Search

Tularemia is a severe infectious disease caused by the Gram-negative bacteria Francisella tularensis. F. tularensis is currently divided into three subspecies, holarctica, tularensis, and mediasiatica, which differ in their virulence and geographic distribution. Subspecies mediasiatica is the least studied because of its very low documented virulence for humans and limited geographic distribution. It was discovered in sparsely populated regions of Central Asia. Since 2011, a new subsp. mediasiatica lineage was identified in Altai (Russia). In 2021, we isolated one subsp. mediasiatica strain in Krasnoyarsk Territory. In spite of its geographic origin, 500 km east from Altai, this strain belongs to the Altai lineage and contributes surprisingly little genetic diversity to previous knowledge. [ABSTRACT FROM AUTHOR]

Highlights • Different levels of anthropogenic disturbance led to discrepant levels of river degradation. • Bacterial communities showed diverse changes in response to disturbance extent. • Bacterial taxa showed diverse changes in response to disturbance extent. • Bacterial taxa could be used to assess and monitor changes of river ecosystems. Abstract Bacterial communities play crucial roles in biogeochemical cycles in riverine ecosystems. However, the use of bacteria as bio-indicators to assess the pollution of water environments is not as common as macroorganisms, especially in large rivers disturbed by anthropogenic activities. In this study, we explored the relationship between geographical distribution of bacterial communities and associated environmental variables, and further selected effective indicators in Songhua River, a crucial river highly disturbed by various anthropogenic activities in Northeastern China. Our results revealed significant differences of environmental variables between the highly-disturbed area (HDA) and the lightly-disturbed area (LDA), with HDA encountering a higher level of nutrient pollution than LDA. The bacterial community composition was significantly different between the two areas (p < 0.05), with nitrate (NO 3 -N) being selected as the most important factor for this dissimilarity. By assigning bacteria into HDA- and LDA-associated groups whose abundance was significantly higher (p < 0.05) in a specific group, we further examined the variation of bacterial communities in different areas. Furthermore, to indicate the degradation status of river ecosystems, we selected Cyanobacteria Family I, Planctomycetaceae, FukuN18 freshwater group, and Rhizobiales Incertae Sedis at the family level, and Pirellula, Synechococcus, Alsobacter, and Prochlorococcus at the genus level as bio-indicators. To indicate the remediation of river ecosystems, we recommended Comamonadaceae and Xanthomonadaceae at the family level, and Limnohabitans, Flavobacterium, Limnobacter, Rhodoferax, Zavarzinia, Pseudarcicella, and Pseudorhodobacter at the genus level. Some indicator taxa were specific to Songhua River, suggesting the importance of river-specific indicators based on unique ecological features of a river ecosystem; while some were common among rivers, supporting the generalization of these indicator taxa in river ecosystems. [ABSTRACT FROM AUTHOR]

Aquaculture ponds are simple and unique ecosystems, which are affected intensively by human activities. In this mini-review, we focus our attention on the distribution and community diversity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in pond water and sediments, as well as the possible ecological mechanisms involved. Moreover, we discuss the possibility of increasing the activity of ammonia-oxidizing organisms in order to improve the water quality in aquaculture ponds. Compared with eutrophic lakes, the significantly higher ammonia concentration in pond water does not lead to significantly higher AOB levels, and the abundance of AOA is too low to quantify accurately. Similar to eutrophic lakes, high abundances of AOA and AOB are present in the surface sediments at the same time, where the oxidation of ammonia is performed mainly by AOB. AOB and AOA exhibit significant seasonal variations in aquaculture ponds, which are affected by the temperature, pH, and dissolved oxygen. The dominant AOB species are Nitrosomonas and the Nitrosospira lineage in pond environments. Nitrososphaera or members of the Nitrososphaera-like cluster dominate the AOA species in surface sediments, whereas the Nitrosopumilus cluster dominates the deeper sediments. AOB and AOA can be enriched on artificial substrates suspended in the pond water, thereby potentially improving the water quality. [ABSTRACT FROM AUTHOR]

Thermosipho species inhabit thermal environments such as marine hydrothermal vents, petroleum reservoirs, and terrestrial hot springs. A 16S rRNA phylogeny of available Thermosipho spp. sequences suggested habitat specialists adapted to living in hydrothermal vents only, and habitat generalists inhabiting oil reservoirs, hydrothermal vents, and hotsprings. Comparative genomics of 15 Thermosipho genomes separated them into three distinct species with different habitat distributions: The widely distributed T. africanus and the more specialized, T. melanesiensis and T. affectus. Moreover, the species can be differentiated on the basis of genome size (GS), genome content, and immune system composition. For instance, the T. africanus genomes are largest and contained the most carbohydrate metabolism genes, which could explain why these isolates were obtained from ecologically more divergent habitats. Nonetheless, all the Thermosipho genomes, like other Thermotogae genomes, show evidence of genome streamlining. GS differences between the species could further be correlated to differences in defense capacities against foreign DNA, which influence recombination via HGT. The smallest genomes are found in T. affectus that contain both CRISPR-cas Type I and III systems, but no RM system genes. We suggest that this has caused these genomes to be almost devoid of mobile elements, contrasting the two other species genomes that contain a higher abundance of mobile elements combined with different immune system configurations. Taken together, the comparative genomic analyses of Thermosipho spp. revealed genetic variation allowing habitat differentiation within the genus as well as differentiation with respect to invading mobile DNA. [ABSTRACT FROM AUTHOR]

ABSTRACT: Chiggers were collected from the central and southern parts of South Korea between April and November, 2009 with the aim of investigating the seasonal and geographical distribution of Or. A total of 1136 chiggers were identified. They included eight species belonging to four genera, as follows: Leptotrombidium scutellare (27.2%, n = 309), L. pallidum (54.6%, n = 621), L. orientale (6.25%, n = 71), L. palpale (1.59%, n = 18), L. zetum (2.0%, n = 23), Euschoengastia koreaensis (1.5%, n = 17), Cheladonta ikaoensis (0.08%, n = 1) and Neotrombicula japonica (1.05%, n = 12). The density of L. pallidum was high from April to May, whereas L. scutallare was not found in spring, being observed from October. Serotype‐specific nested PCR targeting the 56 kDa protein gene and sequencing analysis identified that the strains of 1136 O. tsutsugamushi in the chiggers as Boryong (6.8%), Kanda (0.4%), Oishi (0.3%), Jecheon (0.1%), Youngworl (0.1%) and Wonju (0.1%). Our findings indicate that L. pallidum and L. scutellare are dominant species in Korea and have geographical and seasonal variations. [ABSTRACT FROM AUTHOR]

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]

Objective: To investigate the distribution of Mycobacterium tuberculosis genotypes across Africa. Methods: The SITVIT2 global repository and PUBMED were searched for spoligotype and published genotype data respectively, of M. tuberculosis from Africa. M. tuberculosis lineages in Africa were described and compared across regions and with those from 7 European and 6 South-Asian countries. Further analysis of the major lineages and sub-lineages using Principal Component analysis (PCA) and hierarchical cluster analysis were done to describe clustering by geographical regions. Evolutionary relationships were assessed using phylogenetic tree analysis. Results: A total of 14727 isolates from 35 African countries were included in the analysis and of these 13607 were assigned to one of 10 major lineages, whilst 1120 were unknown. There were differences in geographical distribution of major lineages and their sub-lineages with regional clustering. Southern African countries were grouped based on high prevalence of LAM11-ZWE strains; strains which have an origin in Portugal. The grouping of North African countries was due to the high percentage of LAM9 strains, which have an origin in the Eastern Mediterranean region. East African countries were grouped based on Central Asian (CAS) and East-African Indian (EAI) strain lineage possibly reflecting historic sea trade with Asia, while West African Countries were grouped based on Cameroon lineage of unknown origin. A high percentage of the Haarlem lineage isolates were observed in the Central African Republic, Guinea, Gambia and Tunisia, however, a mixed distribution prevented close clustering. Conclusions: This study highlighted that the TB epidemic in Africa is driven by regional epidemics characterized by genetically distinct lineages of M. tuberculosis. M. tuberculosis in these regions may have been introduced from either Europe or Asia and has spread through pastoralism, mining and war. The vast array of genotypes and their associated phenotypes should be considered when designing future vaccines, diagnostics and anti-TB drugs. [ABSTRACT FROM AUTHOR]

Isolation frequency of nontuberculous mycobacterial (NTM) differs per region. Differences in isolation frequency as well as frequencies in clinical relevance are relevant for daily clinical practice. We conducted a systematic review, searching PubMed to assess these differences. Mycobacterium avium complex (MAC) is the most frequently isolated species and the majority of MAC isolates are causative agents of clinically relevant disease, that is, the patient ultimately meets American Thoracic Society/Infectious Disease Society of America diagnostic criteria for NTM pulmonary disease. Differences in isolation frequency between MAC species are seen in different continents. Another species that shows a remarkable difference in isolation frequency is M. abscessus complex, which is common in Asia and Oceania, in contrast to Europe, North America, and South America. Furthermore, differences in isolation frequency are seen between different continents, and also between regions or cities. These differences might drive local epidemiology of NTM pulmonary disease, and knowledge of the local situation is thus essential for daily clinical practice. To be fully able to assess this problem, larger multicenter studies with uniform microbiological methods are needed. [ABSTRACT FROM AUTHOR]

This study evaluated whether outdoor cultivation of Spirulina sp. in different geographical locations affected its growth and biomass quality, with respect to the chemical composition, volatile compound and heavy metal content, and thermal stability. The positive effect of solar radiation and temperature on biomass productivity in Spirulina sp. cultivated in the northeast was directly related to its improved nutritional characteristics, which occurred with an increase in protein, phycocyanin, and polyunsaturated fatty acid (mainly γ-linolenic) content. The biomass produced in Northeast and South Brazil showed high thermal stability and had volatile compounds that could be used as biomarkers of Spirulina , and their parameters were within the limits of internationally recognized standards for food additives; hence, they have been considered safe foods. However, the growth of crops in south Brazil occurred at lower rates due to low temperatures and luminous intensities, indicative of the robustness of microalgae in relation to these parameters. [ABSTRACT FROM AUTHOR]

Microorganisms are globally distributed but new evidence shows that the microbial structure of their communities can vary due to geographical location and environmental parameters. In this study, 50 samples including brines and sediments from Europe, Spanish-Atlantic and South America were analysed by applying the operational phylogenetic unit (OPU) approach in order to understand whether microbial community structures in hypersaline environments exhibited biogeographical patterns. The fine-tuned identification of approximately 1000 OPUs (almost equivalent to “species”) using multivariate analysis revealed regionally distinct taxa compositions. This segregation was more diffuse at the genus level and pointed to a phylogenetic and metabolic redundancy at the higher taxa level, where their different species acquired distinct advantages related to the regional physicochemical idiosyncrasies. The presence of previously undescribed groups was also shown in these environments, such as Parcubacteria, or members of Nanohaloarchaeota in anaerobic hypersaline sediments. Finally, an important OPU overlap was observed between anoxic sediments and their overlaying brines, indicating versatile metabolism for the pelagic organisms. [ABSTRACT FROM AUTHOR]

Lactobacillus wasatchensis, an obligate heterofermentative nonstarter lactic acid bacteria (NSLAB) implicated in causing gas defects in aged cheeses, was originally isolated from an aged Cheddar produced in Logan, Utah. To determine the geographical distribution of this organism, we isolated slow-growing NSLAB from cheeses collected in different regions of the United States, Australia, New Zealand, and Ireland. Seven of the cheeses showed significant gas defects and 12 did not. Nonstarter lactic acid bacteria were isolated from these cheeses on de Man, Rogosa, and Sharpe medium supplemented with ribose, a preferred substrate for Lb. wasatchensis. Identification was confirmed with 16S rRNA gene sequencing and the API50CH (bioMérieux, Marcy l'Etoile, France) carbohydrate panel. Isolates were also compared with one another by using repetitive element sequence-based PCR (rep-PCR). Lactobacillus wasatchensis was isolated only from cheeses demonstrating late-gas development and was found in samples from 6 of the 7 cheeses. This supports laboratory evidence that this organism is a causative agent of late gas production defects. The rep-PCR analysis produced distinct genetic fingerprints for isolates from each cheese, indicating that Lb. wasatchensis is found in several regions across the United States and is not a local phenomenon. [ABSTRACT FROM AUTHOR]

Knowledge of the spatial organization of the gut microbiota is important for understanding the physical andmolecular interactions among its members. These interactions are thought to influence microbial succession, community stability, syntrophic relationships, and resiliency in the face of perturbations. The complexity and dynamism of the gut microbiota pose considerable challenges for quantitative analysis of its spatial organization. Here, we illustrate an approach for addressing this challenge, using (i) a model, defined 15-member consortium of phylogenetically diverse, sequenced human gut bacterial strains introduced into adult gnotobiotic mice fed a polysaccharide-rich diet, and (ii) in situ hybridization and spectral imaging analysis methods that allow simultaneous detection of multiple bacterial strains at multiple spatial scales. Differences in the binding affinities of strains for substrates such as mucus or food particles, combined with more rapid replication in a preferred microhabitat, could, in principle, lead to localized clonally expanded aggregates composed of one or a few taxa. However, our results reveal a colonic community that is mixed at micrometer scales, with distinct spatial distributions of some taxa relative to one another, notably at the border between the mucosa and the lumen. Our data suggest that lumen and mucosa in the proximal colon should be conceptualized not as stratified compartments but as components of an incompletely mixed bioreactor. Employing the experimental approaches described should allow direct tests of whether and how specified host and microbial factors influence the nature and functional contributions of "microscale" mixing to the dynamic operations of the microbiota in health and disease. [ABSTRACT FROM AUTHOR]

Efficient and correct evaluation of sampling results with respect to hypotheses about the concentration or distribution of bacteria generally requires knowledge about the performance of the detection method. To assess the sensitivity of the detection method an experiment is usually performed where the target matrix is spiked (i.e. artificially contaminated) with different concentrations of the bacteria, followed by analyses of the samples using the pre-enrichment method and the analytical detection method of interest. For safety reasons or because of economic or time limits it is not always possible to perform exactly such an experiment, with the desired number of samples. In this paper, we show how heterogeneous data from diverse sources may be combined within a single model to obtain not only estimates of detection probabilities, but also, crucially, uncertainty estimates. We indicate how such results can then be used to obtain optimal conclusions about presence of bacteria, and illustrate how strongly the sampling results speak in favour of or against contamination. In our example, we consider the case when B. cereus is used as surrogate for B. anthracis , for safety reasons. The statistical modelling of the detection probabilities and of the growth characteristics of the bacteria types is based on data from four experiments where different matrices of food were spiked with B. anthracis or B. cereus and analysed using plate counts and qPCR. We show how flexible and complex Bayesian models, together with inference tools such as OpenBUGS, can be used to merge information about detection probability curves. Two different modelling approaches, differing in whether the pre-enrichment step and the PCR detection step are modelled separately or together, are applied. The relative importance on the detection curves for various existing data sets are evaluated and illustrated. [ABSTRACT FROM AUTHOR]

Background: Artemisinin-resistant Plasmodium falciparum malaria parasites are now present across much of mainland Southeast Asia, where ongoing surveys are measuring and mapping their spatial distribution. These efforts require substantial resources. Here we propose a generic 'smart surveillance' methodology to identify optimal candidate sites for future sampling and thus map the distribution of artemisinin resistance most efficiently. Methods: The approach uses the 'uncertainty' map generated iteratively by a geostatistical model to determine optimal locations for subsequent sampling. Results: The methodology is illustrated using recent data on the prevalence of the K13-propeller polymorphism (a genetic marker of artemisinin resistance) in the Greater Mekong Subregion. Conclusion: This methodology, which has broader application to geostatistical mapping in general, could improve the quality and efficiency of drug resistance mapping and thereby guide practical operations to eliminate malaria in affected areas. [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]

Background: Burkholderia pseudomallei is a soil saprophytic bacterium that causes melioidosis. The infection occurs through cutaneous inoculation, inhalation or ingestion. Bacteriophages (phages) in the same ecosystem may significantly impact the biology of this bacterium in the environment, and in their culturability in the laboratory. Methods/Principal Findings: The soil samples were analysed for the presence of bacteria using culture methods, and for phages using plaque assays on B. pseudomallei strain 1106a lawns. Of the 86 soil samples collected from northeastern Thailand, B. pseudomallei was cultured from 23 (26.7%) samples; no phage capable of infecting B. pseudomallei was detected in these samples. In contrast, phages capable of infecting B. pseudomallei, but no bacteria, were present in 10 (11.6%) samples. B. pseudomallei and their phages were co-isolated from only 3 (3.5%) of soil samples. Since phage capable of infecting B. pseudomallei could not have appeared in the samples without the prior presence of bacteria, or exposure to bacteria nearby, our data suggest that all phage-positive/bacteria-negative samples have had B. pseudomallei in or in a close proximity to them. Taken together, these findings indicate that the presence of phages may influence the success of B. pseudomallei isolation. Transmission electron microscopy revealed that the isolated phages are podoviruses. The temperate phages residing in soil-isolated strains of B. pseudomallei that were resistant to the dominant soil borne phages could be induced by mitomycin C. These induced-temperate phages were closely related, but not identical, to the more dominant soil-isolated phage type. Conclusion/Significance: The presence of podoviruses capable of infecting B. pseudomallei may affect the success of the pathogen isolation from the soil. The currently used culture-based methods of B. pseudomallei isolation appear to under-estimate the bacterial abundance. The detection of phage capable of infecting B. pseudomallei from environmental samples could be a useful preliminary test to indicate the likely presence of B. pseudomallei in environmental samples. [ABSTRACT FROM AUTHOR]

There has been a marked increase in the distribution, intensity and frequency of proliferations of some species of the benthic mat-forming, toxin-producing genus Phormidium in rivers globally over the last decade. This review summarises current knowledge on their taxonomy, distribution, toxin content, environmental drivers of proliferations, and monitoring and management strategies in New Zealand. Although toxic Phormidium proliferation occurs in rivers worldwide little is known about these factors in most countries. Proliferations, defined as >20% cover of a riverbed, have been identified in 103 rivers across New Zealand. Morphological and molecular data indicate the main species responsible is Phormidium autumnale . In New Zealand Phormidium produces anatoxins (anatoxin-a, homoanatoxin-a, dihydroanatoxin-a, and dihydrohomoanatoxin-a) and these were detected in 67% of 771 samples from 40 rivers. The highest concentration measured was 712 mg kg −1 dried weight (Oreti River, Southland), with considerable spatial and temporal variability in anatoxin concentrations between and within rivers. A synthesis of field based studies suggests that Phormidium proliferations are most likely when there is some enrichment of dissolved inorganic nitrogen but when water-column dissolved reactive phosphorus is less than 0.01 mg L −1 . Once established Phormidium -dominated mats trap sediment and internal mat biogeochemistry can mobilise sediment-bound phosphorus, which is then available for growth. Removal of Phormidium -dominated mats is primarily due to shear stress and substrate disturbance, although there is also evidence for autogenic detachment. A combination of factors including; changes to riparian margins, increased nitrate and fine sediment loads, and alterations in flow regimes are likely to have contributed to the rise in Phormidium proliferations. [ABSTRACT FROM AUTHOR]

Poultry and poultry products are commonly considered as the major vehicle of Campylobacter infection in humans worldwide. To reduce the number of human cases, the epidemiology of Campylobacter in poultry must be better understood. Therefore, the objective of the present study was to determine the distribution and genetic relatedness of Campylobacter in the Thai chicken production industry. During June to October 2012, entire broiler production processes (i.e., breeder flock, hatchery, broiler farm and slaughterhouse) of five broiler production chains were investigated chronologically. Representative isolates of C. jejuni from each production stage were characterized by flaA SVR sequencing and multilocus sequence typing (MLST). Amongst 311 selected isolates, 29 flaA SVR alleles and 17 sequence types (STs) were identified. The common clonal complexes (CCs) found in this study were CC-45, CC-353, CC-354 and CC-574. C. jejuni isolated from breeders were distantly related to those isolated from broilers and chicken carcasses, while C. jejuni isolates from the slaughterhouse environment and meat products were similar to those isolated from broiler flocks. Genotypic identification of C. jejuni in slaughterhouses indicated that broilers were the main source of Campylobacter contamination of chicken meat during processing. To effectively reduce Campylobacter in poultry meat products, control and prevention strategies should be aimed at both farm and slaughterhouse levels. [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]

C rocosphaera watsonii is a unicellular nitrogen ( N2)-fixing cyanobacterium with ecological importance in oligotrophic oceans. In cultivated strains there are two phenotypes of C . watsonii (large and small cells) with differences that could differentially impact biogeochemical processes. Recent work has shown the phenotypes diverged through loss or addition of type-specific genes in a fraction of their genomes, whereas the rest of the genomes were maintained at 99-100% DNA identity. Previous molecular assays for C . watsonii abundances targeted the conserved regions and therefore could not differentiate between phenotypes, so their relative distributions in natural communities were unknown. To determine phenotype distributions, this study developed and applied type-specific quantitative polymerase chain reaction assays to samples from the North and South Pacific. Abundances of both C rocosphaera types declined sharply with depth between 45 and 75 m in both sites. In surface water small cells were 10-100 times more abundant than large cells in the N. Pacific, whereas in the S. Pacific the two phenotypes were nearly equal. Evidence for large cell aggregation was only found in N. Pacific samples. The differences in C . watsonii sub-populations in the North and South Pacific have direct implications for biogeochemistry and carbon export in oligotrophic gyres. [ABSTRACT FROM AUTHOR]

It has been known that continental shelves around the Arctic Ocean play a major role in the ventilation of the deep basins as a consequence of shelf-basin exchange. In the present study, we found that bacterial assemblage of the surface sediment was different from that of seawater while seawater harboured local bacterial assemblages in response to the Arctic hydrography. This finding suggests that the Arctic seafloor sediments may have distinctive bacterial biogeography. Moreover, the distribution of bacterial assemblages and physicochemical properties in surface sediments changed gradually from the Arctic continental shelf to deep-sea basin. Based on the results, bacterial biogeography in the Arctic seafloor sediments may be influenced by winnowing and re-deposition of surface sediments through the sediment gravity flow. The present study offers a deeper understanding of shelf convection and its role for the construction of bacterial assemblages in the Arctic Ocean. [ABSTRACT FROM AUTHOR]

Urinary tract infections (UTIs) are one of the most common diseases by which humans seek medical help and are caused mainly by uropathogenic Escherichia coli (UPEC). Studying the virulence and antibiotic resistance of UPEC with respect to various phylogenetic groups is of utmost importance in developing new therapeutic agents. Thus, in this study, we analysed the virulence factors, antibiotic resistance and phylogenetic groups among various UPEC isolates from children with UTIs. The phylogenetic analysis revealed that majority of the strains responsible for UTIs belonged to the phylogenetic groups B2 and D. Of the 58 E. coli isolates, 79.31% belonged to group B2, 15.51% to group D, 3.44% to group A and 1.72% to B1. Simultaneously, the number of virulence factors and antibiotic resistance exhibited were also significantly high in groups B2 and D compared to other groups. Among the isolates, 44.8% were multidrug resistant and of that 73% belonged to the phylogenetic group B2, indicating the compatibility of antibiotic resistance and certain strains carrying virulence factor genes. The antibiotic resistance profiling of UPEC strains elucidates that the antimicrobial agents such as chloramphenicol, cefoxitin, cefepime, ceftazidime might still be used in the therapy for treating UTIs. [ABSTRACT FROM AUTHOR]

Acute bacterial meningitis causes high morbidity and mortality; the associated clinical symptoms often are insensitive or non-specific; and the pathogenic bacteria are geographically diverse. Clinical diagnosis requires a rapid and accurate methodology. This study aimed to develop a new multiplex polymerase chain reaction (mPCR) assay to detect simultaneously six major bacteria that cause adult bacterial meningitis in Taiwan: Klebsiella pneumoniae, Pseudomonas aeruginosa, Streptococcus pneumoniae, Staphylococcus aureus, Escherichia coli, and Acinetobacter baumannii. Species-specific primers for the six bacteria were developed using reference strains. The specificities of the mPCRs for these bacteria were validated, and the sensitivities were evaluated via serial dilutions. The mPCR assay specifically detected all of the six pathogens, particularly with sensitivities of 12 colony forming units (CFU)/mL, 90 CFU/mL, and 390 CFU/mL for E. coli, S. pneumoniae, and K. pneumoniae, respectively. This mPCR assay is a rapid and specific tool to detect the six major bacterial pathogens that cause acute adult meningitis in Taiwan, particularly sensitive for detecting E. coli, S. pneumoniae, and K. pneumoniae. The assay may facilitate early diagnosis and guidance for antimicrobial therapy for adult patients with this deadly disease in Taiwan. [ABSTRACT FROM AUTHOR]

The aim of this study was to elucidate how flooding of the Changjiang River affects the assemblage composition of phycoerythrin-rich (PE-rich) Synechococcus at the surface of the East China Sea (ECS). During non-flooding summers (e.g., 2009), PE-rich Synechococcus usually thrive at the outer edge of the Changjiang River diluted water coverage (CDW; salinity ≤31 PSU). In the summer of 2010, a severe flood occurred in the Changjiang River basin. The plentiful freshwater injection resulted in the expansion of the CDW over half of the ECS and caused PE-rich cells to show a uniform distribution pattern, with decreased abundance compared with the non-flooding summer. The phylogenetic diversity of 16S rRNA gene sequences indicated that the flooding event also shifted the picoplankton community composition from being dominated by Synechococcus, mainly attributed to the clade II lineage, to various orders of heterotrophic bacteria, including Actinobacteria, Flavobacteria, α- Proteobacteria, and γ- Proteobacteria. As an increasing number of studies have proposed that global warming might result in more frequent floods, combining this perspective with the information obtained from our previous [] and this studies yield a more comprehensive understanding of the relationship between the composition of the marine Synechococcus assemblage and global environmental changes. [ABSTRACT FROM AUTHOR]

There were only 9 taxa of Chamaesiphon A. Braun & Grunow, reported so far from India. This includes 6 species and 3 varieties. In the present study, two species of genus Chamaesiphon i.e. C. amethystinus and C. polonicus were reported from the Eastern Himalayas, as new records from India. Further, a taxonomic key to the Indian taxa of the genus Chamaesiphon along with their distribution in India as well as the globe have been provided. The taxonomic status of two endemic species was also evaluated. (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [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]

The cyanobacteria P rochlorococcus and S ynechococcus are important marine primary producers. We explored their distributions and covariance along a physico-chemical gradient from coastal to open ocean waters in the Northeastern Pacific Ocean. An inter-annual pattern was delineated in the dynamic transition zone where upwelled and eastern boundary current waters mix, and two new S ynechococcus clades, Eastern Pacific Clade ( EPC) 1 and EPC2, were identified. By applying state-of-the-art phylogenetic analysis tools to bar-coded 16S amplicon datasets, we observed higher abundance of P rochlorococcus high-light I ( HLI) and low-light I ( LLI) in years when more oligotrophic water intruded farther inshore, while under stronger upwelling S ynechococcus I and IV dominated. However, contributions of some cyanobacterial clades were proportionally relatively constant, e.g. S ynechococcus EPC2. In addition to supporting observations that P rochlorococcus LLI thrive at higher irradiances than other LL taxa, the results suggest LLI tolerate lower temperatures than previously reported. The phylogenetic precision of our 16S rRNA gene analytical approach and depth of bar-coded sequencing also facilitated detection of clades at low abundance in unexpected places. These include P rochlorococcus at the coast and C yanobium-related sequences offshore, although it remains unclear whether these came from resident or potentially advected cells. Our study enhances understanding of cyanobacterial distributions in an ecologically important eastern boundary system. [ABSTRACT FROM AUTHOR]

The underlying mechanisms of microbial community assembly in connective coastal environments are unclear. The coastal water area of northern Zhejiang, East China Sea, is a complex marine ecosystem with multiple environmental gradients, where the distributions and determinants of bacterioplankton communities remain unclear. We collected surface water samples from 95 sites across eight zones in this area for investigating bacterial community with 16S r RNA gene high-throughput sequencing. Bacterial alpha-diversity exhibits strong associations with water chemical parameters and latitude, with 75.5% of variation explained by suspended particle. The composition of dominant phyla can group the sampling sites into four bacterial provinces, and most key discriminant phyla and families/genera of each province strongly associate with specific environmental features, suggesting that local environmental conditions shape the biogeographic provincialism of bacterial taxa. At a broader and finer phylogenetic scale, bacterial beta-diversity is dominantly explained by the shared variation of environmental and spatial factors (63.3%); meanwhile, the environmental determinants of bacterial β-diversity generally exhibit spatially structured patterns, suggesting that bacterial assembly in surface water is highly controlled by spatially structured environmental gradients in this area. This study provides evidence for the unique biogeographic pattern of bacterioplankton communities at an entire scale of this marine ecosystem. [ABSTRACT FROM AUTHOR]

The genus Pseudomonas is one of the most heterogeneous groups of eubacteria, presents in all major natural environments and in wide range of associations with plants and animals. The wide distribution of these bacteria is due to the use of specific mechanisms to adapt to environmental modifications. Generally, bacterial adaptation is only considered under the aspect of genes and protein expression, but lipids also play a pivotal role in bacterial functioning and homeostasis. This review resumes the mechanisms and regulations of pseudomonal glycerophospholipid synthesis, and the roles of glycerophospholipids in bacterial metabolism and homeostasis. Recently discovered specific pathways of P . aeruginosa lipid synthesis indicate the lineage dependent mechanisms of fatty acids homeostasis. Pseudomonas glycerophospholipids ensure structure functions and play important roles in bacterial adaptation to environmental modifications. The lipidome of Pseudomonas contains a typical eukaryotic glycerophospholipid – phosphatidylcholine –, which is involved in bacteria–host interactions. The ability of Pseudomonas to exploit eukaryotic lipids shows specific and original strategies developed by these microorganisms to succeed in their infectious process. All compiled data provide the demonstration of the importance of studying the Pseudomonas lipidome to inhibit the infectious potential of these highly versatile germs. [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]

Deep lakes are of specific interest in the study of archaeal assemblages as chemical stratification in the water column allows niche differentiation and distinct community structure. Active archaeal community and potential nitrifiers were investigated monthly over 1 year by pyrosequencing 16 S rRNA transcripts and genes, and by quantification of archaeal amoA genes in two deep lakes. Our results showed that the active archaeal community patterns of spatial and temporal distribution were different between these lakes. The meromictic lake characterized by a stable redox gradient but variability in nutrient concentrations exhibited large temporal rearrangements of the dominant euryarchaeal phylotypes, suggesting a variety of ecological niches and dynamic archaeal communities in the hypolimnion of this lake. Conversely, T haumarchaeota Marine Group I (MGI) largely dominated in the second lake where deeper water layers exhibited only short periods of complete anoxia and constant low ammonia concentrations. Investigations conducted on archaeal amoA transcripts abundance suggested that not all lacustrine T haumarchaeota conduct the process of nitrification. A high number of 16 S rRNA transcripts associated to crenarchaeal group C3 or the Miscellaneous Euryarchaeotic Group indicates the potential for these uncharacterized groups to contribute to nutrient cycling in lakes. [ABSTRACT FROM AUTHOR]

The existence of microbial communities and the complex interactions that govern their dynamics have received considerable attention in recent years. Advances in genomic sequencing technologies have greatly enhanced our understanding of 'what is there'. However, the question as to 'what are they doing' remains less well defined. The continual development of the genomic and metagenomic sequence databases provides an exciting opportunity to interrogate the distribution and prevalence of key microbial systems across a diverse set of ecosystems. The widely distributed type VI secretion system ( T6SS) has been shown to play a significant role in bacterial-bacterial and bacterial-host interactions. While several T6SS effectors have been shown to target the cell wall and membrane of competing cells, little is known about the roles these proteins play in different ecosystems. Therefore, the prevalence of a key T6SS effector superfamily known as type six lipase effectors ( Tle) was studied in over 2000 metagenomic datasets representing diverse ecosystems and host niches. Increased Tle representation in environmental categories strongly supports the hypothesis of niche specialization and suggests that these effectors may play important niche-specific roles. [ABSTRACT FROM AUTHOR]

The discovery of denitrifying anaerobic methane oxidation with nitrite as electron acceptor mediated by ' C andidatus Methylomirabilis oxyfera' connected the biogeochemical carbon and nitrogen cycle in a new way. However, it is important to have a comprehensive understanding about the distribution of M . oxyfera-like bacteria in the terrestrial realm, especially the wetland ecosystems that are known as the largest natural source of atmospheric methane. Here, our molecular evidence demonstrated that a wide geographical distribution of M . oxyfera-like bacteria at oxic/anoxic interfaces of various wetlands ( n = 91) over the Chinese territory. Intriguingly, the M . oxyfera-like bacteria were detected in some extreme environments, indicating that M . oxyfera-like bacteria occupied a wide range of habitats. Quantitative polymerase chain reaction estimated that the abundance of M . oxyfera-like bacteria ranged from 2.2 × 103 to 2.3 × 107 copies g−1 dry soil, and up to around 0.62% of the total number of bacteria. Moreover, the M . oxyfera-like bacteria showed high biodiversity in wetland ecosystems based on the analysis of 462 pmoA and 287 16S rRNA gene sequences. The current study revealed the widespread distribution and biogeography of M . oxyfera-like bacteria in the terrestrial system. [ABSTRACT FROM AUTHOR]

Unraveling the distribution patterns of plants and animals along the elevational gradients has been attracting growing scientific interests of ecologists, whether the microbial communities exhibit similar elevational patterns, however, remains largely less documented. Here, we investigate the biogeographic distribution of soil archaeal and bacterial communities across three vertical climate zones (3,106-4,479 m.a.s.l.) in Mt. Shegyla on the Tibetan Plateau, by combining quantitative PCR and high-throughput barcoded pyrosequencing approaches. Our results found that the ratio of bacterial to archaeal 16S rRNA gene abundance was negatively related with elevation. Acidobacteria dominated in the bacterial communities, Marine benthic group A dominated in the archaeal communities, and the relative abundance of both taxa changed significantly with elevation. At the taxonomic levels of domain, phylum, and class, more bacterial taxa than archaeal exhibited declining trend in diversity along the increasing elevational gradient, as revealed by Shannon and Faith's phylogenetic diversity indices. Unweighted UniFrac distance clustering showed that the bacterial communities from the mountainous temperate zone clustered together, whereas those from the subalpine cool temperate zone clustered together. However, the partitioning effect of elevational zones on the archaeal community was much weaker compared to that on bacteria. Redundancy analysis revealed that soil geochemical factors explained 58.3 % of the bacterial community variance and 75.4 % of the archaeal community variance. Taken together, we provide evidence that soil bacteria exhibited more apparent elevational zonation feature and decreased diversity pattern than archaea with increasing elevation, and distribution patterns of soil microbes are strongly regulated by soil properties along elevational gradient in this plateau montane ecosystem. [ABSTRACT FROM AUTHOR]

Mesorhizobium muleiense , Mesorhizobium mediterraneum and Mesorhizobium ciceri are chickpea ( Cicer arietinum L.) rhizobia that share a high similarity of the symbiotic genes nodC and nifH , but they have different geographic distributions. M. muleiense has been isolated and found only in alkaline soils of Xinjiang, China, whereas the other two strains have been found in the Mediterranean and India. To investigate the species stability of M. muleiense during natural evolution and its capability of competitive nodulation against the other two exotic species, re-sampling of nodules in the field and competition experiments between the three species were conducted. The results showed that the predominant microsymbiont associated with chickpea grown in Xinjiang was still M. muleiense , but the predominant genotypes of M. muleiense had changed significantly during the four years since a previous survey. The data also showed that M. mediterraneum and M. ciceri were more competitive than the residential strain of M. muleiense CCBAU 83963 T in sterilized vermiculite or soils from Xinjiang. However, in non-sterilized soils, M. muleiense was the predominant nodule occupier. These results indicated that natural or adapting evolution of M. muleiense was occurring in fields subjected to changing environmental factors. In addition, the biogeography and symbiotic associations of rhizobia with their host legumes were also influenced by biological factors in the soil, such as indigenous rhizobia and other organisms. [ABSTRACT FROM AUTHOR]

The F irmicutes constitute a phylum of bacteria that can be found in a wide variety of habitats, from soil to the gastrointestinal tract of animals, where they have to thrive in complex communities. Competition in these communities usually involves the production of compounds such as antimicrobial peptides ( AMPs) to eliminate competitor organisms. Animals and plants also produce AMPs to control their associated microbiota. In turn, defence mechanisms have evolved to prevent the action of these compounds. The close association of some F irmicutes with humans as prominent pathogens or commensal organisms has driven a considerable research effort on defence mechanisms used by these bacteria against antimicrobial compounds. This review focuses on the most recent advances on two well-characterized defence mechanisms against AMPs: the modification of the cell wall by D-alanylation and the role of peptide antibiotic-specific adenosine triphosphate-binding cassette transporters. [ABSTRACT FROM AUTHOR]

Among the bacterial pathogens of Eucalyptus in Brazil, Ralstonia solanacearum is considered one of the most important because of the characteristics of the pathogen, like the high diversity among the strains related to host range, high virulence, broad geographical distribution and its damage to the crop in recent years. Given its importance and the lack of research on this pathosystem, the present study aimed to perform a molecular characterization of different strains of infected Eucalyptus plants in Brazil. A total of 19 bacterial cultures isolated from Eucalyptus in different regions of Brazil were analysed. A 372-bp product generated by multiplex- PCR amplification using Nmult primers identified all the strains analysed as belonging to phylotype II. Eighteen strains were grouped into subclade IIA and one into subclade IIB. The phylogenetic tree generated from the gene sequences of endoglucanase ( egl) confirmed the classification of the strains into phylotype II and separated the strains into sequevars. Strains AMC22, IBSBF2568 and IBSBF2576 were grouped into a single clade, as were strains UFV18 and UFV20, with 89% and 78% a posteriori probability, respectively, forming two new potential sequevars not yet defined. We also identified strains belonging to sequevars 41 (100% probability) and 37 (88% probability). However, most of the strains did not fit into any previously described sequevar and did not form distinct clades. The results of the analysis of fragments amplified using the ERIC- PCR technique indicated the existence of genetic diversity among the strains studied, with a generally high correlation between similarity and the geographical origin of the strains. [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]

Background: Architectural design has the potential to influence the microbiology of the built environment, with implications for human health and well-being, but the impact of design on the microbial biogeography of buildings remains poorly understood. In this study we combined microbiological data with information on the function, form, and organization of spaces from a classroom and office building to understand how design choices influence the biogeography of the built environment microbiome. Results: Sequencing of the bacterial 16S gene from dust samples revealed that indoor bacterial communities were extremely diverse, containing more than 32,750 OTUs (operational taxonomic units, 97% sequence similarity cutoff), but most communities were dominated by Proteobacteria, Firmicutes, and Deinococci. Architectural design characteristics related to space type, building arrangement, human use and movement, and ventilation source had a large influence on the structure of bacterial communities. Restrooms contained bacterial communities that were highly distinct from all other rooms, and spaces with high human occupant diversity and a high degree of connectedness to other spaces via ventilation or human movement contained a distinct set of bacterial taxa when compared to spaces with low occupant diversity and low connectedness. Within offices, the source of ventilation air had the greatest effect on bacterial community structure. Conclusions: Our study indicates that humans have a guiding impact on the microbial biodiversity in buildings, both indirectly through the effects of architectural design on microbial community structure, and more directly through the effects of human occupancy and use patterns on the microbes found in different spaces and space types. The impact of design decisions in structuring the indoor microbiome offers the possibility to use ecological knowledge to shape our buildings in a way that will select for an indoor microbiome that promotes our health and well-being. [ABSTRACT FROM AUTHOR]

Highlights: [•] We examined genetic diversity and geographic distribution of Brucella melitensis and Brucella abortus in Italy. [•] MLVA-16 distinguished 56 genotypes for B. melitensis, most isolates were in the West Mediterranean lineage. [•] MLVA-16 distinguished 32 genotypes for B. abortus but 77.8% of isolates had the same MLVA-11 genotype. [•] One B. melitensis from human had an identical genotype as a sheep isolate suggesting a possible epidemiological link. [•] Isolates with genotypes not typically found in Italy were readily identified. [ABSTRACT FROM AUTHOR]

In the first comprehensive geographical survey of distribution in Great Britain, Mycobacterium avium ssp. paratuberculosis ( MAP) was detected in 115 of 1092 (10.5%) soil cores, in the range of 5 × 102 to 3 × 106 MAP cell equivalents ( CE) g−1 wet weight soil with the majority of the positive PCR reactions ( n = 75; 65%) occurring around the limit of detection (500-5000 CE g−1 wet weight soil). The distribution of MAP significantly increased from North to South and was significantly correlated with increasing cattle numbers over the same longitudinal axis. Similarly MAP occurrence significantly increased towards easterly latitudes although none of the parameters measured were associated. Comparisons of land use indicated that MAP was widely distributed in both farming and non-farming areas. Soil core samples taken from the rivers Wyre and Douglas catchments ( Lancashire, UK) and river Tywi ( South Wales) were negative for MAP. However, river monitoring showed a consistent presence of MAPs throughout those catchments over a 6-month period. We concluded that MAP is widely distributed within and outside the confines of the farming environment; its geographical distribution is wider than originally anticipated and; monitoring rivers describes the MAP status of catchment better than individual soil samples. [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: Bacteria communities growing in constructed wetlands play a major role on the removal of pollutants from wastewater and the presence of a stable community is a critical factor affecting their performance. With this work we aimed at finding how long it takes for bacterial communities to stabilise in constructed wetlands and at answering specific questions regarding their abundance, spatial distribution and their relative importance on the treatment processes. To this end the numerical model BIO_PORE was used to simulate the dynamics of 6 functional bacteria groups (heterotrophic, autotrophic nitrifying, fermenting, acetotrophic methanogenic, acetotrophic sulphate reducing and sulphide oxidising bacteria) within a wetland for a period of 3years. Three indicators of bacterial stabilisation were used: 1) total biomass; b) effluent pollutant concentrations and c) Shannon's diversity index. Results indicate that aerobic bacteria dominated the wetland until the 80th day of operation. Anaerobic bacteria dominated the wetland from that moment and until the end of the studied period. Bacteria stability was reached between 400 and 700days after starting operation. Once the wetland reached stability, sulphate reducing bacteria accounted for the highest biomass of all bacterial groups (46%). The distribution of bacterial communities obtained after bacterial stability is consistent with available experimental results, and was clearly controlled by dissolved oxygen (SO) concentrations and H2S toxicity. After stability, the progressive accumulation of inert solids pushed the location of the active bacteria zone towards the outlet section. [Copyright &y& Elsevier]

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]

Edwardsiella tarda is one of the serious fish pathogens, infecting both cultured and wild fish species. Research on edwardsiellosis has revealed that E. tarda has a broad host range and geographic distribution, and contains important virulence factors that enhance bacterial survival and pathogenesis in hosts. Although recent progress in edwardsiellosis research has enabled the development of numerous, highly effective vaccine candidates, these efforts have not been translated into a commercialized vaccine. The present review aims to provide an overview of the identification, pathology, diagnosis and virulence factors of E. tarda in fish, and describe recent strategies for developing vaccines against edwardsiellosis. The hope is that this presentation will be useful not only from the standpoint of understanding the pathogenesis of E. tarda, but also from the perspective of facilitating the development of effective vaccines. [ABSTRACT FROM AUTHOR]

We report the diversity and distribution of Francisella species in Norwegian coastal and fresh waters following a nationwide survey in which water and sediment samples were collected from locations spanning almost the entire Norwegian coastline. In total, samples were obtained from 149 and 64 seawater and freshwater sites, respectively. DNA extracts from these environmental samples were initially screened by polymerase chain reaction (PCR) using Francisella genus-specific 16S rDNA primers. Positive samples were then amplified with genus-specific primers targeting Francisella succinate dehydrogenase A gene and Francisella philomiragia group-specific sequences for the SAICAR synthetase/phosphoribosylamine-glycine ligase gene. Francisella-related bacteria were identified in approximately 30% of seawater sampled sites, mainly in southern Norway, although a single positive sample was identified in the far north of the country. No PCR positives were identified from the freshwater sources. Sequences related to recognised species, both pathogenic and environmental, were identified, with the majority closely associated with F. philomiragia. However, a number of identified sequences probably represent previously undescribed species. Our data provide evidence of a significant background of Francisella spp. in geographical areas associated with outbreaks of fish francisellosis in Norway. [ABSTRACT FROM AUTHOR]

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]