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PubMed2006

Control of microbial communities by the macrofauna: a sensitive interaction in the context of extreme summer temperatures?

Climate models predict an increasing frequency of extremely hot summer events in the northern hemisphere for the near future. We hypothesised that microbial grazing by the metazoan macrofauna is an interaction that becomes unbalanced at high temperatures due to the different development of the grazing rates of the metazoans and the growth rates of the microbial community with increasing temperature. In order to test this hypothesis, we performed grazing experiments in which we measured the impact of increasing temperatures on the development of the grazing rates of riverine mussels in relation to the growth rates of a unicellular prey community (a natural heterotrophic flagellate community from a large river). In a first experimental series using Corbicula fluminea as a grazer and under the addition of a carbon source (yeast extract), the increase of the prey's growth rates was considerably stronger than that of the predator's grazing rates when temperatures were increased from 19 to over 25 degrees C. This was also the outcome when the mussels had been acclimatized to warm temperatures. Hereafter, specific experiments with natural river water at temperatures of 25 and 30 degrees C were performed. Again, a strong decrease of the mussels' grazing rates in relation to the flagellate growth rates with increasing temperature occurred for two mussel species (C. fluminea and Dreissena polymorpha). When performing the same experiment using a benthic microbial predator community (biofilms dominated by ciliates) instead of the benthic mussels, an increase of the grazing rates relative to the growth rates with temperature could be observed. Our data suggest that predator-prey interactions (between metazoans and microbes) that are balanced at moderate temperatures could become unbalanced at high temperatures. This could have significant effects on the structure and function of microbial communities in light of the predicted increasing frequency of summer heat waves.

Animals↗

PubMed1999

Influence of an Elevated Atmospheric CO2 Content on Soil and Rhizosphere Bacterial Communities Beneath Lolium perenne and Trifolium repens under Field Conditions.

> Abstract The increase in atmospheric CO2 content alters C3 plant photosynthetic rate, leading to changes in rhizodeposition and other root activities. This may influence the activity, the biomass, and the structure of soil and rhizosphere microbial communities and therefore the nutrient cycling rates and the plant growth. The present paper focuses on bacterial numbers and on community structure. The rhizospheres of two grassland plants, Lolium perenne (ryegrass) and Trifolium repens (white clover), were divided into three fractions: the bulk soil, the rhizospheric soil, and the rhizoplane-endorhizosphere. The elevated atmospheric CO2 content increased the most probable numbers of heterotrophic bacteria in the rhizosphere of L. perenne. However, this effect lasted only at the beginning of the vegetation period for T. repens. Community structure was assessed after isolation of DNA, PCR amplification, and construction of cloned 16S rDNA libraries. Amplified ribosomal DNA restriction analysis (ARDRA) and colony hybridization with an oligonucleotide probe designed to detect Pseudomonas spp. showed under elevated atmospheric CO2 content an increased dominance of pseudomonads in the rhizosphere of L. perenne and a decreased dominance in the rhizosphere of T. repens. This work provides evidence for a CO2-induced alteration in the structure of the rhizosphere bacterial populations, suggesting a possible alteration of the plant-growth-promoting-rhizobacterial (PGPR) effect.http://link.springer-ny.com/link/service/journals/00248/bibs/38n1p39.html

Journal Article↗

PubMed2004

[Preliminary application of PCR-DGGE to analyzing microbial diversity in biofilters treating air loaded with ammonia].

As a new DNA fingerprinting technique, denaturing gradient gel electrophoresis (DGGE) can be used to analyze the microbial diversity in different environmental samples. Three biofilters treating air loaded with ammonia will be studied with respect to microbial diversity by applying cultivation-independent molecular methods DGGE. The principal objectives of this paper include the development and application of a suitable set of molecular tools to deliver information about the possible microbial community changes within carriers during treatment of ammonia-contaminated gas. Carriers were sampled at different time during operation of biofilters. After extraction and purification of the genomic DNA, the 16S rRNA genes (V3 region) were amplified by using the specific primers. These amplified DNA fragments were then separated by paralleled DGGE. The profile of DGGE showed that the same carrier at different time had the different bands' patterns. The structural diversity of the microbial community was examined by the Shannon index of general diversity H. Shannon indexes of three kinds of carriers all showed a decrease with time, which had a similar trend to NH3 removal efficiency.

Air Pollutants↗

PubMed1997

Population structure and physiological changes within a hot spring microbial mat community following disturbance.

The influence of disturbance on a hot spring cyanobacterial mat community was investigated by physically removing the top 3.0 mm, which included the entire cyanobacterial layer. Changes in 16S rRNA-defined populations were monitored by denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA gene segments. Some previously absent cyanobacterial populations colonized the disturbed areas, while some populations which were present before the disturbance remained absent for up to 40 days. Changes in physiological activity were measured by oxygen microelectrode analyses and by 14CO2 incorporation into cyanobacterial molecular components. These investigations indicated substantial differences between the disturbed and undisturbed mats, including an unexplained light-induced oxygen consumption in the freshly exposed mat, increased carbon partitioning by phototrophs into growth-related macromolecules, bimodal vertical photosynthesis profiles, and delayed recovery of respiration relative to photosynthesis.

Cyanobacteria↗

PubMed2005

Stable isotope probing analysis of the influence of liming on root exudate utilization by soil microorganisms.

Rhizosphere microorganisms play an important role in soil carbon flow, through turnover of root exudates, but there is little information on which organisms are actively involved or on the influence of environmental conditions on active communities. In this study, a 13CO2 pulse labelling field experiment was performed in an upland grassland soil, followed by RNA-stable isotope probing (SIP) analysis, to determine the effect of liming on the structure of the rhizosphere microbial community metabolizing root exudates. The lower limit of detection for SIP was determined in soil samples inoculated with a range of concentrations of 13C-labelled Pseudomonas fluorescens and was found to lie between 10(5) and 10(6) cells per gram of soil. The technique was capable of detecting microbial communities actively assimilating root exudates derived from recent photo-assimilate in the field. Denaturing gradient gel electrophoresis (DGGE) profiles of bacteria, archaea and fungi derived from fractions obtained from caesium trifluoroacetate (CsTFA) density gradient ultracentrifugation indicated that active communities in limed soils were more complex than those in unlimed soils and were more active in utilization of recently exuded 13C compounds. In limed soils, the majority of the community detected by standard RNA-DGGE analysis appeared to be utilizing root exudates. In unlimed soils, DGGE profiles from 12C and 13C RNA fractions differed, suggesting that a proportion of the active community was utilizing other sources of organic carbon. These differences may reflect differences in the amount of root exudation under the different conditions.

Bacteria↗

PubMed2006

Biodegradability of imidazolium and pyridinium ionic liquids by an activated sludge microbial community.

Ionic liquids (ILs) are novel organic salts that have enormous potential for industrial use as green replacements for harmful volatile organic solvents. Varying the cationic components can alter the chemical and physical properties of ILs, including solubility, to suit a variety of industrial processes. However, to complement designer engineering, it is crucial to proactively characterize the biological impacts of new chemicals, in order to fully define them as environmentally friendly. Before introduction of ILs into the environment, we performed an analysis of the biodegradability of six ILs by activated sludge microorganisms collected from the South Bend, Indiana wastewater treatment plant. We examined biodegradability of 1-butyl, 1-hexyl and 1-octyl derivatives of 3-methyl-imidazolium and 3-methyl-pyridinium bromide compounds using the standard Organisation for Economic Cooperation and Development dissolved organic carbon Die-Away Test, changes in total dissolved nitrogen concentrations, and 1H-nuclear magnetic resonance analysis of initial and final chemical structures. Further, we examined microbial community profiles throughout the incubation period using denaturing gradient gel electrophoresis (DNA-PCR-DGGE). Our results suggest that hexyl and octyl substituted pyridinium-based ILs can be fully mineralized, but that imidazolium-based ILs are only partially mineralized. Butyl substituted ILs with either cation, were not biodegradable. Biodegradation rates also increase with longer alkyl chain length, which may be related to enhanced selection of a microbial community. Finally, DGGE analysis suggests that certain microorganisms are enriched by ILs used as a carbon source. Based on these results, we suggest that further IL design and synthesis include pyridinium cations and longer alkyl substitutions for rapid biodegradability.

Electrophoresis↗

PubMed2025

Spatial Metabolomics Reveals the Role of Penicillic Acid in Cheese Rind Microbiome Disruption by a Spoilage Fungus.

Microbial interactions in cheese rinds influence community structure, food safety, and product quality. But the chemical mechanisms that mediate microbial interactions in cheeses and other fermented foods are generally not known. Here, we investigate how the spoilage mold Aspergillus westerdijkiae chemically inhibits beneficial cheese-rind bacteria using a combination of omics technologies. In cheese rind community and co-culture experiments, A. westerdijkiae strongly inhibited most cheese rind community members. In co-culture with Staphylococcus equorum, A. westerdijkiae strongly affected bacterial gene expression, including upregulation of a putative bceAB gene cluster that is associated with resistance to antimicrobial compounds in other bacteria. Mass spectrometry imaging (MSI) revealed spatially localized production of secondary metabolites, including penicillic acid and ochratoxin B at the fungal-bacterial interface. Integration of LC-MS/MS and genome annotations confirmed the presence of additional bioactive metabolites, such as notoamides and circumdatins. Fungal metabolic responses varied by bacterial partner, suggesting species-specific chemical strategies. Notably, penicillic acid levels increased 2.5-fold during interaction with Brachybacterium, and experiments with purified penicillic acid showed inhibition of a range of cheese rind bacteria. These findings show that A. westerdijkiae deploys a context-dependent arsenal of mycotoxins and other metabolites, disrupting microbial community assembly in cheese rinds.

Aspergillus westerdijkiae↗

PubMed2006

[Effects of hydraulic retention time (HRT) on nitrification performance and microbial community of conventional activated sludge (CAS)].

A conventional activated sludge system was used to treat the ammonium-bearing inorganic wastewater for 260 days under decreased HRTs. When treating 500 mg x L(-1) NH4+ -N wastewater, over 98% ammonia removal could be obtained at HRT > or =20 h. Sharp washout of biomass occurred when HRT was further decreased, resulting in the accumulation of ammonium and nitrite. Changes in the community structure were monitored by microbial quinone and conventional analytical methods. Quinone profiles indicated that ammonia-oxidizing bacteria (AOB) in beta-Protevbacteria and Nitrobacteria in alpha-Proteobacteria were the predominant species to oxidize ammonia and nitrite, respectively. The number of AOB decreased with the reduction of biomass in bioreactor, while that of nitrite-oxidizing bacteria (NOB) changed little and fluctuated at 10(5) CFU x L(-1)

Biodiversity↗

PubMed1998

In situ gene expression in mixed-culture biofilms: evidence of metabolic interactions between community members.

Microbial communities growing in laboratory-based flow chambers were investigated in order to study compartmentalization of specific gene expression. Among the community members studied, the focus was in particular on Pseudomonas putida and a strain of an Acinetobacter sp., and the genes studied are involved in the biodegradation of toluene and related aromatic compounds. The upper-pathway promoter (Pu) and the meta-pathway promoter (Pm) from the TOL plasmid were fused independently to the gene coding for the green fluorescent protein (GFP), and expression from these promoters was studied in P. putida, which was a dominant community member. Biofilms were cultured in flow chambers, which in combination with scanning confocal laser microscopy allowed direct monitoring of promoter activity with single-cell spatial resolution. Expression from the Pu promoter was homogeneously induced by benzyl alcohol in both community and pure-culture biofilms, while the Pm promoter was induced in the mixed community but not in a pure-culture biofilm. By sequentially adding community members, induction of Pm was shown to be a consequence of direct metabolic interactions between an Acinetobacter species and P. putida. Furthermore, in fixed biofilm samples organism identity was determined and gene expression was visualized at the same time by combining GFP expression with in situ hybridization with fluorescence-labeled 16S rRNA targeting probes. This combination of techniques is a powerful approach for investigating structure-function relationships in microbial communities.

Acinetobacter↗

PubMed2006

Use of multiplex terminal restriction fragment length polymorphism for rapid and simultaneous analysis of different components of the soil microbial community.

A multiplex terminal restriction fragment length polymorphism (M-TRFLP) fingerprinting method was developed and validated for simultaneous analysis of the diversity and community structure of two or more microbial taxa (up to four taxa). The reproducibility and robustness of the method were examined using soil samples collected from different habitats. DNA was PCR amplified separately from soil samples using individual taxon-specific primers for bacteria, archaea, and fungi. The same samples were also subjected to a multiplex PCR with the primers for all three taxa. The terminal restriction fragment length polymorphism profiles generated for the two sets of PCR products were almost identical not only in terms of the presence of peaks but also in terms of the relative peak intensity. The M-TRFLP method was then used to investigate rhizosphere bacterial, fungal, and rhizobial/agrobacterial communities associated with the dwarf shrub Calluna vulgaris growing in either open moorland, a mature pine forest, or a transition zone between these two habitats containing naturally regenerating pine trees. Rhizosphere microbial communities associated with Vaccinium myrtillus collected from the native pine forest were also investigated. In this study, individual PCR products from the three taxa were also pooled before restriction digestion and fragment size analysis. The terminal restriction fragment length polymorphism profiles obtained with PCR products amplified individually and with multiplexed and pooled PCR products were found to be consistent with each other in terms of the number, position, and relative intensity of peaks. The results presented here confirm that M-TRFLP analysis is a highly reproducible and robust molecular tool for simultaneous investigation of multiple taxa, which allows more complete and higher resolution of microbial communities to be obtained more rapidly and economically.

Archaea↗

PubMed2002

Community structure and function in prokaryotic marine plankton.

Molecular biodiversity studies of microbial communities have provided invaluable information on the existence of heretofore unknown organisms and on community composition. Cloning and 'fingerprinting' techniques have been used many times to study prokaryote community composition of marine plankton. There are still many opportunities for new discoveries in this area, but the results have also opened new questions about the activities of these organisms and their function, going beyond just listing taxa or counting organisms. Rarely can the broad function be inferred from phylogenetic position alone (e.g. cyanobacteria). The recent discovery of abundant non-cyanobacterial marine phototrophs points to our inability to link phylogenetic position with function in a detailed way. One approach we have found fruitful is to combine fluorescence in situ hybridization with microautoradiography, a technique dubbed STARFISH. A recent application has shown that ubiquitous archaea from the deep sea, phylogenetically related to extreme thermophiles, are active in the uptake of amino acids from ambient (nanomolar) concentrations. This suggests the group is at least partly heterotrophic and able to compete successfully with bacteria for nutrients. Other as-yet uncultivated groups are also amenable to similar studies.

Animals↗

PubMed2000

Quantification of biofilm structures by the novel computer program COMSTAT.

The structural organization of four microbial communities was analysed by a novel computer program, COMSTAT, which comprises ten features for quantifying three-dimensional biofilm image stacks. Monospecies biofilms of each of the four bacteria, Pseudomonas: putida, P. aureofaciens, P. fluorescens and P. aeruginosa, tagged with the green fluorescent protein (GFP) were grown in flow chambers with a defined minimal medium as substrate. Analysis by the COMSTAT program of four variables describing biofilm structure - mean thickness, roughness, substratum coverage and surface to volume ratio - showed that the four Pseudomonas: strains represent different modes of biofilm growth. P. putida had a unique developmental pattern starting with single cells on the substratum growing into micro-colonies, which were eventually succeeded by long filaments and elongated cell clusters. P. aeruginosa colonized the entire substratum, and formed flat, uniform biofilms. P. aureofaciens resembled P. aeruginosa, but had a stronger tendency to form micro-colonies. Finally, the biofilm structures of P. fluorescens had a phenotype intermediate between those of P. putida and P. aureofaciens. Analysis of biofilms of P. aureofaciens growing on 0.03 mM, 0.1 mM or 0.5 mM citrate minimal media showed that mean biofilm thickness increased with increasing citrate concentration. Moreover, biofilm roughness increased with lower citrate concentrations, whereas surface to volume ratio increased with higher citrate concentrations.

Biofilms↗

PubMed2003

In situ growth of the novel SM1 euryarchaeon from a string-of-pearls-like microbial community in its cold biotope, its physical separation and insights into its structure and physiology.

Recently, a unique archaeal/bacterial community that grows in a macroscopically visible string-of-pearls-like structure in cold (~10 degrees C), sulfurous marsh water was discovered. Here, a new technique is described that allows the fast and reliable growth of these string-of-pearls-like microbial communities in larger quantities on polyethylene nets in nature. The microbial net population, estimated to consist of about 10,000 single pearls, can be harvested once a week and the archaeal cells selectively separated by density gradient centrifugation. As in native pearls, the archaeal cell fraction obtained consisted of a single type of coccoid cells only, 0.6 micro m in diameter. This novel type of euryarchaea has been tentatively named SM1 euryarchaeon. Electron microscopy and immuno-fluorescence in situ hybridization (immuno-FISH) revealed that about 100 pili-like fibers, up to 3 micro m in length, emanate radially from the surface of each cell. The SM1 euryarchaeal cells exhibited a viability of about 90%. The optimal conditions for viability were temperatures between -2 degrees C and 20 degrees C, pH 5-9, and low salt conditions; cell viability was independent of oxygen partial pressures. The cultures stained gram-positive, the cell wall was sensitive to SDS, EDTA and Proteinase K treatment. The cells did not exhibit the typical fluorescence for methanogens and did not contain coenzyme F(420). The G+C-content was 34.5 mol%.

Archaea↗

PubMed2002

Arctic microorganisms respond more to elevated UV-B radiation than CO2.

Surface ultraviolet-B radiation and atmospheric CO2 concentrations have increased as a result of ozone depletion and burning of fossil fuels. The effects are likely to be most apparent in polar regions where ozone holes have developed and ecosystems are particularly sensitive to disturbance. Polar plant communities are dependent on nutrient cycling by soil microorganisms, which represent a significant and highly labile portion of soil carbon (C) and nitrogen (N). It was thought that the soil microbial biomass was unlikely to be affected by exposure of their associated plant communities to increased UV-B. In contrast, increasing atmospheric CO2 concentrations were thought to have a strong effect as a result of greater below-ground C allocation. In addition, there is a growing belief that ozone depletion is of only minor environmental concern because the impacts of UV-B radiation on plant communities are often very subtle. Here we show that 5 years of exposure of a subarctic heath to enhanced UV-B radiation both alone and in combination with elevated CO2 resulted in significant changes in the C:N ratio and in the bacterial community structure of the soil microbial biomass.

Arctic Regions↗

PubMed2003

Bacterial community structure and location in Stilton cheese.

The microbial diversity occurring in Stilton cheese was evaluated by 16S ribosomal DNA analysis with PCR-denaturing gradient gel electrophoresis. DNA templates for PCR experiments were directly extracted from the cheese as well as bulk cells harvested from a variety of viable-count media. The variable V3 and V4-V5 regions of the 16S genes were analyzed. Closest relatives of Lactococcus lactis, Enterococcus faecalis, Lactobacillus plantarum, Lactobacillus curvatus, Leuconostoc mesenteroides, Staphylococcus equorum, and Staphylococcus sp. were identified by sequencing of the DGGE fragments. Fluorescently labeled oligonucleotide probes were developed to detect Lactococcus lactis, Lactobacillus plantarum, and Leuconostoc mesenteroides in fluorescence in situ hybridization (FISH) experiments, and their specificity for the species occurring in the community of Stilton cheese was checked in FISH experiments carried out with reference cultures. The combined use of these probes and the bacterial probe Eub338 in FISH experiments on Stilton cheese sections allowed the assessment of the spatial distribution of the different microbial species in the dairy matrix. Microbial colonies of bacteria showed a differential location in the different parts of the cheese examined: the core, the veins, and the crust. Lactococci were found in the internal part of the veins as mixed colonies and as single colonies within the core. Lactobacillus plantarum was detected only underneath the surface, while Leuconostoc microcolonies were homogeneously distributed in all parts observed. The combined molecular approach is shown to be useful to simultaneously describe the structure and location of the bacterial flora in cheese. The differential distribution of species found suggests specific ecological reasons for the establishment of sites of actual microbial growth in the cheese, with implications of significance in understanding the ecology of food systems and with the aim of achieving optimization of the fermentation technologies as well as preservation of traditional products.

Cheese↗

PubMed2001

Phylogenetic structure of unusual aquatic microbial formations in Nullarbor caves, Australia.

The nature of unusual aquatic microbial formations in flooded passages of cave systems in the Nullarbor region of Australia was investigated using electron microscopy and DNA analysis. The caves are located in a semiarid region but intersect the watertable at depths of approximately 100 m below the surface. Throughout submerged portions of the caves divers have noted the presence of unusual microbial formations. These 'microbial mantles' comprise sheets or tongues of mucoid material in which small crystals are embedded. Examination of the biomass revealed it to be primarily composed of densely packed, unbranched filaments, together with spherical-, rod- and spiral-shaped cells, and microcrystals of calcite in a mucoid matrix. Molecular phylogenetic analysis of the community structure revealed approximately 12% of clones showed high similarity to autotrophic nitrite-oxidizing bacteria (Nitrospira moscoviensis). The remainder of the clones exhibited a high proportion of phylogenetically novel sequence types. Chemical analysis of water samples revealed high levels of sulphate and nitrate together with significant nitrite. The community structure, the presence of nitrite in the water, and the apparent absence of aquatic macrofauna, suggest these microbial structures may represent biochemically novel, chemoautotrophic communities dependent on nitrite oxidation.

Australia↗

PubMed2006

The influence of soil heavy metals pollution on soil microbial biomass, enzyme activity, and community composition near a copper smelter.

The environmental risk of heavy metal pollution is pronounced in soils adjacent to large industrial complexes. It is important to investigate the functioning of soil microorganisms in ecosystems exposed to long-term contamination by heavy metals. We studied the potential effects of heavy metals on microbial biomass, activity, and community composition in soil near a copper smelter in China. The results showed that microbial biomass C was negatively affected by the elevated metal levels and was closely correlated with heavy metal stress. Enzyme activity was greatly depressed by conditions in the heavy metal-contaminated sites. Good correlation was observed between enzyme activity and the distance from the smelter. Elevated metal loadings resulted in changes in the activity of the soil microbe, as indicated by changes in their metabolic profiles from correlation analysis. Significant decrease of soil phosphatase activities was found in the soils 200 m away from the smelter. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis demonstrated that heavy metals pollution had a significant impact on bacterial and actinomycetic community structure. There were negative correlations between soil microbial biomass, phosphatase activity, and NH(4)NO(3) extractable heavy metals. The soil microorganism activity and community composition could be predicted significantly using the availability of Cu and Zn. By combining different monitoring approaches from different viewpoints, the set of methods applied in this study were sensitive to site differences and contributed to a better understanding of heavy metals effects on the structure, size and activity of microbial communities in soils. The data presented demonstrate the role of heavy metals pollution in understanding the heavy metal toxicity to soil microorganism near a copper smelter in China.

Actinobacteria↗

PubMed2000

Effect of soil aggregate size on methanogenesis and archaeal community structure in anoxic rice field soil.

In anoxically incubated slurries of Italian rice field soil, CH(4) production is initiated after a lag phase during which ferric iron and sulfate are reduced. The production of CH(4) was affected by the size of soil aggregates used for the preparation of the soil slurry. Rates of CH(4) production were lowest with small aggregates (<50 and 50-100 µm), were highest with aggregates of 200-2000 µm size and were intermediate with aggregates of 2000-15000 µm size. The different amounts of CH(4) accumulated were positively correlated to the concentrations of acetate, propionate and caproate that transiently accumulated in the slurries prepared from different aggregate sizes and also to the organic carbon content. The addition of organic debris that was collected from large-size aggregates to the aggregate size fractions <200 and <50 µm resulted in an increase of CH(4) production to amounts that were comparable to those measured in unamended aggregates of 200-2000 µm size, indicating that CH(4) production in the different aggregate size fractions was limited by substrate. The distribution of archaeal small-subunit rRNA genes in the different soil aggregate fractions was analyzed by terminal restriction fragment length polymorphism which allowed seven different archaeal ribotypes to be distinguished. Ribotype-182 (consisting of members of the Methanosarcinaceae and rice cluster VI), ribotype-389 (rice cluster I and II) and ribotype-820 (undigested DNA, rice cluster IV and members of the Methanosarcinaceae) accounted for >20, >30 and >10% of the total, respectively. The other ribotypes accounted for <10% of the total. The relative quantity of the individual ribotypes changed only slightly with incubation time and was almost the same among the different soil aggregate fractions. Ribotype-389, for example, slightly decreased with time, whereas ribotype-182 slightly increased. At the end of incubation, the relative quantity of ribotype-182 seemed to be slightly higher in soil fractions with larger than with smaller aggregates, whereas it was the opposite with ribotype-80 (Methanomicrobiaceae) and ribotype-88 (Methanobacteriaceae). Ribotype-280 (Methanosaetaceae and rice cluster V), ribotype-375 (rice cluster III), ribotype-389 and ribotype-820, on the other hand, were not much different among the different soil aggregate size fractions. However, the differences were not significant relative to the errors encountered during the extraction of polymerase chain reaction (PCR)-amplifiable DNA from soil. In conclusion, soil aggregate size and incubation time showed a strong effect on the function but only a small effect on the structure of the methanogenic microbial community.

Journal Article↗