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Rushan cheese, an essential part of the Bai culture, has been produced and consumed for centuries by the Bai people living mostly in Yunnan province of China, however, studies on the naturally occurring microbial communities of Rushan cheese are lacking. In this study, we applied high throughput sequencing technique to analyze the microbial compositions of Rushan cheese samples from three different geographical origins (i.e., Weishan, Eryuan, and Jianchuan). The microbiota in Weishan, Eryuan and Jianchuan Rushan cheese samples were distinct in terms of taxonomic composition and abundance. Linear discriminant analysis (LDA) of effect size (LEfSe) analysis found the characteristic taxonomic species in Weishan Rushan cheese samples were Lactobacillus pentosus , Lactobacillus crustorum , Lactobacillus brevis , Leuconostoc mesenteroides , and Pediococcus pentosaceus ; the representing taxonomic species in Eryuan Rushan cheese samples were Lactobacillus kefiranofaciens , Lactococcus lactis , Acetobacter pasteurianus and Moraxella osloensis ; by comparison, Acinetobacter was enriched in Jianchuan Rushan cheese samples. Characterization of the microbial diversity in Rushan cheese samples from different geographical origins will contribute to the understanding of microorganisms responsible for the Rushan cheese fermentation, and enable us to develop bioresources derived from Rushan cheese in the future. [ABSTRACT FROM AUTHOR]

The accumulation of toxic inorganic nitrogen is one of the major water quality problems in intensive aquaculture systems, thus the N removal in aquaculture systems is an important issue for the sustainable development of aquaculture. To understand one of the major microbial N removal processes, anaerobic ammonium oxidation (anammox), phylogenetic diversity, and distribution of anammox bacteria in sediments of four different marine aquaculture zones in Hong Kong (HK) were investigated. The 16S rRNA genes analysis indicated that sequences detected from Cheung Sha Wan (CSW) and Sok Kwu Wan (SKW) were closely related to several clusters within the Scalindua genus of anammox bacteria, including a new habitat-specific group, while only several sequences related to Scalindua and Kuenenia were detected in Sham Wan (SW) and Yim Tin Tsai East (YTTE). Most of the sequences obtained in SW and YTTE with the same PCR primers showed a low similarity to the known anammox bacteria, forming several novel groups within the Planctomycetes. However, results from the hydrazine oxidoreductase (HZO) encoding gene showed that only sequences from SW were related to the genus of Kuenenia, and sequences from other three sites were closely related to the genus of Scalindua. The community analysis showed that CSW and SKW share similar anammox bacterial community structures while SW and YTTE contain a unique anammox bacterial community. Furthermore, correlations reflect that organic matter is positively correlated with Kuenenia-like anammox bacteria, while the redox potential is significantly correlated with Scalindua-like anammox bacteria in marine aquaculture zones. Our results extend the knowledge of anammox bacteria in marine aquaculture systems and highlight the importance of environmental factors in shaping the community structures of anammox bacteria. [ABSTRACT FROM AUTHOR]

Mycobacterium avium subsp. paratuberculosis (MAP) is the causative bacterium of Johne’s disease (JD) in ruminants. The control of JD in the dairy industry is challenging, but can be improved with a better understanding of the diversity and distribution of MAP subtypes. Previously established molecular typing techniques used to differentiate MAP have not been sufficiently discriminatory and/or reliable to accurately assess the population structure. In this study, the genetic diversity of 182 MAP isolates representing all Canadian provinces was compared to the known global diversity, using single nucleotide polymorphisms identified through whole genome sequencing. MAP isolates from Canada represented a subset of the known global diversity, as there were global isolates intermingled with Canadian isolates, as well as multiple global subtypes that were not found in Canada. One Type III and six “Bison type” isolates were found in Canada as well as one Type II subtype that represented 86% of all Canadian isolates. Rarefaction estimated larger subtype richness in Québec than in other Canadian provinces using a strict definition of MAP subtypes and lower subtype richness in the Atlantic region using a relaxed definition. Significant phylogeographic clustering was observed at the inter-provincial but not at the intra-provincial level, although most major clades were found in all provinces. The large number of shared subtypes among provinces suggests that cattle movement is a major driver of MAP transmission at the herd level, which is further supported by the lack of spatial clustering on an intra-provincial scale. [ABSTRACT FROM AUTHOR]

Bacteria of the class D ehalococcoidia ( DEH) (phylum C hloroflexi) are widely distributed in the marine subsurface and are especially prevalent in deep marine sediments. Nevertheless, little is known about the specific distributions of DEH subgroups at different sites and depths. This study therefore specifically examined the distributions of DEH through depths of various marine sediment cores by quantitative PCR and pyrosequencing using newly designed DEH 16 S rRNA gene targeting primers. Quantification of DEH showed populations may establish in shallow sediments (i.e. upper centimetres), although as low relative proportions of total Bacteria, yet often became more prevalent in deeper sediments. Pyrosequencing revealed pronounced diversity co-exists within single biogeochemical zones, and that clear and sometimes abrupt shifts in relative proportions of DEH subgroups occur with depth. These shifts indicate varying metabolic properties exist among DEH subgroups. The distributional changes in DEH subgroups with depth may be related to a combination of biogeochemical factors including the availability of electron acceptors such as sulfate, the composition of organic matter and depositional regimes. Collectively, the results suggest DEH exhibit wider metabolic and genomic diversity than previously recognized, and this contributes to their widespread occurrence in the marine subsurface. [ABSTRACT FROM AUTHOR]

Ammonia-oxidizing thaumarcheota ( AOA) and ammonia-oxidizing bacteria ( AOB) differentially influence soil and atmospheric chemistry, but soil properties that control their distributions are poorly understood. In this study, the ammonia monooxygenase gene ( amoA) was used to identify and quantify presumptive AOA and AOB and relate their distributions to soil properties in two experimental fields planted with different varieties of switchgrass ( P anicum virgatum), a potential bioenergy feedstock. Differences in ammonia oxidizer diversity were associated primarily with soil properties of the two field sites, with pH displaying significant correlations with both AOA and AOB population structure. Percent nitrogen (%N), carbon to nitrogen ratios (C : N), and pH were also correlated with shifts nitrifier population structure. N itrosotalea-like and N itrosospira cluster II populations were more highly represented in acidic soils, whereas populations affiliated with N itrososphaera and N itrosospira cluster 3 A.1 were relatively more abundant in alkaline soils. AOA were the dominant functional group in all plots based on quantitative polymerase chain reaction and high-throughput sequencing analyses. These data suggest that AOA contribute significantly to nitrification rates in carbon and nitrogen rich soils influenced by perennial grasses. [ABSTRACT FROM AUTHOR]

Black soils (Mollisols) are one of the most important soil resources for maintaining food security of China and are mainly distributed in northeast China. To understand which environmental factors influence the microbial communities and how the communities are distributed in the black soils, we collected 26 soil samples with different soil carbon contents across the black soil zone in northeast China, and the soil bacterial community compositions were estimated using high resolution bar-coded pyrosequencing. A total of 355,813 bacterial 16S rDNA sequences were obtained, which were classified into at least 35 bacterial groups. The dominant groups across all samples (>5% of all sequences) were Acidobacteria, Actinobacteria, Proteobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes and Planctomycetes. The composition and diversity of the soil bacterial community were dominantly affected by both soil pH and soil total carbon content, and the effect of soil pH was stronger than that of soil carbon content. Variance partitioning analysis showed that geographic distance contributed 14.75% of the bacterial community variation, and soil environmental factors explained approximately 37.52% of the variation. Pairwise analysis showed that a relatively higher diversity of the bacterial community was observed at lower latitudes, suggesting that a latitudinal diversity gradient of the bacterial community might be present in the black soil zone. In general, our results indicated that contemporary factors, such as soil pH and soil carbon content, were more important than the historical factor of geographic distance in shaping the bacterial community in the black soil zone in northeast China. [ABSTRACT FROM AUTHOR]

Despite an exceptional number of bacterial cells and species in soils, bacterial diversity seems to have little effect on soil processes, such as respiration or nitrification, that can be affected by interactions between bacterial cells. The aim of this study is to understand how bacterial cells are distributed in soil to better understand the scaling between cell-to-cell interactions and what can be measured in a few milligrams, or more, of soil. Based on the analysis of 744 images of observed bacterial distributions in soil thin sections taken at different depths, we found that the inter-cell distance was, on average 12.46 µm and that these inter-cell distances were shorter near the soil surface (10.38 µm) than at depth (>18 µm), due to changes in cell densities. These images were also used to develop a spatial statistical model, based on Log Gaussian Cox Processes, to analyse the 2D distribution of cells and construct realistic 3D bacterial distributions. Our analyses suggest that despite the very high number of cells and species in soil, bacteria only interact with a few other individuals. For example, at bacterial densities commonly found in bulk soil (108 cells g−1 soil), the number of neighbours a single bacterium has within an interaction distance of ca. 20 µm is relatively limited (120 cells on average). Making conservative assumptions about the distribution of species, we show that such neighbourhoods contain less than 100 species. This value did not change appreciably as a function of the overall diversity in soil, suggesting that the diversity of soil bacterial communities may be species-saturated. All in all, this work provides precise data on bacterial distributions, a novel way to model them at the micrometer scale as well as some new insights on the degree of interactions between individual bacterial cells in soils. [ABSTRACT FROM AUTHOR]

Genomic approaches to characterizing bacterial communities are revealing significant differences in diversity and composition between environments. But bacterial distributions have not been mapped at a global scale. Although current community surveys are way too sparse to map global diversity patterns directly, there is now sufficient data to fit accurate models of how bacterial distributions vary across different environments and to make global scale maps from these models. We apply this approach to map the global distributions of bacteria in marine surface waters. Our spatially and temporally explicit predictions suggest that bacterial diversity peaks in temperate latitudes across the world's oceans. These global peaks are seasonal, occurring 6 months apart in the two hemispheres, in the boreal and austral winters. This pattern is quite different from the tropical, seasonally consistent diversity patterns observed for most macroorganisms. However, like other marine organisms, surface water bacteria are particularly diverse in regions of high human environmental impacts on the oceans. Our maps provide the first picture of bacterial distributions at a global scale and suggest important differences between the diversity patterns of bacteria compared with other organisms. [ABSTRACT FROM AUTHOR]

Abstract: Molecular characterization of 117 Bacillus thuringiensis (Bt) isolates from various geographical locations was previously done by PCR amplification of cry genes. In present investigation, diversity of cry genes from different soil types and climatic environments was studied using rarefaction method. Presence of cry1, cry2, cry3, 7, 8, cry4, cry5, 12, 14, 21, cry11, cry13 and cyt1 genes from Bt strains isolated from various regions of India was determined by PCR amplification. A varied distribution of cry genes and their profiles was found in four soil types. The cry1 gene was the most abundant in the isolates from four soil types and geographical regions. A higher degree of cry gene diversity was observed in isolates from alluvial soil. Rarefaction analysis indicated that more cry genes could be found from various soil types. Distribution of cry genes in semi arid, subtropical humid and tropical dry regions was varied but the degree of cry gene diversity determined by rarefaction analysis was similar. No major difference in distribution and diversity of cry genes was found in agricultural and non-agricultural samples except the absence of cry3 and cry13 genes in isolates of non-agricultural samples. We report the utility of rarefaction analysis to compare cry gene diversity from different geographical regions. [Copyright &y& Elsevier]

In this study, genetic diversity of Chlamydia pneumoniae was investigated and the relationships between sequences amplified of different sources, clinical conditions and geographical regions of central Argentina were established. Samples amplified were similar to human C. pneumoniae patterns and show the high clonality of the population. [ABSTRACT FROM AUTHOR]