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Petr Baldrian - One of the best experts on this subject based on the ideXlab platform.
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cellulose and hemicellulose decomposition by Forest Soil bacteria proceeds by the action of structurally variable enzymatic systems
Scientific Reports, 2016Co-Authors: Ruben Lopezmondejar, Daniela Zuhlke, Dorte Becher, Katharina Riedel, Petr BaldrianAbstract:Evidence shows that bacteria contribute actively to the decomposition of cellulose and hemicellulose in Forest Soil; however, their role in this process is still unclear. Here we performed the screening and identification of bacteria showing potential cellulolytic activity from litter and organic Soil of a temperate oak Forest. The genomes of three cellulolytic isolates previously described as abundant in this ecosystem were sequenced and their proteomes were characterized during the growth on plant biomass and on microcrystalline cellulose. Pedobacter and Mucilaginibacter showed complex enzymatic systems containing highly diverse carbohydrate-active enzymes for the degradation of cellulose and hemicellulose, which were functionally redundant for endoglucanases, β-glucosidases, endoxylanases, β-xylosidases, mannosidases and carbohydrate-binding modules. Luteibacter did not express any glycosyl hydrolases traditionally recognized as cellulases. Instead, cellulose decomposition was likely performed by an expressed GH23 family protein containing a cellulose-binding domain. Interestingly, the presence of plant lignocellulose as well as crystalline cellulose both trigger the production of a wide set of hydrolytic proteins including cellulases, hemicellulases and other glycosyl hydrolases. Our findings highlight the extensive and unexplored structural diversity of enzymatic systems in cellulolytic Soil bacteria and indicate the roles of multiple abundant bacterial taxa in the decomposition of cellulose and other plant polysaccharides.
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microbial activity in Forest Soil reflects the changes in ecosystem properties between summer and winter
Environmental Microbiology, 2016Co-Authors: Lucia žifcakova, Tomas Větrovský, Adina Howe, Petr BaldrianAbstract:Summary Understanding the ecology of coniferous Forests is very important because these environments represent globally largest carbon sinks. Metatranscriptomics, microbial community and enzyme analyses were combined to describe the detailed role of microbial taxa in the functioning of the Picea abies-dominated coniferous Forest Soil in two contrasting seasons. These seasons were the summer, representing the peak of plant photosynthetic activity, and late winter, after an extended period with no photosynthate input. The results show that microbial communities were characterized by a high activity of fungi especially in litter where their contribution to microbial transcription was over 50%. Differences in abundance between summer and winter were recorded for 26–33% of bacterial genera and < 15% of fungal genera, but the transcript profiles of fungi, archaea and most bacterial phyla were significantly different among seasons. Further, the seasonal differences were larger in Soil than in litter. Most importantly, fungal contribution to total microbial transcription in Soil decreased from 33% in summer to 16% in winter. In particular, the activity of the abundant ectomycorrhizal fungi was reduced in winter, which indicates that plant photosynthetic production was likely one of the major drivers of changes in the functioning of microbial communities in this coniferous Forest.
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production of extracellular enzymes and degradation of biopolymers by saprotrophic microfungi from the upper layers of Forest Soil
Plant and Soil, 2011Co-Authors: Petr Baldrian, Jana Vořiskova, Petra Dobiasova, Věra Merhautova, Ludmila Lisa, Vendula ValaskovaAbstract:Production of extracellular enzymes participating in the degradation of biopolymers was studied in 29 strains of nonbasidiomycetous microfungi isolated from Quercus petraea Forest Soil based on the frequency of occurrence. Most of the isolates were ascomycetes and belonged to the genera Acremonium, Alternaria, Cladosporium, Geomyces, Hypocrea, Myrothecium, Ochrocladosporium, and Penicillium (18 isolates), and two isolates were zygomycetes. Only six isolates showed phenol oxidation activity which was low and none of the strains were able to degrade humic acids. Approximately half of the strains were able to degrade cellulose and all but six degraded chitin. Most strains produced significant amounts of the cellulolytic enzymes cellobiohydrolase and β-glucosidase and the chitinolytic enzymes chitinase, chitobiosidase, and N-acetylglucosaminidase. The highest cellulase activities were found in Penicillium strains, and the highest activity of chitinolytic enzymes was found in Acremonium sp. The production of the hemicellulose-degrading enzymes α-galactosidase, β-galactosidase, and α-mannosidase was mostly low. The microfungal strains were able to produce significant growth on a range of 41–87, out of 95 simple C-containing substrates tested in a Biolog™ assay, monosaccharides being for all strains the most rapidly metabolized C-sources. Comparison with saprotrophic basidiomycetes from the same environment showed that microfungi have similar cellulolytic capabilities and higher chitinase activities which testifies for their active role in the decomposition of both lignocellulose and dead fungal biomass, important pools of Soil carbon.
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spatial variability of enzyme activities and microbial biomass in the upper layers of quercus petraea Forest Soil
Soil Biology & Biochemistry, 2008Co-Authors: Jaroslav Snajdr, Vendula Valaskova, Veˇra Merhautova, Jana Herinkova, Tomas Cajthaml, Petr BaldrianAbstract:Abstract Extracellular lignocellulose-degrading enzymes are responsible for the transformation of organic matter in hardwood Forest Soils. The spatial variability on a 12 × 12 m plot and vertical distribution (0–8 cm) of the ligninolytic enzymes laccase and Mn-peroxidase, the polysaccharide-specific hydrolytic enzymes endoglucanase, endoxylanase, cellobiohydrolase, 1,4-β-glucosidase, 1,4-β-xylosidase and 1,4-β- N -acetylglucosaminidase and the phosphorus-mineralizing acid phosphatase were studied in a Quercus petraea Forest Soil profile. Activities of all tested enzymes exhibited high spatial variability in the L and H horizons. Acid phosphatase and 1,4-β- N -acetylglucosaminidase exhibited low variability in both horizons, while the variability of Mn-peroxidase activity in the L horizon, and endoxylanase and cellobiohydrolase activities in the H horizon were very high. The L horizon contained 4× more microbial biomass (based on PLFA) and 7× fungal biomass (based on ergosterol content) than the H horizon. The L horizon also contained relatively more fungi-specific and less actinomycete-specific PLFA. There were no significant correlations between enzyme activities and total microbial biomass. In the L horizon cellulose and hemicellulose-degrading enzymes correlated with each other and also with 1,4-β- N -acetylglucosaminidase and acid phosphatase activities. Laccase, Mn-peroxidase and acid phosphatase activities correlated in the H horizon. The Soil profile showed a gradient of pH, organic carbon and humic compound content, microbial biomass and enzyme activities, all decreasing with Soil depth. Ligninolytic enzymes showed preferential localization in the upper part of the H horizon. Differences in enzyme activities were accompanied by differences in the microbial community composition where the relative amount of fungal biomass decreased and actinomycete biomass increased with Soil depth. The results also showed that the vertical gradients occur at a small scale: the upper and lower parts of the H horizon only 1 cm apart were significantly different with respect to seven out of nine activities, microbial biomass content and community composition.
Gerhard Rambold - One of the best experts on this subject based on the ideXlab platform.
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Insights into fungal communities colonizing the acarosphere in a Forest Soil habitat
Mycological Progress, 2018Co-Authors: Sebastian Werner, Derek Peršoh, Gerhard RamboldAbstract:Knowledge on the diversity and ecology of microfungi associated with Soil-dwelling mites is rather limited. To get insights into associations between the two highly diverse groups, we studied composition and potential function of mite-associated fungal communities occurring in Soil. Two different mite species living in temperate region pine Forest Soil were screened for associated fungi. The fungal community was assessed by restriction fragment length polymorphism (RFLP) analyses in a predatory ( Leptogamasus obesus ) and a predominantly saprobic ( Oppiella subpectinata ) mite species as well as in the organic Soil layer. Key fungi were identified by sequencing, and community composition was exemplarily compared between the RFLP and a 454 metabarcoding approach. Composition of the fungal communities differed between mite species and between mites and organic Soil layer. The mites were predominantly associated with Zygomycota, less frequently with Ascomycota, and rarely with Basidiomycota. The bulk Soil was colonized by roughly equal proportions of the three phyla. Fungal taxa being known to exhibit chitinolytic activity were predominantly restricted to mites. Compositional and functional differences between the communities suggest that mites represent a particular microhabitat for fungi, the “acarosphere.” This mobile habitat may contribute to nutrient cycling by combining fungal and animal decomposition activities and serve as vector for Soil-inhabiting fungi.
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Fungal guilds are evenly distributed along a vertical spruce Forest Soil profile while individual fungi show pronounced niche partitioning
Mycological Progress, 2018Co-Authors: Derek Peršoh, Nancy Stolle, Andreas Brachmann, Dominik Begerow, Gerhard RamboldAbstract:Saprotrophic and ectomycorrhizal (EcM) Forest fungi decompose organic matter and mobilize nutrients for host plants, respectively. Competition between the two guilds may cause the so-called Gadgil effect, i.e., decreased litter decomposition rates resulting in increased carbon storage in Soil. The Gadgil effect was supposed to even affect global climate, highlighting the necessity to understand fungal distribution and interactions in Soil. Searching for evidence of competition between saprotrophic and mycorrhizal fungi, we analyzed the distribution of fungi along a well-stratified vertical spruce Forest Soil profile in two seasons, i.e., autumn and the following spring. The different Soil strata (i.e., two mineral horizons and two organic layers) underneath the litter layer were colonized by distinct fungal communities, which included roughly consistent proportions of all fungal guilds and phyla at each time. However, the community composition changed quantitatively between the sampling dates. Along the vertical Soil profile, it differed mostly between the organic layers and the mineral Soil, which is supposed to be due to differences in the predominant energy sources (i.e., aboveground litter and rhizodeposition, respectively). Network analyses revealed co-occurrences (i.e., positive correlations of individual abundances) to outweigh mutual exclusions (i.e., negative correlations) between individual fungi in each Soil stratum and season. This also applied for interactions between saprotrophic and EcM fungi. Network analyses therefore provided no indications for a possible Gadgil effect. However, considering individual nutrient use efficiencies might refine insights from network analyses in future studies and facilitate linking community dynamics to ecosystem processes.
Stephane Dubé - One of the best experts on this subject based on the ideXlab platform.
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Biogeography and organic matter removal shape long-term effects of timber harvesting on Forest Soil microbial communities
The ISME Journal, 2017Co-Authors: Roland C Wilhelm, Erick Cardenas, Kendra R Maas, Hilary Leung, Larisa Mcneil, Shannon Berch, William Chapman, Graeme Hope, J M Kranabetter, Stephane DubéAbstract:The growing demand for renewable, carbon-neutral materials and energy is leading to intensified Forest land-use. The long-term ecological challenges associated with maintaining Soil fertility in managed Forests are not yet known, in part due to the complexity of Soil microbial communities and the heterogeneity of Forest Soils. This study determined the long-term effects of timber harvesting, accompanied by varied organic matter (OM) removal, on bacterial and fungal Soil populations in 11- to 17-year-old reForested coniferous plantations at 18 sites across North America. Analysis of highly replicated 16 S rRNA gene and ITS region pyrotag libraries and shotgun metagenomes demonstrated consistent changes in microbial communities in harvested plots that included the expansion of desiccation- and heat-tolerant organisms and decline in diversity of ectomycorrhizal fungi. However, the majority of taxa, including the most abundant and cosmopolitan groups, were unaffected by harvesting. Shifts in microbial populations that corresponded to increased temperature and Soil dryness were moderated by OM retention, which also selected for sub-populations of fungal decomposers. Biogeographical differences in the distribution of taxa as well as local edaphic and environmental conditions produced substantial variation in the effects of harvesting. This extensive molecular-based investigation of Forest Soil advances our understanding of Forest disturbance and lays the foundation for monitoring long-term impacts of timber harvesting.
Ralf Conrad - One of the best experts on this subject based on the ideXlab platform.
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Impact of short-term storage temperature on determination of microbial community composition and abundance in aerated Forest Soil and anoxic pond sediment samples
Systematic and Applied Microbiology, 2014Co-Authors: Franziska B. Brandt, Björn Breidenbach, Kristof Brenzinger, Ralf ConradAbstract:Sampling strategy is important for unbiased analysis of the characteristics of microbial communities in the environment. During field work it is not always possible to analyze fresh samples immediately or store them frozen. Therefore, the effect of short-term storage temperature was investigated on the abundance and composition of bacterial, archaeal and denitrifying communities in environmental samples from two different sampling sites. Oxic Forest Soil and anoxic pond sediment were investigated by measuring microbial abundance (DNA) and transcriptional activity (RNA). Prior to investigating the effect of storage temperature, samples were immediately analyzed, in order to represent the original situation in the habitat. The effect of storage temperature was then determined after 11 days at different low temperatures (room temperature, 4. °C, -22. °C and -80. °C). Community profiling using terminal restriction fragment length polymorphism (T-RFLP) showed no significant differences between the immediately analyzed reference sample and the samples stored at different incubation temperatures, both for DNA and RNA extracts. The abundance of microbial communities was determined using quantitative PCR and it also revealed a stable community size at all temperatures tested. By contrast, incubation at an elevated temperature (37. °C) resulted in changed bacterial community composition. In conclusion, short-term storage, even at room temperature, did not affect microbial community composition, abundance and transcriptional activity in aerated Forest Soil and anoxic pond sediment.
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molecular analyses of novel methanotrophic communities in Forest Soil that oxidize atmospheric methane
Applied and Environmental Microbiology, 2000Co-Authors: Thilo Henckel, Udo Jackel, Sylvia Schnell, Ralf ConradAbstract:Forest and other upland Soils are important sinks for atmospheric CH{sub 4}, consuming 20 to 60 Tg of CH{sub 4} per year. Consumption of atmospheric CH{sub 4} by Soil is a microbiological process. However, little is known about the methanotrophic bacterial community in Forest Soils. The authors measured vertical profiles of atmospheric CH{sub 4} oxidation rates in a German Forest Soil and characterized the methanotrophic populations by PCR and denaturing gradient gel electrophoresis (DGGE) with primer sets targeting the pmoA gene, coding for the {alpha} subunit of the particulate methane monooxygenase, and the small-subunit rRNA gene (SSU rDNA) of all life. The Forest Soil was a sink for atmospheric CH{sub 4} in situ and in vitro at all times. In winter, atmospheric CH{sub 4} was oxidized in a well-defined subsurface Soil layer, whereas in summer, the complete Soil core was active. The content of total extractable DNA was about 10-fold higher in summer than in winter. It decreased with Soil depth from about 40 to 1 {micro}g DNA per g (dry weight) of Soil. The PCR product concentration of SSU rDNA of all life was constant both in winter and in summer. However, the PCR product concentration of pmoA changedmore » with depth and season. pmoA was detected only in Soil layers with active CH{sub 4} oxidation, i.e., 6 to 16 cm deep in winter and throughout the Soil core in summer. The same methanotrophic populations were present in winter and summer. Layers with high CH{sub 4} consumption rates also exhibited more bands of pmoA in DGGE, indicating that high CH{sub 4} oxidation activity was positively correlated with the number of methanotrophic populations present. The pmoA sequences derived from excised DGGE bands were only distantly related to those of known methanotrophs, indicating the existence of unknown methanotrophs involved in atmospheric CH{sub 4} consumption.« less
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influence of an increased ph on the composition of the nitrate reducing microbial populations in an anaerobically incubated acidic Forest Soil
Systematic and Applied Microbiology, 1992Co-Authors: Martin Blosl, Ralf ConradAbstract:Summary Change of Soil pH greatly affects the rate and the percentual production of nitrite, NO, N 2 O, N 2 and NH 4 + from the reduction of nitrate. The pH effect may be due to a change in the composition of the nitrate-reducing bacterial community in Soil. The pH of slurries of an acidic (pH 4) Soil from the Bavarian Forest was increased to pH 7 by the addition of alkali and then incubated under anaerobic conditions for 30 h. Then, the Soil slurries were assayed for the most probable number (MPN) counts of nitrate-reducing bacteria and for the distribution of nitrate-respiring (i.e. reducing nitrate no nitrite), nitrate-ammonifying (i.e. reducing nitrate to ammonia), and denitrifying (i.e. reducing nitrate to N 2 ) bacteria among randomly isolated nitrate-reducing bacteria. As result, the MPN counts had increased by up to 3 orders of magnitude in the slurries adjusted to pH 7 compared to those left at pH 4. MPN counts of nitrate reducers at pH 7 were higher in complex versus defined mineral media. All (100%) of the nitrate reducers (n = 17) isolated at pH 4 had the properties of nitrate respirers. Most (86%) of the nitrate reducers (n = 163) isolated at pH 7 were also nitrate respirers, 15% were nitrate ammonifiers and 7% were denitrifiers. The results indicate that the metabolic types of nitrate reducers became more diverse upon neutralization of the acidic Forest Soil. However, all of the isolated nitrate reducers were able to produce small amounts of NO and N 2 O. All (100%) of a selection (n = 18) of isolated nitrate reducers were facultatively anaerobic and catalasepositive, most (72%) were Gram + and 39% formed spores.
Vendula Valaskova - One of the best experts on this subject based on the ideXlab platform.
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production of extracellular enzymes and degradation of biopolymers by saprotrophic microfungi from the upper layers of Forest Soil
Plant and Soil, 2011Co-Authors: Petr Baldrian, Jana Vořiskova, Petra Dobiasova, Věra Merhautova, Ludmila Lisa, Vendula ValaskovaAbstract:Production of extracellular enzymes participating in the degradation of biopolymers was studied in 29 strains of nonbasidiomycetous microfungi isolated from Quercus petraea Forest Soil based on the frequency of occurrence. Most of the isolates were ascomycetes and belonged to the genera Acremonium, Alternaria, Cladosporium, Geomyces, Hypocrea, Myrothecium, Ochrocladosporium, and Penicillium (18 isolates), and two isolates were zygomycetes. Only six isolates showed phenol oxidation activity which was low and none of the strains were able to degrade humic acids. Approximately half of the strains were able to degrade cellulose and all but six degraded chitin. Most strains produced significant amounts of the cellulolytic enzymes cellobiohydrolase and β-glucosidase and the chitinolytic enzymes chitinase, chitobiosidase, and N-acetylglucosaminidase. The highest cellulase activities were found in Penicillium strains, and the highest activity of chitinolytic enzymes was found in Acremonium sp. The production of the hemicellulose-degrading enzymes α-galactosidase, β-galactosidase, and α-mannosidase was mostly low. The microfungal strains were able to produce significant growth on a range of 41–87, out of 95 simple C-containing substrates tested in a Biolog™ assay, monosaccharides being for all strains the most rapidly metabolized C-sources. Comparison with saprotrophic basidiomycetes from the same environment showed that microfungi have similar cellulolytic capabilities and higher chitinase activities which testifies for their active role in the decomposition of both lignocellulose and dead fungal biomass, important pools of Soil carbon.
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spatial variability of enzyme activities and microbial biomass in the upper layers of quercus petraea Forest Soil
Soil Biology & Biochemistry, 2008Co-Authors: Jaroslav Snajdr, Vendula Valaskova, Veˇra Merhautova, Jana Herinkova, Tomas Cajthaml, Petr BaldrianAbstract:Abstract Extracellular lignocellulose-degrading enzymes are responsible for the transformation of organic matter in hardwood Forest Soils. The spatial variability on a 12 × 12 m plot and vertical distribution (0–8 cm) of the ligninolytic enzymes laccase and Mn-peroxidase, the polysaccharide-specific hydrolytic enzymes endoglucanase, endoxylanase, cellobiohydrolase, 1,4-β-glucosidase, 1,4-β-xylosidase and 1,4-β- N -acetylglucosaminidase and the phosphorus-mineralizing acid phosphatase were studied in a Quercus petraea Forest Soil profile. Activities of all tested enzymes exhibited high spatial variability in the L and H horizons. Acid phosphatase and 1,4-β- N -acetylglucosaminidase exhibited low variability in both horizons, while the variability of Mn-peroxidase activity in the L horizon, and endoxylanase and cellobiohydrolase activities in the H horizon were very high. The L horizon contained 4× more microbial biomass (based on PLFA) and 7× fungal biomass (based on ergosterol content) than the H horizon. The L horizon also contained relatively more fungi-specific and less actinomycete-specific PLFA. There were no significant correlations between enzyme activities and total microbial biomass. In the L horizon cellulose and hemicellulose-degrading enzymes correlated with each other and also with 1,4-β- N -acetylglucosaminidase and acid phosphatase activities. Laccase, Mn-peroxidase and acid phosphatase activities correlated in the H horizon. The Soil profile showed a gradient of pH, organic carbon and humic compound content, microbial biomass and enzyme activities, all decreasing with Soil depth. Ligninolytic enzymes showed preferential localization in the upper part of the H horizon. Differences in enzyme activities were accompanied by differences in the microbial community composition where the relative amount of fungal biomass decreased and actinomycete biomass increased with Soil depth. The results also showed that the vertical gradients occur at a small scale: the upper and lower parts of the H horizon only 1 cm apart were significantly different with respect to seven out of nine activities, microbial biomass content and community composition.