Influence of carbon monoxide on metabolite formation in Methanosarcina acetivorans

Methanogenic archaea conserve energy for growth by reducing some one- and two-carbon compounds to methane and concomitantly generating an ion motive force. Growth of Methanosarcina acetivorans on carbon monoxide (CO) is peculiar as it involves formation of, besides methane, formate, acetate and methylated thiols. It has been argued that methane formation is partially inhibited under carboxidotrophic conditions and that the other products result from either detoxification of CO or from bypassing methanogenesis with other pathways for energy conservation. To gain a deeper understanding of the CO-dependent physiology of M. acetivorans we analyzed metabolite formation in resting cells. The initial rates of methane, acetate, formate, and dimethylsulfide formation increased differentially with increasing CO concentrations but were maximal already at the same moderate CO partial pressure. Strikingly, further increase of the amount of CO was not inhibitory. The maximal rate of methane formation from CO was approximately fivefold lower than that from methanol, consistent with the previously observed significant downregulation of the energy converting sodium-dependent methyltransferase. The rate of dimethylsulfide formation from CO was only 1–2% of that of methane formation under any conditions tested. Implications of the data presented for previously proposed pathways of CO utilization are discussed.     

Molecular investigations into a globally important carbon pool: permafrost‐protected carbon in Alaskan soils

The fate of carbon (C) contained within permafrost in boreal forest environments is an important consideration for the current and future carbon cycle as soils warm in northern latitudes. Currently, little is known about the microbiology or chemistry of permafrost soils that may affect its decomposition once soils thaw. We tested the hypothesis that low microbial abundances and activities in permafrost soils limit decomposition rates compared with active layer soils. We examined active layer and permafrost soils near Fairbanks, AK, the Yukon River, and the Arctic Circle. Soils were incubated in the lab under aerobic and anaerobic conditions. Gas fluxes at ?5 and 5 °C were measured to calculate temperature response quotients (Q₁₀). The Q₁₀ was lower in permafrost soils (average 2.7) compared with active layer soils (average 7.5). Soil nutrients, leachable dissolved organic C (DOC) quality and quantity, and nuclear magnetic resonance spectroscopy of the soils revealed that the organic matter within permafrost soils is as labile, or even more so, than surface soils. Microbial abundances (fungi, bacteria, and subgroups: methanogens and Basidiomycetes) and exoenzyme activities involved in decomposition were lower in permafrost soils compared with active layer soils, which, together with the chemical data, supports the reduced Q₁₀ values. CH₄ fluxes were correlated with methanogen abundance and the highest CH₄ production came from active layer soils. These results suggest that permafrost soils have high inherent decomposability, but low microbial abundances and activities reduce the temperature sensitivity of C fluxes. Despite these inherent limitations, however, respiration per unit soil C was higher in permafrost soils compared with active layer soils, suggesting that decomposition and heterotrophic respiration may contribute to a positive feedback to warming of this eco region.     

Managing methanogens and homoacetogens to promote reductive dechlorination of trichloroethene with direct delivery of H2 in a membrane biofilm reactor

A study with H(2)-based membrane biofilm reactors (MBfRs) was undertaken to examine the effectiveness of direct H(2) delivery in ex-situ reductive dechlorination of chlorinated ethenes. Trichloroethene (TCE) could be reductively dechlorinated to ethene with up to 95% efficiency as long as the pH-increase effects of methanogens and homoacetogens were managed and dechlorinators were selected for during start-up by creating H(2) limitation. Based on quantitative PCR, the dominant bacterial groups in the biofilm at the end of reactor operation were Dehalococcoides, Geobacter, and homoacetogens. Pyrosequencing confirmed the dominance of the dechlorinators and identified Acetobacterium as the key homoacetogen. Homoacetogens outcompeted methanogens for bicarbonate, based on the effluent concentration of acetate, by suppressing methanogens during batch start-up. This was corroborated by the methanogenesis functional gene mcrA, which was 1-2 orders of magnitude lower than the FTHFS functional gene for homoacetogens. Imaging of the MBfR fibers using scanning electron microscopy showed a distinct Dehalococcoides-like morphology in the fiber biofilm. These results support that direct addition of H(2) can allow for efficient and complete reductive dechlorination, and they shed light into how H(2)-fed biofilms, when operated to manage methanogenic and homoacetogenic activity, can be used for ex-situ bioremediation of chlorinated ethenes.     

氢营养型产甲烷代谢途径研究进展

产甲烷古菌是一类极端厌氧的古菌域微生物,可以利用CO_2、甲醇、乙酸等简单化合物产甲烷并获得能量。目前能够培养的氢营养型(CO_2/H_2)产甲烷古菌的种类较多,而且在三类产甲烷代谢类型中,氢营养型产甲烷途径的产能效率最高,并具有多种模式的特殊能量利用系统。近年来,随着质谱、光谱和晶体技术的发展与运用,人们对产甲烷代谢途径的研究进一步深入,尤其是对氢营养型产甲烷途径的生化机制有了新的认识,揭示了产甲烷古菌在能量极限条件下独特、高效的能量利用模式。本文从能量储存、代谢途径、蛋白功能与催化机制等方面概述产甲烷古菌利用CO_2/H_2产甲烷的详细过程,并对产甲烷古菌代谢途径的研究方向与技术发展进行展望。     

Community structure – Ecosystem function relationships in the Congo Basin methane cycle depend on the physiological scale of function

Belowground ecosystem processes can be highly variable and difficult to predict using microbial community data. Here, we argue that this stems from at least three issues: (a) complex covariance structure of samples (with environmental conditions or spatial proximity) can make distinguishing biotic drivers a challenge; (b) communities can control ecosystem processes through multiple mechanisms, making the identification of these controls a challenge; and (c) ecosystem function assessments can be broad in physiological scale, encapsulating multiple processes with unique microbially mediated controls. We test these assertions using methane (CH₄)‐cycling processes in soil samples collected along a wetland‐to‐upland habitat gradient in the Congo Basin. We perform our measurements of function under controlled laboratory conditions and statistically control for environmental covariates to aid in identifying biotic drivers. We divide measurements of microbial communities into four attributes (abundance, activity, composition, and diversity) that represent different forms of community control. Lastly, our process measurements differ in physiological scale, including broader processes (gross methanogenesis and methanotrophy) that involve more mediating groups, to finer processes (hydrogenotrophic methanogenesis and high‐affinity CH₄ oxidation) with fewer mediating groups. We observed that finer scale processes can be more readily predicted from microbial community structure than broader scale processes. In addition, the nature of those relationships differed, with broad processes limited by abundance while fine‐scale processes were associated with diversity and composition. These findings demonstrate the importance of carefully defining the physiological scale of ecosystem function and performing community measurements that represent the range of possible controls on ecosystem processes.     

In Situ Cultivation of Subsurface Microorganisms in a Deep Mafic Sill: Implications for SLiMEs

An in situ culturing device was incubated within a flowing borehole in a mafic sill at 1.474 km depth in Evander Au mine, South Africa. The device was designed to enrich methanogenic, Fe^{3 +}-reducing and SO₄ ^{2 ?}-reducing microorganisms using acetate, formate, methanol, Fe^{3 +}-citrate and SO₄ ^{2 ?} enriched agar and sand cartridges. At the end of the 33 day incubation geochemical analyses detected elevated H₂, acetate, CH₄ and Fe concentrations and depleted SO₄ ^{2 ?} concentrations. 16S rDNA sequences and PLFA analyses revealed that the microbial community composition of the substrate-bearing cartridges were distinct from that of the original borehole water and the non-substrate-bearing control cartridge. 16S rDNA and dissimilatory sulfite reductase, dsrAB, gene sequences indicated the device successfully targeted SO₄ ^{2 ?} reducing bacteria (SRB), which were not detected in the original borehole water. 16S rDNA sequences also revealed a shift in the microbial community from one relying on H₂ based methanogenesis to one suggestive of H₂ based acetogenesis supporting aceticlastic methanogenesis and SO₄ ^{2 ?} reduction compatible with the subsurface lithoautotrophic hypothesis.     

Colonization of sulfide‐oxygen interfaces on hot spring tufa by Thermothrix thiopara

Cream‐colored streamers of Thermothrix thiopara were found at the sulfide‐oxygen interfaces of active tufa mounds where reducing geothermal groundwaters mixed with the oxidizing atmosphere. In the Jemez hot springs, the molar ratio of sulfide to oxygen was 0.3 to 0.8 at streamer locations within the interface. This corresponded to the optimum stoichiometric proportion (0.5) necessary for sulfur metabolism. The mechanism of cell positioning at the interface was studied by shifting the interface location with a plastic cover to extend reducing conditions from the mouth of the spring to the edge of the plastic. Macroscopically visible streamers of filamentous cells became established at the new interface within a period of eight days. They could then be reestablished at the original interface by removing the cover.

Calcite crystals, pyrite crystals, and membrane enrichment vials were incubated on both sides of the interface and the kinetics of colonization determined. The preferential attachment of rod‐shaped cells to pyrite appeared to be the mechanism by which cells located themselves where pyrite occurred in situ, upstream from the interface. The formation of filamentous cells from rod‐shaped cells was induced by oxygen‐limited growth conditions. This moved the cells slightly downstream and directly within the interface.     

Methanogenic Microbial Community Composition of Oily Sludge and Its Enrichment Amended with Alkanes Incubated for Over 500 Days

Methanogenic microbial community is responsive to the availability of hydrocarbons and such information is critical for the assessment of hydrocarbon degradation in remediation and also in biologically enhanced recovery of energy from non-producing oil reserves. In this study, methanogenic enrichment cultures from oily sludge amended with n-alkanes (C₁₅-C₂₀) showed a development of active methanogenic alkanes-degrading consortium for over a total of 1000 days of incubation at 37°C. Total genomic DNAs were extracted from three types of samples, the original oily sludge (OS), the sludge after incubation for 500 days under methanogenic condition without any external carbon addition (EC), and the enrichment culture from the EC amended with n-alkanes (ET) incubated for another 500 days. The phylogenetic diversities of microbial communities of the three samples were analyzed by PCR amplification of partial 16S rRNA genes. The catabolic genes encoding benzylsuccinate synthase (bssA) and alkylsuccinate synthase (assA) were also examined by PCR amplification. These results provide important evidence in that microbial populations in an oily sludge shifted from methanogenic aromatic compounds degrading communities to potential methanogenic alkane-degrading communities when the enrichment was supplemented with n-alkanes and incubated under anaerobic conditions.     

Linking Belowground Carbon Allocation to Anaerobic CH4 and CO2 Production in a Forested Peatland,New York State

Heterotrophic soil microorganisms rely on carbon (C) allocated belowground in plant production, but belowground C allocation (BCA) by plants is a poorly quantified part of ecosystem C cycling, especially, in peat soil. We applied a C balance approach to quantify BCA in a mixed conifer-red maple (Acer rubrum) forest on deep peat soil. Direct measurements of CH₄ and CO₂ fluxes across the soil surface (soil respiration), production of fine and small plant roots, and aboveground litterfall were used to estimate respiration by roots, by mycorrhizae and by free-living soil microorganisms. Measurements occurred in two consecutive years. Soil respiration rates averaged 1.2 bm μmol m^{? 2} s^{? 1} for CO₂ and 0.58 nmol m^{? 2} s^{? 1} for CH₄ (371 to 403 g C m^{? 2} year^{? 1}). Carbon in aboveground litter (144 g C m^{? 2} year^{? 1}) was 84% greater than C in root production (78 g C m^{? 2} year^{? 1}). Complementary in vitro assays located high rates of anaerobic microbial activity, including methanogenesis, in a dense layer of roots overlying the peat soil and in large-sized fragments within the peat matrix. Large-sized fragments were decomposing roots and aboveground leaf and twig litter, indicating that relatively fresh plant production supported most of the anaerobic microbial activity. Respiration by free-living soil microorganisms in deep peat accounted for, at most, 29 to 38 g C m^{? 2} year^{? 1}. These data emphasize the close coupling between plant production, ecosystem-level C cycling and soil microbial ecology, which BCA can help reveal.