Wiley
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Linking autotrophic activity in environmental samples with specific bacterial taxa by detection of <sup>13</sup>C‐labelled fatty acids Summary A method for the detection of physiologically active autotrophic bacteria in complex microbial communities was developed based on labelling with the stable isotope 13 C. Labelling of autotrophic nitrifying, sulphur‐oxidizing and iron‐oxidizing populations was performed in situ by incubation with NaH[13 C]O3 . Incorporated label into fatty acid methyl esters (FAMEs) was detected and quantified using gas chromatography‐mass spectrometry in single ion monitoring mode. Before the analyses of different environmental samples, the protocol was evaluated in pure culture experiments. In different environmental samples a selective labelling of fatty acids demonstrated which microbial taxa were responsible for the respective chemolithoautotrophic activity. The most strongly labelled fatty acids of a sample from a sulphide treating biofilter from an animal rendering plant were cis ‐7‐hexadecenoic acid (16:1 cis7) and 11‐methyl hexadecanoic acid (16:0 11methyl), which are as‐yet not known for any sulphide‐oxidizing autotroph. The fatty acid labelling pattern of an experimental biotrickling filter sample supplied with dimethyl disulphide clearly indicated the presence and activity of sulphide‐oxidizing bacteria of the genus Thiobacillus . For a third environmental sample from an acid mining lake sediment, the assignment of autotrophic activity to bacteria of the genus Leptospirillum but not to Acidithiobacillus could be made by this method, as the fatty acid patterns of these bacteria show clear differences.
Wiley - Tập 5 Số 11 - Trang 1155-1167 - 2003
Formation of propionate and butyrate by the human colonic microbiota Summary The human gut microbiota ferments dietary non‐digestible carbohydrates into short‐chain fatty acids (SCFA). These microbial products are utilized by the host and propionate and butyrate in particular exert a range of health‐promoting functions. Here an overview of the metabolic pathways utilized by gut microbes to produce these two SCFA from dietary carbohydrates and from amino acids resulting from protein breakdown is provided. This overview emphasizes the important role played by cross‐feeding of intermediary metabolites (in particular lactate, succinate and 1,2‐propanediol) between different gut bacteria. The ecophysiology, including growth requirements and responses to environmental factors, of major propionate and butyrate producing bacteria are discussed in relation to dietary modulation of these metabolites. A detailed understanding of SCFA metabolism by the gut microbiota is necessary to underpin effective strategies to optimize SCFA supply to the host.
Wiley - Tập 19 Số 1 - Trang 29-41 - 2017
Responses of Clostridia to oxygen: from detoxification to adaptive strategies Summary Clostridia comprise bacteria of environmental, biotechnological and medical interest and many commensals of the gut microbiota. Because of their strictly anaerobic lifestyle, oxygen is a major stress for Clostridia. However, recent data showed that these bacteria can cope with O2 better than expected for obligate anaerobes through their ability to scavenge, detoxify and consume O2 . Upon O2 exposure, Clostridia redirect their central metabolism onto pathways less O2 ‐sensitive and induce the expression of genes encoding enzymes involved in O2 ‐reduction and in the repair of oxidized damaged molecules. While Faecalibacterium prausnitzii efficiently consumes O2 through a specific extracellular electron shuttling system requiring riboflavin, enzymes such as rubrerythrins and flavodiiron proteins with NAD(P)H‐dependent O2 ‐ and/or H2 O2 ‐reductase activities are usually encoded in other Clostridia. These two classes of enzymes play indeed a pivotal role in O2 tolerance in Clostridioides difficile and Clostridium acetobutylicum . Two main signalling pathways triggering O2 ‐induced responses have been described so far in Clostridia. PerR acts as a key regulator of the O2 ‐ and/or reactive oxygen species–defence machinery while in C . difficile , σB , the sigma factor of the general stress response also plays a crucial role in O2 tolerance by controlling the expression of genes involved in O2 scavenging and repair systems.
Wiley - Tập 23 Số 8 - Trang 4112-4125 - 2021
Forest microsite effects on community composition of ectomycorrhizal fungi on seedlings of <i>Picea abies</i> and <i>Betula pendula</i> Summary Niche differentiation in soil horizons, host species and natural nutrient gradients contribute to the high diversity of ectomycorrhizal fungi in boreal forests. This study aims at documenting the diversity and community composition of ectomycorrhizal fungi of Norway spruce (Picea abies ) and silver birch (Betula pendula ) seedlings in five most abundant microsites in three Estonian old‐growth forests. Undisturbed forest floor, windthrow mounds and pits harboured more species than brown‐ and white‐rotted wood. Several species of ectomycorrhizal fungi were differentially represented on either hosts, microsites and sites. Generally, the most frequent species in dead wood were also common in forest floor soil. Ordination analyses suggested that decay type determined the composition of EcM fungal community in dead wood. Root connections with in‐growing mature tree roots from below affected the occurrence of certain fungal species on seedling roots systems in dead wood. This study demonstrates that ectomycorrhizal fungi differentially establish in certain forest microsites that is attributable to their dispersal and competitive abilities. Elevated microsites, especially decayed wood, act as seed beds for both ectomycorrhizal forest trees and fungi, thus affecting the succession of boreal forest ecosystems.
Wiley - Tập 10 Số 5 - Trang 1189-1201 - 2008
Anaerobic microbial communities and their potential for bioenergy production in heavily biodegraded petroleum reservoirs Summary Most of the oil in low temperature, non‐uplifted reservoirs is biodegraded due to millions of years of microbial activity, including via methanogenesis from crude oil. To evaluate stimulating additional methanogenesis in already heavily biodegraded oil reservoirs, oil sands samples were amended with nutrients and electron acceptors, but oil sands bitumen was the only organic substrate. Methane production was monitored for over 3000 days. Methanogenesis was observed in duplicate microcosms that were unamended, amended with sulfate or that were initially oxic, however methanogenesis was not observed in nitrate‐amended controls. The highest rate of methane production was 0.15 μmol CH4 g−1 oil d−1 , orders of magnitude lower than other reports of methanogenesis from lighter crude oils. Methanogenic Archaea and several potential syntrophic bacterial partners were detected following the incubations. GC–MS and FTICR–MS revealed no significant bitumen alteration for any specific compound or compound class, suggesting that the very slow methanogenesis observed was coupled to bitumen biodegradation in an unspecific manner. After 3000 days, methanogenic communities were amended with benzoate resulting in methanogenesis rates that were 110‐fold greater. This suggests that oil‐to‐methane conversion is limited by the recalcitrant nature of oil sands bitumen, not the microbial communities resident in heavy oil reservoirs.
Wiley - Tập 22 Số 8 - Trang 3049-3065 - 2020
Vesiduction: the fourth way of <scp>HGT</scp> Summary Besides the canonical gene transfer mechanisms transformation, transduction and conjugation, DNA transfer involving extracellular vesicles is still under appreciated. However, this widespread phenomenon has been observed in the three domains of life. Here, we propose the term ‘Vesiduction’ as a fourth mode of intercellular DNA transfer.
Wiley - Tập 22 Số 7 - Trang 2457-2460 - 2020
Microbial pathways for nitrogen loss in an upland soil Summary The distribution and importance of anaerobic ammonium oxidation (anammox) and nitrite‐dependent anaerobic methane oxidation (n‐damo) have been identified in aquatic ecosystems; their role in agricultural upland soils however has not yet been well investigated. In this study, we examined spatio‐temporal distributions of anammox and n‐damo bacteria in soil profiles (300 cm depth) from an agricultural upland. Monitoring nitrogen (N) conversion activity using isotope‐tracing techniques over the course of one year showed denitrification (99.0% N‐loss in the winter and 85.0% N‐loss in the summer) predominated over anammox (1.0% N‐loss in the winter and 14.4% N‐loss in the summer) and n‐damo (0.6% N‐loss in the winter) in surface soils (0–20 cm). While below 20 cm depth, N‐loss was dominated by anammox (79.4 ± 14.3% in the winter and 65.4 ± 12.5% in the summer) and n‐damo was not detected. Phylogenetic analysis showed that Candidatus Brocadia anammoxidans dominated the anammox community in the surface soil and Candidatus Brocadia fulgida dominated below 20 cm depth. Dissimilatory nitrate reduction to ammonium (DNRA), another nitrite reduction process, was found to play a limited role (4.9 ± 3.5%) in the surface soil compared with denitrification; below 80 cm DNRA rates were much higher than rates of anammox and denitrification. Ammonium oxidation was the main source of
Wiley - Tập 20 Số 5 - Trang 1723-1738 - 2018
Metagenomic analysis reveals distinct patterns of denitrification gene abundance across soil moisture, nitrate gradients Summary This study coupled a landscape‐scale metagenomic survey of denitrification gene abundance in soils with in situ denitrification measurements to show how environmental factors shape distinct denitrification communities that exhibit varying denitrification activity. Across a hydrologic gradient, the distribution of total denitrification genes (nap/nar + nirK/nirS + cNor/qNor + nosZ) inferred from metagenomic read abundance exhibited no consistent patterns. However, when genes were considered independently, nirS , cNor and nosZ read abundance was positively associated with areas of higher soil moisture, higher nitrate and higher annual denitrification rates, whereas nirK and qNor read abundance was negatively associated with these factors. These results suggest that environmental conditions, in particular soil moisture and nitrate, select for distinct denitrification communities that are characterized by differential abundance of genes encoding apparently functionally redundant proteins. In contrast, taxonomic analysis did not identify notable variability in denitrifying community composition across sites. While the capacity to denitrify was ubiquitous across sites, denitrification genes with higher energetic costs, such as nirS and cNor , appear to confer a selective advantage in microbial communities experiencing more frequent soil saturation and greater nitrate inputs. This study suggests metagenomics can help identify denitrification hotspots that could be protected or enhanced to treat non‐point source nitrogen pollution.
Wiley - Tập 21 Số 4 - Trang 1255-1266 - 2019
The quantitative significance of <i>Syntrophaceae</i> and syntrophic partnerships in methanogenic degradation of crude oil alkanes Summary Libraries of 16S rRNA genes cloned from methanogenic oil degrading microcosms amended with North Sea crude oil and inoculated with estuarine sediment indicated that bacteria from the genera Smithella (Deltaproteobacteria, Syntrophaceace ) and Marinobacter sp. (Gammaproteobacteria ) were enriched during degradation. Growth yields and doubling times (36 days for both Smithella and Marinobacter ) were determined using qPCR and quantitative data on alkanes, which were the predominant hydrocarbons degraded. The growth yield of the Smithella sp. [0.020 g(cell‐C) /g(alkane‐C) ], assuming it utilized all alkanes removed was consistent with yields of bacteria that degrade hydrocarbons and other organic compounds in methanogenic consortia. Over 450 days of incubation predominance and exponential growth of Smithella was coincident with alkane removal and exponential accumulation of methane. This growth is consistent with Smithella's occurrence in near surface anoxic hydrocarbon degrading systems and their complete oxidation of crude oil alkanes to acetate and/or hydrogen in syntrophic partnership with methanogens in such systems. The calculated growth yield of the Marinobacter sp., assuming it grew on alkanes, was [0.0005 g(cell‐C) /g(alkane‐C) ] suggesting that it played a minor role in alkane degradation. The dominant methanogens were hydrogenotrophs (Methanocalculus spp. from the Methanomicrobiales ). Enrichment of hydrogen‐oxidizing methanogens relative to acetoclastic methanogens was consistent with syntrophic acetate oxidation measured in methanogenic crude oil degrading enrichment cultures. qPCR of the Methanomicrobiales indicated growth characteristics consistent with measured rates of methane production and growth in partnership with Smithella .
Wiley - Tập 13 Số 11 - Trang 2957-2975 - 2011
Analysis of methanotrophic bacteria in Movile Cave by stable isotope probing Summary Movile Cave is an unusual groundwater ecosystem that is supported by in situ chemoautotrophic production. The cave atmosphere contains 1–2% methane (CH4 ), although much higher concentrations are found in gas bubbles that keep microbial mats afloat on the water surface. As previous analyses of stable carbon isotope ratios have suggested that methane oxidation occurs in this environment, we hypothesized that aerobic methane‐oxidizing bacteria (methanotrophs) are active in Movile Cave. To identify the active methanotrophs in the water and mat material from Movile Cave, a microcosm was incubated with a 10%13 CH4 headspace in a DNA‐based stable isotope probing (DNA‐SIP) experiment. Using improved centrifugation conditions, a 13 C‐labelled DNA fraction was collected and used as a template for polymerase chain reaction amplification. Analysis of genes encoding the small‐subunit rRNA and key enzymes in the methane oxidation pathway of methanotrophs identified that strains of Methylomonas , Methylococcus and Methylocystis/Methylosinus had assimilated the 13 CH4 , and that these methanotrophs contain genes encoding both known types of methane monooxygenase (MMO). Sequences of non‐methanotrophic bacteria and an alga provided evidence for turnover of CH4 due to possible cross‐feeding on 13 C‐labelled metabolites or biomass. Our results suggest that aerobic methanotrophs actively convert CH4 into complex organic compounds in Movile Cave and thus help to sustain a diverse community of microorganisms in this closed ecosystem.
Wiley - Tập 6 Số 2 - Trang 111-120 - 2004
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