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- Bacteria (3)
- Nitrogen (3)
- Stable isotope probing (3)
- Succession (3)
- Basidiomycetes (2)
- Fourier transform infrared - attenuated total reflexion (FTIR-ATR) spectroscopy (2)
- Fungal decay (2)
- Fungi (2)
- IRMS (2)
- Methane oxidation (2)
Nitrogen sources of oligoporus placenta and trametes versicolor evaluated in a 2³ experimental plan
(2012)
Four full-factorial 2³ experimental plans were applied to evaluate the nitrogen (N) sources of Oligoporus placenta and Trametes versicolor and their interaction with the atmospheric N2-assimilating bacterium Beijerinckia acida. The effects of N from peptone, of sapwood and of N from gaseous N2 on fungal, bacterial and fungal–bacterial activity were investigated. The activities were determined by quantification of biomass, formation of CO2, consumption of O2 and laccase activity. The significance of each effect was tested according to t-test recommendation.
The activity of both fungi was enhanced by peptone rather than sapwood or gaseous N2. Nevertheless, comparative studies under an N2-free gas mixture as well as under air revealed that the presence of N2 affected bacterial growth and bacterial–fungal cocultivations. Elemental analysis isotope ratio mass spectrometry (IRMS) of the bacterial and fungal biomass enabled estimation of N transfer and underlined gaseous N2 as requisite for fungal–bacterial interactions. Combining full-factorial experimental plans with an analytical set-up comprising gas chromatography, IRMS and enzymatic activity allowed synergistic effects to be revealed, fungal N sources to be traced, and symbiotic fungal–bacterial interactions to be investigated.
The main wood degraders in aerobic terrestrial ecosystems belong to the white- and brown-rot fungi, where their biomass can be created on wood decay only. However, total sulfur (S) concentration in wood is very low and only little is known about the different sulfur compounds in wood today. Sulfur-starved brown-rot fungi Gloeophyllum trabeum and Oligoporus placenta were incubated on sterilized pine wood blocks whereas Lentinus cyathiformis and the white-rot fungi Trametes versicolor were incubated on sterilized beech wood blocks. After 19 weeks of incubation, the S oxidation status was analyzed in wood, in degraded wood, and in biomass of wood-degrading fungi by synchrotron based S K-edge XANES, and total S and sulfate were quantified. Total sulfur and sulfate content in pine wood blocks were approximately 50 and 1 µg g-1, respectively, while in beech wood approximately 100 and 20 µg g-1 were found, respectively. Sulfur in beech was dominated by sulfate-esters. In contrast, pine wood also contained larger amounts of reduced S. Three out of four selected fungi caused a reduction of the S oxidation state in wood from oxidized S (sulfate-ester, sulfate) to intermediate S (sulfonate, sulfoxide) or reduced S (thiols, e.g., proteins, peptides, enzyme cofactors). Only O. placenta shifted thiol to sulfonate. Growth experiments of these fungi on selective minimal media showed that in particular cysteine (thiol), sulfonates, and sulfate enhanced total mycelium growth. Consequently, wood-degrading fungi were able to utilize a large variety of different wood S sources for growth but preferentially transformed in vivo sulfate-esters and thiol into biomass structures.
Material performance testing of wood-plastic composites (WPC) requires adequate and time-efficient evaluation of the resistance against fungal colonisation and decay. This study investigates the effects of weathering on WPCs and subsequent material degradation by fungi. Weathering using UV radiation, water spray and repeated frost incidents caused micro- and macro-cracks. Fourier transform infrared spectroscopy (FTIR) demonstrated delignification of wood particles at the weathered WPC surface. Despite of increased surface area, accessibility for fungal hyphae and moisture content, weathering enhanced mass loss due to fungal decay only subtly but not significantly. These potentially enhancing effects for fungal decay are assumed to be outbalanced by delignification due to photo-oxidation and leaching of degradation products resulting in loss of nutrient sources essential for fungal growth.
As a glacier retreats, it leaves behind it a forefield that has a natural gradient of soil formation age. We systematically sampled the Damma glacier forefield (Switzerland) along a temporal gradient of soils deglaciated between 1956 and 2002. A significant change in organic carbon content, sulfate concentration, pH, water and nucleic acid content was observed along the forefield chronosequence. Based on 16S rRNA gene based fingerprinting, the structure of the bacterial community also shifted along the forefield. Shifts in the structure of the bacterial community were significantly correlated to changes of pH, soil water content and soil age. To test the impacts of an array of environmental variables including soil age, soil water content, and different anions on the structure of the bacterial community we incubated different glacier forefield soils under specific treatment conditions for 30 days at 25 °C. The incubation of recently deglaciated soils resulted into an increase of bacteria from the family Methylocystaceae and from the class Betaproteobacteria while the community composition from matured soil changed to a lesser extent. The total nitrogen concentration in matured soil doubled during incubation, whereas the nitrogen concentrations in recently deglaciated soil stayed constant. This suggested that the microbial ecosystem functioned differently in the mature versus the recently deglaciated soils. Only soil age and soil water content could be singled out as having significant effects on the structure and composition of the bacterial community, despite the fact that bacterial communities in glacier forefields are exposed to other steep environmental gradients.
Methanotrophs in the rhizosphere of rice field ecosystems attenuate the emissions of CH4 into the atmosphere and thus play an important role for the global cycle of this greenhouse gas. Therefore, we measured the activity and composition of the methanotrophic community in the rhizosphere of rice microcosms. Methane oxidation was determined by measuring the CH4 flux in the presence and absence of difluoromethane as a specific inhibitor for methane oxidation. Methane oxidation started on day 24 and reached the maximum on day 32 after transplantation. The total methanotrophic community was analysed by terminal restriction fragment length polymorphism (T-RFLP) and cloning/sequencing of the pmoA gene, which encodes a subunit of particulate methane monooxygenase. The metabolically active methanotrophic community was analysed by stable isotope probing of microbial phospholipid fatty acids (PLFA-SIP) using 13C-labelled CH4 directly added to the rhizospheric region. Rhizospheric soil and root samples were collected after exposure to 13CH4 for 8 and 18 days. Both T-RFLP/cloning and PLFA-SIP approaches showed that type I and type II methanotrophic populations changed over time with respect to activity and population size in the rhizospheric soil and on the rice roots. However, type I methanotrophs were more active than type II methanotrophs at both time points indicating they were of particular importance in the rhizosphere. PLFA-SIP showed that the active methanotrophic populations exhibit a pronounced spatial and temporal variation in rice microcosms.
Most of the methane (CH4) emission from rice fields is derived from plant photosynthates,
which are converted to CH4. Rice cluster I (RC-1) archaea colonizing the
rhizosphere were found to be the methanogens responsible for this process. Hence, RC-1
methanogens seem to play a crucial role in emission of the greenhouse gas CH4. We
determined the community composition and activity of methanogens colonizing the
roots of eight different rice cultivars after growth on both Italian rice soil and river bank
soil, which contained different communities of methanogenic archaea. The community
composition was analyzed by terminal restriction fragment length polymorphism and
cloning/sequencing of the archaeal 16S rRNA gene and the mcrA gene coding for a
subunit of the methyl coenzyme M reductase. When grown on rice field soil, the
methanogenic community of the different rice cultivars was always dominated by RC-1
methanogens. In contrast, roots were colonized by Methanomicrobiales when grown on
river bank soil, in which RC-1 methanogens were initially not detectable. Roots
colonized with Methanomicrobiales compared with RC-1 exhibited lower CH4 production
and CH4 emission rates. The results show that the type of methanogens colonizing
rice roots has a potentially important impact on the global CH4 cycle.
Bacterial community succession corresponds to changes in the phylogenetic identity, growth-response time and rRNA operon (rrn) copy number of culturable populations. To test this hypothesis, we compared the bacterial fractions culturable from the oxic zone of flooded, unplanted paddy soil microcosms after 1-day (early succession) and 70-day (late succession) incubation periods. The proportion of bacteria that was cultivable on solid media corresponded for early and late succession to 3740% and 3135% of total DAPI cell counts, which were 7.40 (±0.36) × 108 and 5.54 (±0.28) × 108 cells per gram of dry soil, respectively. In colony-forming curve analysis, late successional bacteria showed a significant delay in their growth response compared with those from early succession. A total of 59 early successional isolates grouped into 16 species-level clusters (SLC) plus three Bacilli-like SLC, while 66 late successional isolates formed 25 SLC plus five Bacilli-like SLC. Except Bacilli-like spp., isolates from early succession always belonged to different SLC than those from late succession. Betaproteobacteria and Gammaproteobacteria were typical of the early stage, while Alphaproteobacteria and Actinobacteria prevailed in late succession. Considering all SLC except those assigned to Bacilli, growth-response time and rrn copy number were significantly correlated with successional stage. Isolates of most early successional SLC (14 of 16) formed visible colonies within 1 (11 SLC) or 2 days (three SLC) and contained = 4 rrn copies. In contrast, isolates of late successional SLC (23 of 25) formed visible colonies within 2 days (four SLC) or, in most cases, only within 315 days (19 SLC) and contained = 2 rrn copies. Regardless of whether isolated from early or late succession, Bacilli-like isolates always showed a colony-forming time of 2 days and had 911 rrn copies.
Emissions of the greenhouse gas CH4, which is often produced in contaminated aquifers, are reduced or eliminated by microbial CH4 oxidation in the overlying vadose zone. The aim of this field study was to estimate kinetic parameters and isotope fractionation factors for CH4 oxidation in situ in the vadose zone above a methanogenic aquifer in Studen, Switzerland, and to characterize the involved methanotrophic communities. To quantify kinetic parameters, several field tests, so-called gas push-pull tests (GPPTs), with CH4 injection concentrations ranging from 17 to 80 mL L-1 were performed. An apparent Vmax of 0.70 ± 0.15 mmol CH4 (L soil air)-1 h-1 and an apparent Km of 0.28 ± 0.09 mmol CH4 (L soil air)-1 was estimated for CH4 oxidation at 2.7 m depth, close to the groundwater table. At 1.1 m depth, Km (0.13 ± 0.02 mmol CH4 (L soil air)-1) was in a similar range, but Vmax (0.076 ± 0.006 mmol CH4 (L soil air)-1 h-1) was an order of magnitude lower. At 2.7 m, apparent first-order rate constants determined from a CH4 gas profile (1.9 h-1) and from a single GPPT (2.0 ± 0.03 h-1) were in good agreement. Above the groundwater table, a Vmax much higher than the in situ CH4 oxidation rate prior to GPPTs indicated a high buffer capacity for CH4. At both depths, known methanotrophic species affiliated with Methylosarcina and Methylocystis were detected by cloning and sequencing. Apparent stable carbon isotope fractionation factors a for CH4 oxidation determined during GPPTs ranged from 1.006 to 1.032. Variability was likely due to differences in methanotrophic activity and CH4 availability leading to different degrees of mass transfer limitation. This complicates the use of stable isotopes as an independent quantification method.
Methane-oxidizing bacteria (MOB) in soil are not only controlled by their main substrates, methane and oxygen, but also by nitrogen availability. We compared an unfertilized control with a urea-fertilized treatment and applied RNA-stable-isotope-probing to follow activity changes upon fertilization as closely as possible. Nitrogen fertilization of an Italian rice field soil increased the CH4 oxidation rates sevenfold. In the fertilized treatment, isopycnic separation of 13C-enriched RNA became possible after 7 days when 300 µmol 13CH4 gdry soil-1 had been consumed. Terminal-restriction fragment length polymorphism (T-RFLP) fingerprints and clone libraries documented that the type I methanotrophic genera Methylomicrobium and Methylocaldum assimilated 13CH4 nearly exclusively. Although previous studies had shown that the same soil contains a much larger diversity of MOB, including both type I and type II, nitrogen fertilization apparently activated only a small subset of the overall diversity of MOB, type I MOB in particular.
Methanotrophs in the rhizosphere play an important role in global climate change since they attenuate methane emission from rice field ecosystems into the atmosphere. Most of the CH4 is emitted via transport through the plant gas vascular system. We used this transport for stable isotope probing (SIP) of the methanotrophs in the rhizosphere under field conditions and pulse-labelled rice plants in a Chinese rice field with CH4 (99% 13C) for 7 days. The rate of 13CH4 loss rate during 13C application was comparable to the CH4 oxidation rate measured by the difluoromethane inhibition technique. The methanotrophic communities on the roots and in the rhizospheric soil were analyzed by terminal-restriction fragment length polymorphism (T-RFLP), cloning and sequencing of the particulate methane monooxygenase (pmoA) gene. Populations of type I methanotrophs were larger than those of type II. Both methane oxidation rates and composition of methanotrophic communities suggested that there was little difference between urea-fertilized and unfertilized fields. SIP of phospholipid fatty acids (PLFA-SIP) and rRNA (RNA-SIP) were used to analyze the metabolically active methanotrophic community in rhizospheric soil. PLFA of type I compared with type II methanotrophs was labelled more strongly with 13C, reaching a maximum of 6.8 atom-% . T-RFLP analysis and cloning/sequencing of 16S rRNA genes showed that methanotrophs, especially of type I, were slightly enriched in the 'heavy' fractions. Our results indicate that CH4 oxidation in the rice rhizosphere under in situ conditions is mainly due to type I methanotrophs.