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Soil Bacterial Communities (soil + bacterial_community)
Selected AbstractsTranscriptional activity of paddy soil bacterial communitiesENVIRONMENTAL MICROBIOLOGY, Issue 4 2009Pravin Malla Shrestha Summary Bulk mRNA was used to explore the transcriptional activity of bacterial communities in oxic versus anoxic paddy soil. Two microbial cDNA libraries were constructed from composite samples using semi-randomly primed RT-PCR. cDNAs averaged 500,600 bp in length and were treated as expressed sequence tags (ESTs). Clustering analysis of 805 random cDNAs resulted in 179 and 155 different ESTs for the oxic and anoxic zones respectively. Using an E -value threshold of e,10, a total of 218 different ESTs could be assigned by blastx, while 116 ESTs were predicted novel. Both the proportion and significance of the EST assignments increased with cDNA length. Taxonomic assignment was more powerful in discriminating between the aerobic and anaerobic bacterial communities than functional inference, as most ESTs in both oxygen zones were putative indicators of similar housekeeping functions, in particular ABC-type transporters. A few ESTs were putative indicators for community function in a biogeochemical context, such as ,-oxidation of long-chain fatty acids specifically in the oxic zone. Expressed sequence tags assigned to Alpha- and Betaproteobacteria were predominantly found in the oxic zone, while those affiliated with Deltaproteobacteria were more frequently detected in the anoxic zone. At the genus level, multiple assignments to Bradyrhizobium and Geobacter were unique to the oxic and anoxic zones respectively. The phylum-level affiliations of 93 16S rRNA sequences corresponded well with two taxonomically distinct EST patterns. Expressed sequence tags affiliated with Acidobacteria and Chloroflexi were frequently detected in both oxygen zones. In summary, the soil metatranscriptome is accessible for global analysis and such studies have great potential in elucidating the taxonomic and functional status of soil bacterial communities, but study significance depends on the number and length of cDNAs being randomly analysed. [source] Bacterial community structure of glacier forefields on siliceous and calcareous bedrockEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 6 2009A. Lazzaro Summary Forefields of retreating glaciers represent unique opportunities to investigate the initial phases of soil formation and microbial interactions with mineral surfaces. An open question concerns the physical and chemical driving-factors affecting the establishment of microbial communities in these young ecosystems. In this study we compared the bacterial community structure of six glacier forefield soils belonging to two contrasting bedrock categories (calcareous and siliceous) through T-RFLP profiling of the 16S rRNA gene. The community profiles were correlated with an array of physical (soil texture, water holding capacity, hours of sunshine, temperature, rainfall and exposure) and chemical (TC, TN, DOC, extractable nutrients and pH) factors using canonical correspondence analysis (CCA). A first comparison of the T-RFLP profiles suggested that the degree of operational taxonomic unit (OTU) diversity of these soils was similar, and that community structure was dominated by ubiquitous taxa. CCA showed that both physical (e.g. hours of sunshine or rainfall) and chemical factors (e.g. SO2,4 or PO3,4) played an equal role in shaping the soil bacterial communities. OTUs unique to specific sites appeared to be strongly influenced by the climatic regime and by texture. Overall, the community structure of the six glacial forefields showed no clear dependence on the bedrock categories. [source] Growth response of the bacterial community to pH in soils differing in pHFEMS MICROBIOLOGY ECOLOGY, Issue 1 2010David Fernández-Calviño Abstract The effect of pH on the instantaneous growth of soil bacterial communities was studied in five soils with different pH (4.5,7.8) using leucine (Leu) and thymidine (TdR) incorporation. The pH dependency of bacterial growth was modelled using three different unimodal functions, and the pHopt for growth and the pH range in which growth was >50% of the optimal growth were compared. Leu and TdR incorporation yielded very similar results. The best fits were obtained using a third-degree polynomial function and the cardinal pH model. However, a simple second-degree function was adequate in most cases, yielding very similar pHopt values to the other two models. Bacterial growth was highly influenced by pH, showing optimum growth at a pH related to the soil pH. The lowest pHopt was found in the most acidic soil and the highest pHopt in the soil with the highest pH. The pHopt for bacterial growth was close to the soil pH measured in water, but higher (0.7,2.1 units) than the pH measured with 0.1 M KCl. The pH range in which bacterial growth was >50% of that at optimum was, on average, 1.7 units below and above the optimum pH. [source] Comparison of DNA- and RNA-based bacterial community structures in soil exposed to 2,4-dichlorophenolJOURNAL OF APPLIED MICROBIOLOGY, Issue 6 2009L. Lillis Abstract Aims:, To examine the effect of the pollutant 2,4-dichlorophenol on DNA- and RNA-based bacterial communities in soil. Methods and Results:, Soil was exposed to 100 mg kg,1 of 2,4-dichlorophenol (2,4-DCP), and degradation was monitored over 35 days. DNA and RNA were coextracted, and terminal restriction fragment length polymorphism (T-RFLP) was used to report changes in bacterial communities in response to the presence of the chlorophenol. The phylogenetic composition of the soil during degradation was determined by creating a clone library of amplified 16S rRNA sequences from both DNA and reverse-transcribed RNA from exposed soil. Resulting clones were sequenced, and putative identities were assigned. Conclusions:, A significant difference between active (RNA-based) and total (DNA-based) bacterial community structure was observed for both T-RFLP and phylogenetic analyses in response to 2,4-DCP, with more pronounced changes seen in RNA-based communities. Phylogenetic analysis indicated the dominance of Proteobacteria in both profiles. Significance and Impact of the Study:, This study describes the response of soil bacterial communities to the addition of the xenobiotic compound 2,4-DCP, and highlights the importance of including RNA-based 16S rRNA analysis to complement any molecular study in a perturbed soil. [source] Life history determines biogeographical patterns of soil bacterial communities over multiple spatial scalesMOLECULAR ECOLOGY, Issue 19 2010A. BISSETT Abstract The extent to which the distribution of soil bacteria is controlled by local environment vs. spatial factors (e.g. dispersal, colonization limitation, evolutionary events) is poorly understood and widely debated. Our understanding of biogeographic controls in microbial communities is likely hampered by the enormous environmental variability encountered across spatial scales and the broad diversity of microbial life histories. Here, we constrained environmental factors (soil chemistry, climate, above-ground plant community) to investigate the specific influence of space, by fitting all other variables first, on bacterial communities in soils over distances from m to 102 km. We found strong evidence for a spatial component to bacterial community structure that varies with scale and organism life history (dispersal and survival ability). Geographic distance had no influence over community structure for organisms known to have survival stages, but the converse was true for organisms thought to be less hardy. Community function (substrate utilization) was also shown to be highly correlated with community structure, but not to abiotic factors, suggesting nonstochastic determinants of community structure are important Our results support the view that bacterial soil communities are constrained by both edaphic factors and geographic distance and further show that the relative importance of such constraints depends critically on the taxonomic resolution used to evaluate spatio-temporal patterns of microbial diversity, as well as life history of the groups being investigated, much as is the case for macro-organisms. [source] Temporal and shrub adaptation effect on soil microbial functional diversity in a desert systemEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 6 2009V. Saul-Tcherkas Summary The Negev Desert is characterized by spatial and temporal patterns of resource distribution, in which soil biota are considered to be among the most sensitive biological characteristics, easily influenced by changes related to soil and abiotic factors. Soil water availability and organic matter are among the most important factors, acting as triggers that determine the length of the period of activity. The main source of organic matter in this xeric environment is input from annual and perennial shrubs. In order to persist and propagate in this xeric environment, the plants have developed different ecophysiological adaptations (e.g. the excretion of salt (Reaumuria negevensis) and chemical compounds (Artemisia sieberi) via the leaves). We found that the values of soil moisture obtained for soil samples collected in the vicinity of R. negevensis were larger than for samples collected in the vicinity of Noaea mucronata and A. sieberi and in the open area. The maximum values of CO2 evolution, microbial biomass and Shannon index (H,) were obtained for the samples collected from the vicinity of N. mucronata. Therefore, we assume that the vicinity of N. mucronata afforded the best conditions for the soil bacterial community. In the Negev Desert, we also found that water availability and pulses of rain compared with frequent rainfall influenced CO2 evolution, microbial biomass, qCO2 and the Shannon index (H,). The differences in water amount and availability between the two rainy seasons caused larger values in most of the properties during the first four seasons (December 2005,November 2006) compared with the last four seasons (December 2006,November 2007) for most of the samples. [source] Influence of arbuscular mycorrhizal mycelial exudates on soil bacterial growth and community structureFEMS MICROBIOLOGY ECOLOGY, Issue 2 2007Jonas F. Toljander Abstract Plant root systems colonized by arbuscular mycorrhizal (AM) fungi have previously been shown to influence soil bacterial populations; however, the direct influence of the AM extraradical mycelium itself on bacterial growth and community composition is not well understood. In this study, we investigated the effects of exudates produced by AM extraradical mycelia on the growth and development of an extracted soil bacterial community in vitro. The chemical composition of the mycelial exudates was analysed using proton nuclear magnetic resonance spectrometry. Following the addition of exudates to a bacterial community extracted from soil, bacterial growth and vitality were determined using a bacterial vitality stain and fluorescence microscopy. Changes in community composition were also analysed at various times over the course of 3 days by terminal restriction fragment length polymorphism analysis, in combination with cloning and sequencing of 16S rRNA genes. Mycelial exudates increased bacterial growth and vitality and changed bacterial community composition. Several Gammaproteobacteria, including a taxon within the Enterobacteriaceae, increased in frequency of occurrence in response to AM mycelial exudates. This study is the first attempt to identify carbohydrates from the extraradical mycelium of an AM fungus, and demonstrates the direct effects of mycelial exudates on a soil bacterial community. [source] Temperature-dependent changes in the soil bacterial community in limed and unlimed soilFEMS MICROBIOLOGY ECOLOGY, Issue 1 2003Marie Pettersson Abstract A humus soil with a pH(H2O) of 4.9 was limed to a pH of 7.5 and was incubated together with samples from unlimed and field limed (pH 6.1) soils at 5, 20 and 30°C for up to 80 days. The changes in the phospholipid fatty acid (PLFA) pattern were most rapid for the bacterial community of the soil incubated at 30°C, while no changes were found in the soil incubated at 5°C. The response of the community activity to temperature was measured using the thymidine incorporation method on bacteria extracted from the soil. The bacterial community in soil incubated at 30°C became more adapted to high temperature than that in soil samples incubated at 5°C. When soil samples incubated at 30°C and 20°C were returned to 5°C for 35 days, only small changes in the PLFA pattern were found. No significant shift in community temperature adaptation was found. Thus, higher temperatures (with higher turnover) led to higher rates of change in both the PLFA pattern and the activity response to temperature, compared with lower temperatures. No effect of liming as a way of increasing substrate availability and turnover on the rate of change was observed. Changes in the PLFA pattern appeared sooner than changes in the activity response to temperature, indicating that changes in the PLFA pattern were mainly due to phenotypic acclimation and not to species replacement. [source] Biogeochemical changes induced in uranium mining waste pile samples by uranyl nitrate treatments under anaerobic conditionsGEOBIOLOGY, Issue 3 2009A. GEISSLER Response of the subsurface soil bacterial community of a uranium mining waste pile to treatments with uranyl nitrate over different periods of time was studied under anaerobic conditions. The fate of the added U(VI) without supplementation with electron donors was investigated as well. By using 16S rRNA gene retrieval, we demonstrated that incubation with uranyl nitrate for 4 weeks resulted in a strong reduction in and even disappearance of some of the most predominant bacterial groups of the original sample. Instead, a strong proliferation of denitrifying and uranium-resistant populations of Rahnella spp. from Gammaproteobacteria and of Firmicutes occurred. After longer incubations for 14 weeks with uranyl nitrate, bacterial diversity increased and populations intrinsic to the untreated samples such as Bacteroidetes and Deltaproteobacteria propagated and replaced the above-mentioned uranium-resistant groups. This indicated that U(VI) was immobilized. Mössbauer spectroscopic analysis revealed an increased Fe(III) reduction by increasing the incubation time from four to 14 weeks. This result signified that Fe(III) was used as an electron acceptor by the bacterial community established at the later stages of the treatment. X-ray absorption spectroscopic analysis demonstrated that no detectable amounts of U(VI) were reduced to U(IV) in the time frames of the performed experiments. The reason for this observation is possibly due to the low level of electron donors in the studied oligotrophic environment. Time-resolved laser-induced fluorescence spectroscopic analysis demonstrated that most of the added U(VI) was bound by organic or inorganic phosphate phases both of biotic origin. [source] | |||||||||||||