overlap with bacterial populations of geothermal habitats and natural or anthropogenic hydrocarbon-rich sites. Consistent with earlier observations, our combined evidence from bacterial phylogeny and molecular-isotopic data indicates an important role of some novel deeply branching bacteria in anaerobic methanotrophy. Anaerobic methane oxidation likely represents a significant and widely occurring process in the trophic ecology of methane-rich hydrothermal vents. This study stresses a high diversity among communities capable of anaerobic oxidation of methane.     

Isolation of anaerobic oxalate-degrading bacteria from freshwater lake sediments

Enrichment cultures that anaerobically degraded oxalate were obtained from lake sediment inocula. From these, 5 pure cultures of anaerobic oxalate-degrading bacteria were isolated and partially characterized. The isolates were Gram-negative, non-sporeforming, non-motile, obligate anaerobes. Oxalate was required for growth and was stoichiometrically converted to formate; ¹⁴CO₂ was also recovered when ¹⁴C-oxalate was added. Maximal growth occurred when the oxalate concentration was 50 mM. Acetate stimulated growth in the presence of oxalate, however, ¹⁴C-experiments indicated that acetate was only utilized for cell carbon.The isolates were either spiral-shaped or rod-shaped organisms. The first morphotype grew much more slowly than the second and exhibited 13-fold lower cell yields. These isolates represent a new strain of oxalate-degrading bacteria. The second morphotype was similar to the anaerobic oxalate-degrading bacteria previously found in rumen. This report extends the known habitats in which anaerobic oxalate-degrading organisms have been found to include aquatic sediments.