Spatial Distribution Of Bacterial Communities Research Articles

Molecular Phylogenetic Diversity and Spatial Distribution of Bacterial Communities in Cooling Stage during Swine Manure Composting.

Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and subsequent sub-cloning and sequencing were used in this study to analyze the molecular phylogenetic diversity and spatial distribution of bacterial communities in different spatial locations during the cooling stage of composted swine manure. Total microbial DNA was extracted, and bacterial near full-length 16S rRNA genes were subsequently amplified, cloned, RFLP-screened, and sequenced. A total of 420 positive clones were classified by RFLP and near-full-length 16S rDNA sequences. Approximately 48 operational taxonomic units (OTUs) were found among 139 positive clones from the superstratum sample; 26 among 149 were from the middle-level sample and 35 among 132 were from the substrate sample. Thermobifida fusca was common in the superstratum layer of the pile. Some Bacillus spp. were remarkable in the middle-level layer, and Clostridium sp. was dominant in the substrate layer. Among 109 OTUs, 99 displayed homology with those in the GenBank database. Ten OTUs were not closely related to any known species. The superstratum sample had the highest microbial diversity, and different and distinct bacterial communities were detected in the three different layers. This study demonstrated the spatial characteristics of the microbial community distribution in the cooling stage of swine manure compost.

Spatial distribution of bacterial communities driven by multiple environmental factors in a beach wetland of the largest freshwater lake in China.

The spatial distributions of bacterial communities may be driven by multiple environmental factors. Thus, understanding the relationships between bacterial distribution and environmental factors is critical for understanding wetland stability and the functioning of freshwater lakes. However, little research on the bacterial communities in deep sediment layers exists. In this study, thirty clone libraries of 16S rRNA were constructed from a beach wetland of the Poyang Lake along both horizontal (distance to the water-land junction) and vertical (sediment depth) gradients to assess the effects of sediment properties on bacterial community structure and diversity. Our results showed that bacterial diversity increased along the horizontal gradient and decreased along the vertical gradient. The heterogeneous sediment properties along gradients substantially affected the dominant bacterial groups at the phylum and species levels. For example, the NH+4 concentration decreased with increasing depth, which was positively correlated with the relative abundance of Alphaproteobacteria. The changes in bacterial diversity and dominant bacterial groups showed that the top layer had a different bacterial community structure than the deeper layers. Principal component analysis revealed that both gradients, not each gradient independently, contributed to the shift in the bacterial community structure. A multiple linear regression model explained the changes in bacterial diversity and richness along the depth and distance gradients. Overall, our results suggest that spatial gradients associated with sediment properties shaped the bacterial communities in the Poyang Lake beach wetland.

Spatial distribution of bacterial communities and related biochemical properties in Luzhou-flavor liquor-fermented grains.

Grain fermenting with separate layers in a fermentation pit is the typical and experiential brewing technology for Chinese Luzhou-flavor liquor. However, it is still unclear to what extent the bacterial communities in the different layers of fermented grains (FG) effects the liquor's quality. In this study, the spatial distributions of bacterial communities in Luzhou-flavor liquor FG (top, middle, and bottom layers) from 2 distinctive factories (Jiannanchun and Fenggu) were investigated using culture-independent approaches (phospholipid fatty acid [PLFA] and polymerase chain reaction-denaturing gel electrophoresis [DGGE]). The relationship between bacterial community and biochemical properties was also assessed by Canonical correspondence analysis (CCA). No significant variation in moisture was observed in spatial samples, and the highest content of acidity and total ester was detected in the bottom layer (P < 0.05). A high level of ethanol was observed in the top and middle layers of Fenggu and Jiannanchun, respectively. Significant spatial distribution of the total PLFA was only shown in the 50-y-old pits (P < 0.05), and Gram negative bacteria was the prominent community. Bacterial 16S rDNA DGGE analysis revealed that the most abundant bacterial community was in the top layers of the FG both from Fenggu and Jiannanchun, with Lactobacillaceae accounting for 30% of the total DGGE bands and Lactobacillus acetotolerans was the dominant species. FG samples from the same pit had a highly similar bacterial community structure according to the hierarchal cluster tree. CCA suggested that the moisture, acidity, ethanol, and reducing sugar were the main factors affecting the distribution of L. acetotolerans. Our results will facilitate the knowledge about the spatial distribution of bacterial communities and the relationship with their living environment.

Spatial distribution of bacterial communities in high-altitude freshwater wetland sediment

Sediment microorganisms play a crucial role in a variety of biogeochemical processes in freshwater ecosystems. The objective of the current study was to investigate the spatial distribution of sediment bacterial community structure in Luoshijiang Wetland, located in Yunnan–Kweichow Plateau (China). Wetland sediments at different sites and depths were collected. Clone library analysis indicates bacterial communities varied with both sampling site and sediment depth. A total of fourteen bacterial phyla were identified in sediment samples, including Proteobacteria, Acidobacteria, Actinobacteria, Armatimonadetes, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Spirochaetes, and Verrucomicrobia. Proteobacteria (mainly Betaproteobacteria and Deltaproteobacteria) predominated in wetland sediments. Moreover, the proportions of Alphaproteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadete, and Planctomycetes were significantly correlated with chemical properties.

Spatial distribution of bacterial communities on volumetric and planar anodes in single‐chamber air‐cathode microbial fuel cells

Pyrosequencing was used to characterize bacterial communities in air-cathode microbial fuel cells across a volumetric (graphite fiber brush) and a planar (carbon cloth) anode, where different physical and chemical gradients would be expected associated with the distance between anode location and the air cathode. As expected, the stable operational voltage and the coulombic efficiency (CE) were higher for the volumetric anode than the planar anode (0.57 V and CE = 22% vs. 0.51 V and CE = 12%). The genus Geobacter was the only known exoelectrogen among the observed dominant groups, comprising 57 ± 4% of recovered sequences for the brush and 27 ± 5% for the carbon-cloth anode. While the bacterial communities differed between the two anode materials, results showed that Geobacter spp. and other dominant bacterial groups were homogenously distributed across both planar and volumetric anodes. This lends support to previous community analysis interpretations based on a single biofilm sampling location in these systems.

Soil pH drives the spatial distribution of bacterial communities along elevation on Changbai Mountain

The elevational patterns of diversity for plants and animals have been well established over the past century. However, it is unclear whether there is a general elevational distribution pattern for microbes. Changbai Mountain is one of few well conserved natural ecosystems, where the vertical distribution of vegetation is known to mirror the vegetation horizontal zonation from temperate to frigid zones on the Eurasian continent. Here, we present a comprehensive analysis of soil bacterial community composition and diversity along six elevations representing six typical vegetation types from forest to alpine tundra using a bar-coded pyrosequencing technique. The bacterial communities differed dramatically along elevations (vegetation types), and the community composition was significantly correlated with soil pH, carbon/nitrogen ratio (C/N), moisture or total organic carbon (TOC), respectively. Phylogenetic diversity was positively correlated with soil pH (P = 0.024), while phylotype richness was positively correlated with soil pH (P = 0.004), total nitrogen (TN) (P = 0.030), and negatively correlated with C/N ratio (P = 0.021). Our results emphasize that pH is a better predictor of soil bacterial elevational distribution and also suggest that vegetation types may indirectly affect soil bacterial elevational distribution through altering soil C and N status.

Characterization and spatial distribution of bacterial communities within passively aerated cattle manure composting piles

The bacterial communities in the core, bottom, top, middle-surface, and lower-surface full-scale passively aerated cattle manure compost was investigated using DGGE of PCR-amplified 16S rRNA sequences. Some Bacillus species and strictly anaerobic thermophilic Clostridium species were dominant only in the core and bottom zones. In contrast, bands belonging to mesophilic bacteria such as Bacteroidetes, Clostoridia,alpha and gamma-proteobacteria were detected in surface zones, even in the initial thermophilic stage of the process. Our results clearly show the spatial distribution of the microbial community within full-scale composting piles, which indicates N or C conversion by zone-specific bacterial communities were occurring in each zone of the pile.

Spatial distribution of bacterial communities in sediment of a eutrophic lake revealed by denaturing gradient gel electrophoresis and multivariate analysis

Bacterial community structure and the effects of several environmental factors on the microbial community distribution were investigated in the sediment of the eutrophic Lake Xuanwu. Profiles of bacterial communities were generated using denaturing gradient gel electrophoresis (DGGE), and the results were interpreted with multivariate statistical analysis. Five major variables in sediment were examined in a principal component analysis, which indicates notable differences of physicochemical parameters among different sites of the lake. To assess changes in the genetic diversity of bacterial communities of different sampling sites, DGGE band patterns were analyzed by multidimensional scaling analysis, which indicated that sampling sites having similar environmental characteristics also have the similar microbial communities. Canonical correspondence analysis demonstrated that pH and redox potential had significant effects on the bacterial community composition in the sediments. Analysis of DNA sequences revealed that the dominant bacterial groups in Lake Xuanwu belonged to Proteobacteria, Actinobacteria, Verrucomicrobia, and Nitrospirae, which are commonly isolated from freshwater ecosystems.

Spatial distribution of bacterial communities and phenanthrene degradation in the rhizosphere of Lolium perenne L.

Rhizodegradation of organic pollutants, such as polycyclic aromatic hydrocarbons, is based on the effect of root-produced compounds, known as exudates. These exudates constitute an important and constant carbon source that selects microbial populations in the plant rhizosphere, modifying global as well as specific microbial activities. We conducted an experiment in two-compartment devices to show the selection of bacterial communities by root exudates and phenanthrene as a function of distance to roots. Using direct DNA extraction, PCR amplification, and thermal gradient gel electrophoresis screening, bacterial population profiles were analyzed in parallel to bacterial counts and quantification of phenanthrene biodegradation in three layers (0 to 3, 3 to 6, and 6 to 9 mm from root mat) of unplanted-polluted (phenanthrene), planted-polluted, and planted-unpolluted treatments. Bacterial community differed as a function of the distance to roots, in both the presence and the absence of phenanthrene. In the planted and polluted treatment, biodegradation rates showed a strong gradient with higher values near the roots. In the nonplanted treatment, bacterial communities were comparable in the three layers and phenanthrene biodegradation was high. Surprisingly, no biodegradation was detected in the section of planted polluted treatment farthest from the roots, where the bacterial community structure was similar to those of the nonplanted treatment. We conclude that root exudates and phenanthrene induce modifications of bacterial communities in polluted environments and spatially modify the activity of degrading bacteria.

Spatial distribution of bacterial communities and their relationships with the micro-architecture of soil

Biological soil thin-sections and a combination of image analysis and geostatistical tools were used to conduct a detailed investigation into the distribution of bacteria in soil and their relationship with pores. The presence of spatial patterns in the distribution of bacteria was demonstrated at the microscale, with ranges of spatial autocorrelation of 1 mm and below. Bacterial density gradients were found within bacterial patches in topsoil samples and also in one subsoil sample. Bacterial density patches displayed a mosaic of high and low values in the remaining subsoil samples. Anisotropy was detected in the spatial structure of pores, but was not detected in relation to the distribution of bacteria. No marked trend as a function of distance to the nearest pore was observed in bacterial density values in the topsoil, but in the subsoil bacterial density was greatest close to pores and decreased thereafter. Bacterial aggregation was greatest in the cropped topsoil, though no consistent trends were found in the degree of bacterial aggregation as a function of distance to the nearest pore. The implications of the results presented for modelling and predicting bacterial activity in soil are discussed.