Wiley
Công bố khoa học tiêu biểu
Sắp xếp:
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
Vertical profiles of methanogenesis and methanogens in two contrasting acidic peatlands in central New York State, USA Summary Northern acidic peatlands are important sources of atmospheric methane, yet the methanogens in them are poorly characterized. We examined methanogenic activities and methanogen populations at different depths in two peatlands, McLean bog (MB) and Chicago bog (CB). Both have acidic (pH 3.5–4.5) peat soils, but the pH of the deeper layers of CB is near‐neutral, reflecting its previous existence as a neutral‐pH fen. Acetotrophic and hydrogenotrophic methanogenesis could be stimulated in upper samples from both bogs, and phylotypes of methanogens using H2 /CO2 (Methanomicrobiales ) or acetate (Methanosarcinales ) were identified in 16S rRNA gene clone libraries and by terminal restriction fragment length polymorphism (T‐RFLP) analyses using a novel primer/restriction enzyme set that we developed. Particularly dominant in the upper layers was a clade in the Methanomicrobiales , called E2 here and the R10 or fen group elsewhere, estimated by quantitative polymerase chain reaction to be present at ∼108 cells per gram of dry peat. Methanogenic activity was considerably lower in deeper samples from both bogs. The methanogen populations detected by T‐RFLP in deeper portions of MB were mainly E2 and the uncultured euryarchaeal rice cluster (RC)‐II group, whereas populations in the less acidic CB deep layers were considerably different, and included a Methanomicrobiales clade we call E1‐E1′, as well as RC‐I, RC‐II, marine benthic group D, and a new cluster that we call the subaqueous cluster. E2 was barely detectable in the deeper samples from CB, further evidence for the associations of most organisms in this group with acidic habitats.
Wiley - Tập 8 Số 8 - Trang 1428-1440 - 2006
Methanogen communities and <i>Bacteria</i> along an ecohydrological gradient in a northern raised bog complex Summary Mires forming an ecohydrological gradient from nutrient‐rich, groundwater‐fed mesotrophic and oligotrophic fens to a nutrient‐poor ombrotrophic bog were studied by comparing potential methane (CH4 ) production and methanogenic microbial communities. Methane production was measured from different depths of anoxic peat and methanogen communities were detected by detailed restriction fragment length polymorphism (RFLP) analysis of clone libraries, sequencing and phylogenetic analysis. Potential CH4 production changed along the ecohydrological gradient with the fens displaying much higher production than the ombrotrophic bog. Methanogen diversity also decreased along the gradient. The two fens had very similar diversity of methanogenic methyl‐coenzyme M reductase gene (mcrA ), but in the upper layer of the bog the methanogen diversity was strikingly lower, and only one type of mcrA sequence was retrieved. It was related to the Fen cluster, a group of novel methanogenic sequences found earlier in Finnish mires. Bacterial 16S rDNA sequences from the fens fell into at least nine phyla, but only four phyla were retrieved from the bog. The most common bacterial groups were Deltaproteobacteria , Verrucomicrobia and Acidobacteria .
Wiley - Tập 7 Số 10 - Trang 1547-1557 - 2005
Methanogenesis and methanogenic pathways in a peat from subarctic permafrost Summary Few studies have dealt so far with methanogenic pathways and populations in subarctic and arctic soils. We studied the effects of temperature on rates and pathways of CH4 production and on the relative abundance and structure of the archaeal community in a mildly acidic peat from a permafrost region in Siberia (67°N). We monitored the production of CH4 and CO2 over time and measured the consumption of Fe(II), ethanol and volatile fatty acids. All experiments were performed with and without specific inhibitors [2‐bromoethanesulfonate (BES) for methanogenesis and CH3 F for acetoclastic methanogenesis]. The optimum temperature for methanogenesis was between 26°C and 28°C [4.3 μmol CH4 (g dry weight)−1 day−1 ], but the activity was high even at 4°C [0.75 μmol CH4 (g dry weight)−1 day−1 ], constituting 17% of that at 27°C. The population structure of archaea was studied by terminal restriction fragment length polymorphism analysis and remained constant over a wide temperature range. Acetoclastic methanogenesis accounted for about 70% of the total methanogenesis. Most 16S rRNA gene sequences clustered with Methanosarcinales , correlating with the prevalence of acetoclastic methanogenesis. In addition, sequences clustering with Methanobacteriales were recovered. Fe reduction occurred in parallel to methanogenesis. At lower and higher temperatures Fe reduction was not affected by BES. Because butyrate was consumed during methanogenesis and accumulated when methanogenesis was inhibited (BES and CH3 F), it is proposed to serve as methanogenic precursor, providing acetate and H2 by syntrophic oxidation. In addition, ethanol and caproate occurred as intermediates. Because of thermodynamic constraints, homoacetogenesis could not compete with hydrogenotrophic methanogenesis.
Wiley - Tập 9 Số 4 - Trang 954-964 - 2007
Biogeography of wetland rice methanotrophs Summary We focused on the functional guild of methane oxidizing bacteria (MOB) as model organisms to get deeper insights into microbial biogeography. The pmoA gene was used as a functional and phylogenetic marker for MOB in two approaches: (i) a pmoA database (> 4000 sequences) was evaluated to obtain insights into MOB diversity in Italian rice paddies, and paddy fields worldwide. The results show a wide geographical distribution of pmoA genotypes that seem to be specifically adapted to paddy fields (e.g. Rice Paddy Cluster 1 and Rice Paddy Cluster 2). (ii) On the smaller geographical scale, we designed a factorial experiment including three different locations, two rice varieties and two habitats (soil and roots) within each of three rice fields. Multivariate analysis of terminal restriction fragment analysis profiles revealed different community patterns at the three field sites, located 10–20 km apart. Root samples were characterized by high abundance of type I MOB whereas the rice variety had no effect. With the agronomical practice being nearly identical, historical contingencies might be responsible for the field site differences. Considering a large reservoir of viable yet inactive MOB cells acting as a microbial seed bank, environmental conditions might have selected and activated a different subset at a time thereby shaping the community.
Wiley - Tập 12 Số 4 - Trang 862-872 - 2010
The active methanotrophic community in hydromorphic soils changes in response to changing methane concentration Summary Methanotrophic communities were studied in several periodically water‐saturated gleyic soils. When sampled, each soil had an oxic upper layer and consumed methane from the atmosphere (at 1.75 ppmv). In most gleyic soils the Km(app) values for methane were between 70 and 800 ppmv. These are higher than most values observed in dry upland soils, but lower than those measured in wetlands. Based on cultivation‐independent retrieval of the pmoA ‐gene and quantification of partial pmoA gene sequences, type II (Alphaproteobacteria ) methanotrophs of the genus Methylocystis spp. were abundant (> 107 pmoA target molecules per gram of dry soil). Type I (Gammaproteobacteria ) methanotrophs related to the genera Methylobacter and Methylocaldum /Methylococcus were detected in some soils. Six pmoA sequence types not closely related to sequences from cultivated methanotrophs were detected as well, indicating that diverse uncultivated methanotrophs were present. Three Gleysols were incubated under different mixing ratios of 13 C‐labelled methane to examine 13 C incorporation into phospholipid fatty acids (PLFAs). Phospholipid fatty acids typical of type II methanotrophs, 16:0 and 18:1ω7c, were labelled with 13 C in all soils after incubation under an atmosphere containing 30 ppmv of methane. Incubation under 500 ppmv of methane resulted in labelling of additional PLFAs besides 16:0 and 18:1ω7c, suggesting that the composition of the active methanotrophic community changed in response to increased methane supply. In two soils, 16:1 PLFAs typical of type I methanotrophs were strongly labelled after incubation under the high methane mixing ratio only. Type II methanotrophs are most likely responsible for atmospheric methane uptake in these soils, while type I methanotrophs become active when methane is produced in the soil.
Wiley - Tập 8 Số 2 - Trang 321-333 - 2006
Software platforms to facilitate reconstructing genome‐scale metabolic networks Summary System‐level analyses of microbial metabolism are facilitated by genome‐scale reconstructions of microbial biochemical networks. A reconstruction provides a structured representation of the biochemical transformations occurring within an organism, as well as the genes necessary to carry out these transformations, as determined by the annotated genome sequence and experimental data. Network reconstructions also serve as platforms for constraint‐based computational techniques, which facilitate biological studies in a variety of applications, including evaluation of network properties, metabolic engineering and drug discovery. Bottom‐up metabolic network reconstructions have been developed for dozens of organisms, but until recently, the pace of reconstruction has failed to keep up with advances in genome sequencing. To address this problem, a number of software platforms have been developed to automate parts of the reconstruction process, thereby alleviating much of the manual effort previously required. Here, we review four such platforms in the context of established guidelines for network reconstruction. While many steps of the reconstruction process have been successfully automated, some manual evaluation of the results is still required to ensure a high‐quality reconstruction. Widespread adoption of these platforms by the scientific community is underway and will be further enabled by exchangeable formats across platforms.
Wiley - Tập 16 Số 1 - Trang 49-59 - 2014
The Pel and Psl polysaccharides provide <i>Pseudomonas aeruginosa</i> structural redundancy within the biofilm matrix Summary Extracellular polysaccharides comprise a major component of the biofilm matrix. Many species that are adept at biofilm formation have the capacity to produce multiple types of polysaccharides. Pseudomonas aeruginosa produces at least three extracellular polysaccharides, alginate, Pel and Psl, that have been implicated in biofilm development. Non‐mucoid strains can use either Pel or Psl as the primary matrix structural polysaccharide. In this study, we evaluated a range of clinical and environmental P. aeruginosa isolates for their dependence on Pel and Psl for biofilm development. Mutational analysis demonstrates that Psl plays an important role in surface attachment for most isolates. However, there was significant strain‐to‐strain variability in the contribution of Pel and Psl to mature biofilm structure. This analysis led us to propose four classes of strains based upon their Pel and Psl functional and expression profiles. Our data also suggest that Pel and Psl can serve redundant functions as structural scaffolds in mature biofilms. We propose that redundancy could help preserve the capacity to produce a biofilm when exopolysaccharide genes are subjected to mutation. To test this, we used PAO1, a common lab strain that primarily utilizes Psl in the matrix. As expected, a psl mutant strain initially produced a poor biofilm. After extended cultivation, we demonstrate that this strain acquired mutations that upregulated expression of the Pel polysaccharide, demonstrating the utility of having a redundant scaffold exopolysaccharide. Collectively, our studies revealed both unique and redundant roles for two distinct biofilm exopolysaccharides.
Wiley - Tập 14 Số 8 - Trang 1913-1928 - 2012
Field‐based evidence for copper contamination induced changes of antibiotic resistance in agricultural soils Summary Bacterial resistance to antibiotics and heavy metals are frequently linked, suggesting that exposure to heavy metals might select for bacterial assemblages conferring resistance to antibiotics. However, there is a lack of clear evidence for the heavy metal‐induced changes of antibiotic resistance in a long‐term basis. Here, we used high‐capacity quantitative PCR array to investigate the responses of a broad spectrum of antibiotic resistance genes (ARGs) to 4–5 year copper contamination (0–800 mg kg−1 ) in two contrasting agricultural soils. In total, 157 and 149 unique ARGs were detected in the red and fluvo‐aquic soil, respectively, with multidrug and β‐ lactam as the most dominant ARG types. The highest diversity and abundance of ARGs were observed in medium copper concentrations (100–200 mg kg−1 ) of the red soil and in high copper concentrations (400–800 mg kg−1 ) of the fluvo‐aquic soil. The abundances of total ARGs and several ARG types had significantly positive correlations with mobile genetic elements (MGEs), suggesting mobility potential of ARGs in copper‐contaminated soils. Network analysis revealed significant co‐occurrence patterns between ARGs and microbial taxa, indicating strong associations between ARGs and bacterial communities. Structural equation models showed that the significant impacts of copper contamination on ARG patterns were mainly driven by changes in bacterial community compositions and MGEs. Our results provide field‐based evidence that long‐term Cu contamination significantly changed the diversity, abundance and mobility potential of environmental antibiotic resistance, and caution the un‐perceived risk of the ARG dissemination in heavy metal polluted environments.
Wiley - Tập 18 Số 11 - Trang 3896-3909 - 2016
The human gut microbiome in health: establishment and resilience of microbiota over a lifetime Summary With technological advances in culture‐independent molecular methods, we are uncovering a new facet of our natural history by accounting for the vast diversity of microbial life which colonizes the human body. The human microbiome contributes functional genes and metabolites which affect human physiology and are, therefore, considered an important factor for maintaining health. Much has been described in the past decade based primarily on 16S rRNA gene amplicon sequencing regarding the diversity, structure, stability and dynamics of human microbiota in their various body habitats, most notably within the gastrointestinal tract (GIT). Relatively high levels of variation have been described across different stages of life and geographical locations for the GIT microbiome. These observations may prove helpful for the future contextualization of patterns in other body habitats especially in relation to identifying generalizable trends over human lifetime. Given the large degree of complexity and variability, a key challenge will be how to define baseline healthy microbiomes and how to identify features which reflect deviations therefrom in the future. In this context, metagenomics and functional omics will likely play a central role as they will allow resolution of microbiome‐conferred functionalities associated with health. Such information will be vital for formulating therapeutic interventions aimed at managing microbiota‐mediated health particularly in the GIT over the course of a human lifetime.
Wiley - Tập 18 Số 7 - Trang 2103-2116 - 2016
Tổng số: 139
- 1
- 2
- 3
- 4
- 5
- 6
- 14