Bacterial Genetic Diversity Research Articles

Finding Order in the Chaos: Outstanding Questions in Klebsiella pneumoniae Pathogenesis.

Klebsiella pneumoniae are Gram-negative facultative anaerobes that are found within host-associated commensal microbiomes, but they can also cause a wide range of infections that are often difficult to treat. These infections are caused by different pathotypes of K. pneumoniae, called either classical or hypervirulent strains. These two groups are genetically distinct, inhabit nonoverlapping geographies, and cause different types of harmful infections in humans. These distinct bacterial groups have also been found to interact differently with the host immune system. Initial innate immune defenses against K. pneumoniae infection include complement, macrophages, neutrophils, and monocytes; these defenses are primary strategies employed by the host to clear infections. K. pneumoniae pathogenesis depends upon the interactions between the microbe and each of these host defenses, and it is becoming increasingly apparent that bacterial genetic diversity impacts the outcomes of these interactions. Here, we highlight recent advances in our understanding of K. pneumoniae pathogenesis, with a focus on how bacterial evolution and diversity impact K. pneumoniae interactions with mammalian innate immune host defenses. We also discuss outstanding questions regarding how K. pneumoniae can frustrate normal immune responses, capitalize upon states of immunocompromise, and cause infections with high mortality.

Effects of biochar on bacterial genetic diversity in soil contaminated with cadmium

AbstractBiochar has various ecological effects on heavy metal‐contaminated soils. Biochar can be used to passivate the activity of heavy metals and improve environmental conditions for microbial growth. A greenhouse pot experiment was conducted to explore the diversity of microbes in red soil under cadmium (Cd) stress following the application of wheat straw biochar. The contaminant Cd was prepared at 2.5 mg kg‒1 with deionized water to simulate the heavy metal pollution of red soil under natural conditions, and the proportions of wheat straw biochar used were 2.5% and 10%. The complete genetic diversity of red soil bacteria in this study was evaluated using high‐throughput sequencing. The results showed that the bacterial genetic diversity of Cd‐contaminated red soils was restored with biochar treatment, and recovery with 2.5% biochar was significant. Biochar significantly affected the richness of soil bacteria by 6.79%–21.04%. Forty‐three phyla of bacteria, including Proteobacteria, Acidobacteria and Gemmatimonadetes, constituted the bacterial community in the red soils. Further principal component analysis showed that Cd pollution and biochar application collectively affected the bacterial genetic diversity. Hydrogenophaga, Rubrivivax, Haliscomenobacter, Citrobacter, Methylibium and Azospirillum were indicator strains for Cd‐contaminated red soils, while Steroidobacter, Bradyrhizobium, Anaerolinea, Chloronema Dubinina and Gorlenko were key strains for the biochar remediation of Cd contamination. In conclusion, for soil polluted with 2.5 mg kg Cd‒1, the application of 2.5% wheat straw biochar significantly increases soil microbial abundance and genetic diversity and plays an active role in improving the soil micro‐ecosystem.

The mechanisms underlying antigenic variation and maintenance of genomic integrity in Mycoplasma pneumoniae and Mycoplasma genitalium.

Mycoplasma pneumoniae and Mycoplasma genitalium are important causative agents of infections in humans. Like all other mycoplasmas, these species possess genomes that are significantly smaller than that of other prokaryotes. Moreover, both organisms possess an exceptionally compact set of DNA recombination and repair-associated genes. These genes, however, are sufficient to generate antigenic variation by means of homologous recombination between specific repetitive genomic elements. At the same time, these mycoplasmas have likely evolved strategies to maintain the stability and integrity of their 'minimal' genomes. Previous studies have indicated that there are considerable differences between mycoplasmas and other bacteria in the composition of their DNA recombination and repair machinery. However, the complete repertoire of activities executed by the putative recombination and repair enzymes encoded by Mycoplasma species is not yet fully understood. In this paper, we review the current knowledge on the proteins that likely form part of the DNA repair and recombination pathways of two of the most clinically relevant Mycoplasma species, M. pneumoniae and M. genitalium. The characterization of these proteins will help to define the minimal enzymatic requirements for creating bacterial genetic diversity (antigenic variation) on the one hand, while maintaining genomic integrity on the other.

Effect of monospecific and mixed litters on bacterial communities' structure and functions under contrasting Mediterranean climate conditions

Global climate change is expected to contribute to intense droughts and heatwaves in the Mediterranean basin, motivating ecological research to explore the responses of litter microbial communities to more drastic climatic conditions. Here, we investigated how the functioning of microbial decomposition systems may be affected by litter source and mixing in two contrasting Mediterranean climate contexts: a sub-humid climate in France vs a semi-arid climate in Algeria. Studies included in situ incubation of litter bags of monospecific litters (Pinus halepensis, Pistacia lentiscus, and Quercus ilex) and binary mixtures (Pinus/Pistacia; Pinus/Quercus) of litters in France and Algeria. Following a 12-month incubation, the remaining litter was chemically characterised using elemental analyses and solid-state 13C NMR spectroscopy. Microbial properties evaluated included basal respiration (BR), active microbial biomass (MB), community-level physiological profiling (CLPP), and molecular fingerprinting (T-RFLP). In both countries, negative correlations were observed between MB and ratios of C/N and (aromatics+phenols)/N. Basal respiration was also negatively correlated to both ratios in France; however, the opposite trend was found in Algeria. The effect of litter mixing on MB, BR, and microbial functional diversity (catabolic diversity index ECO H′) also differed between climates. The mixture of Pinus and Quercus litter led to limited heterotrophic CO2 release in the Algerian arid context i.e. a synergistic effect on MB associated with an antagonistic effect on BR. Higher bacterial genetic diversity (Terminal Restriction Fragment TRF richness and evenness) was found in Algeria whereas higher functional diversity (catabolic diversity index ECO H′) was found in France, suggesting that the higher genetic diversity potential in the arid climate context did not lead to functionally diverse bacterial communities. Our findings on the differing effect of litter chemical properties- (aromatics+phenols)/N and C/N- on microbial functioning (BR and MB) in sub-humid and semi-arid climates indicate that the impact of litter chemistry (litter source; litter admixtures) on C cycling is climate-dependent.

Tuber aestivum is associated with changes in soil chemistry and reduced biological quality in a Quercus pubescens stand in Northern Italy

Truffles contribute both directly and indirectly to important dynamics in the soil web, being involved in a large number of ecological functions that are crucial for terrestrial ecosystems. Despite this, the interrelationships between true truffles, i.e. hypogeous ectomycorrhizal fungi producing valuable fruiting bodies, and other elements of the soil system are largely unknown. In this study, we aimed to shed new light on whether and how much Tuber aestivum affects soil microbial activities (evaluated as enzyme activities), abundance (assayed as soil DNA content) and bacterial genetic diversity along with soil chemical properties. We compared chemical and biological variables inside and outside brûlés (i.e. areas inhabited by truffles with scarce vegetation cover around host plants) in two seasons, namely spring and summer, using both a linear mixed model and a multivariate two-block partial least squares approach. The areas with truffle presence had higher pH but lower organic carbon and nitrogen content. Similarly, all enzyme activities were lower inside the brûlé than outside, with the exception of peroxidase. A soil quality index (i.e. AI3) based on three enzyme activities (β-glucosidase, acid phosphomonoesterase and urease) indicated a reduction in soil quality inside the brûlé. Overall, soil DNA content responded to an interaction of truffle presence/absence and season, while bacterial genetic diversity indexes were higher in spring. Despite the observational nature of this study, results point out that T. aestivum can be considered a key species in the soil where it is present as it was associated with changes in chemistry as well as microbial activity that were generally more conspicuous than mere seasonal effects, although the causative nature of these associations still needs to be confirmed.

Dynamics of within-host Mycobacterium tuberculosis diversity and heteroresistance during treatment

BackgroundStudying within-host genetic diversity of Mycobacterium tuberculosis (Mtb) in patients during treatment may identify adaptations to antibiotic and immune pressure. Understanding the significance of genetic heteroresistance, and more specifically heterozygous resistance-associated variants (RAVs), is clinically important given increasing use of rapid molecular tests and whole genome sequencing (WGS). MethodsWe analyse data from six studies in KwaZulu-Natal, South Africa. Most patients (>75%) had baseline rifampicin resistance. Sputum was collected for culture at baseline and at between two and nine intervals until month six. Positive cultures underwent WGS. Mixed infections and reinfections were excluded from analysis. FindingsBaseline Mtb overall genetic diversity (at treatment initiation or major change to regimen) was associated with cavitary disease, not taking antiretroviral therapy if HIV infected, infection with lineage 2 strains and absence of second-line drug resistance on univariate analyses. Baseline genetic diversity was not associated with six-month outcome. Genetic diversity increased from baseline to weeks one and two before returning to previous levels. Baseline genetic heteroresistance was most common for bedaquiline (6/10 [60%] of isolates with RAVs) and fluoroquinolones (9/62 [13%]). Most patients with heterozygous RAVs on WGS with sequential isolates available demonstrated RAV persistence or fixation (17/20, 85%). New RAVs emerged in 9/286 (3%) patients during treatment. We could detect low-frequency RAVs preceding emergent resistance in only one case, although validation of deep sequencing to detect rare variants is required. InterpretationIn this study of single-strain Mtb infections, baseline within-host bacterial genetic diversity did not predict outcome but may reveal adaptations to host and drug pressures. Predicting emergent resistance from low-frequency RAVs requires further work to separate transient from consequential mutations. FundingWellcome Trust, NIH/NIAID

Genetic diversity of bacteria in bioremediation system of iron mine tailing by Robinia pseudoacacia - Ryegrass - Trifolium repens

To exploration the change of microorganism in iron tailing sand restoration, a bioremediation system of iron tailing sand by combination of Robinia pseudoacacia - Ryegrass-Trifolium repens pus soil or bio-matrix flowerpot was designed, the change of bacterial quantity and genetic diversity at different time was determined. The tailings and soil samples C1 (tailings), C2 (tailings adjacent to biologic pot) and C3 (Robinia pseudoacacia rhizosphere soil), were collected on the 180th d, 270th d and the 360th d. The bacterial quantity was determined, the bacterial strains were isolated and purified, and genetic diversity was studied by BOXA1R-PCR and 16S rDNA sequencing. The results showed that along the restoration time increasing, the number of bacteria in C2 and C3 increased from 4.81×105 cfu·g−1 and 11.82×105 cfu·g−1 to 5.99×105 cfu·g−1 and 15.67×105 cfu·g−1 at 270th d, then to 8.96×105 cfu·g−1 and 21.96×105 cfu·g−1 at 360th d, respectively, while there was little change in C1. From these samples, a total of 32, 46 and 52 bacterial strains were isolated, and the genetic diversity was determined by BOXA1R-PCR, the results showed that there were 7, 9 and 10 BOXA1R groups formed, respectively; phylogenetic analysis of representatives suggested that genus Bacillus were the predominant, and bacteria with biological nitrogen fixation ability, distributed in Rhizobium, Ensifer, Azotobacter, etc. were founded during the iron tailing sand bioremediation. The results suggests that bio-matrix flowerpot combining Robinia pseudoacacia - Ryegrass - Trifolium repens cultivar can increase the bacterial quantity and genetic diversity in iron tailing sand significantly, and probably has a good application potential for tailings restoration.

Soil Microbial Diversity, Biomass, and Activity in Two Pine Plantations of Southern Italy Treated with Prescribed Burning

Microbial diversity plays a crucial role in ecosystem processes, including organic matter decomposition and nutrient cycling. This research explores the effect of prescribed burning (PB) on soil microbial diversity, as well as biomass and activity in Mediterranean pine plantations. In burned and adjacent unburned plots of Pinus pinea and P. pinaster plantations of Southern Italy protected areas, the fermentation layer and the 5 cm thick layer of mineral soil underneath were sampled at intervals during the first year after PB. The experimental protocol encompassed measurements of total microbial abundance (Cmic and soil DNA), fungal mycelium, fungal fraction of Cmic, microbial activity, bacterial genetic diversity (16S rDNA PCR-DGGE), microbial metabolic quotient (qCO2), and C mineralization rate (CMR), as well as physical and chemical soil properties. PB caused only temporary (up to 3 h–32 d) reductions in Cmic, DNA amount, fungal mycelium, respiration, and CMR in the P. pinaster plantation, and had no appreciable negative effect on the microbial community in P. pinea plantation, where fire intensity was lower because of less abundant litter fuel. In either plantation, PB did not generally reduce bacterial genetic diversity (evaluated as band richness, Shannon index, and evenness), thus, also accounting for the fast recovery in microbial growth and activity after high-intensity PB in P. pinaster plantation. While confirming PB as a sustainable practice to reduce wildfire risk, also supported by data on plant community obtained in the same plantations, the results suggest that an integrated analysis of microbial diversity, growth, and activity is essential for an accurate description of PB effects on soil microbial communities.

Are Cowpea-Nodulating Bradyrhizobial Communities Influenced by Biochar Amendments in Soils? Genetic Diversity and Symbiotic Effectiveness Assessment of Two Agricultural Soils of Brazilian Drylands

The objective of this study was to evaluate the influence of biochar amendment on the bacterial genetic diversity and symbiosis in cowpea-nodulating rhizobial communities in two agricultural soils of Brazilian drylands. Vertisol and Ultisol surface layer soil samples were collected in the Brazilian semiarid region. The soils were mixed with biochar and cowpea seeds (BRS Marataoa) and sown in pots. Forty-five days after plant emergence, the nodule bacteria were isolated. The genetic variability of the nodule bacteria was evaluated by means of restriction fragment length polymorphism of 16S-23S rRNA intergenic spacer region (IGS-RFLP), and those that shared identical IGS-RFLP profiles were fingerprinted by BOX-PCR. By selecting of representative isolates in the genetic clusters, 27 bacteria were identified by 16S-23S IGS sequencing and symbiotically assessed. The IGS-RFLP dendrogram of the 73 isolates had 20 clusters; the multivariate correspondence analysis grouped both Vertisol treatments, and the Ultisol treatments were placed far away in the biplot. Ultisol showed higher bradyrhizobial diversity than the Vertisol. The fingerprinting indicated the presence of only three clonal colonies, showing high intraspecific diversity. The 16S-23S IGS sequences indicated the prevalence of bacteria related to Bradyrhizobium guangxiense in the Vertisol and Bradyrhizobium zhanjiangense in the Ultisol, in addition to the presence of three putative Microvirga spp. in the Ultisol. The symbiotic efficiency of 22 out of 27 bacteria was comparable with that of the inoculant strain Bradyrhizobium yuanmingense BR 3267. The genetic diversity of the cowpea-nodulating bradyrhizobia was not primarily affected by the biochar application in two agricultural soils of Brazilian drylands. Both soils harbored symbiotically efficient bacteria, without the influence of biochar amendment .

Effects of Host, Sample, and in vitro Culture on Genomic Diversity of Pathogenic Mycobacteria.

Mycobacterium tuberculosis (M. tb), an obligate human pathogen and the etiological agent of tuberculosis (TB), remains a major threat to global public health. Comparative genomics has been invaluable for monitoring the emergence and spread of TB and for gaining insight into adaptation of M. tb. Most genomic studies of M. tb are based on single bacterial isolates that have been cultured for several weeks in vitro. However, in its natural human host, M. tb comprises complex, in some cases massive bacterial populations that diversify over the course of infection and cannot be wholly represented by a single genome. Recently, enrichment via hybridization capture has been used as a rapid diagnostic tool for TB, circumventing culturing protocols and enabling the recovery of M. tb genomes directly from sputum. This method has further applicability to the study of M. tb adaptation, as it enables a higher resolution and more direct analysis of M. tb genetic diversity within hosts with TB. Here we analyzed genomic material from M. tb and Mycobacterium bovis populations captured directly from sputum and from cultured samples using metagenomic and Pool-Seq approaches. We identified effects of sampling, patient, and sample type on bacterial genetic diversity. Bacterial genetic diversity was more variable and on average higher in sputum than in culture samples, suggesting that manipulation in the laboratory reshapes the bacterial population. Using outlier analyses, we identified candidate bacterial genetic loci mediating adaptation to these distinct environments. The study of M. tb in its natural human host is a powerful tool for illuminating host pathogen interactions and understanding the bacterial genetic underpinnings of virulence.

Genetic diversity and community structure of soil bacteria in Chinese fir plantations

To explore the diversity of soil bacteria and changes in the bacterial community structure of Chinese fir plantations of different generations and developmental stages, the genetic diversity of soil bacteria was studied using the 454 sequencing technology. The results showed that the bacterial genetic diversity and community structure of Chinese fir plantation plots under monoculture planting and rotation planting practices were as follows: the Shannon diversity indices of first-generation young plantation of Chinese fir plantations (FYC), second-generation young plantation (SYC), and third-generation young plantation (TYC) initially decreased and then increased to 8.45, 8.1, and 8.43, respectively. Due to different management and tending measures, the phyla showing considerable differences in relative abundance were Cyanobacteria, Nitrospirae, Fibrobacteres, Thermotogae, and Planctomycetes. The bacterial genetic diversity and community structure of Chinese fir plantations at different developmental stages were as follows: the bacterial diversity and the number of operational taxonomic units (OTUs) decreased with increasing forest age; with the increasing forest age of Chinese fir, the bacteria with considerable differences in the relative abundance were Burkholderiales, Xanthomonadales, Ktedonobacteria, Nitrosomonadales, Anaerolineae, and Holophagae. The predominant bacteria of the Chinese fir plantations were Acidothermus, Bradyrhizobium, Lactococcus, Planctomyces, Sorangium, and Bryobacter.

Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia

BackgroundLarge-scale genomic studies of within-host diversity in Staphylococcus aureus bacteraemia (SAB) are needed to understanding bacterial adaptation underlying persistence and thus refining the role of genomics in management of SAB. However, available comparative genomic studies of sequential SAB isolates have tended to focus on selected cases of unusually prolonged bacteraemia, where secondary antimicrobial resistance has developed.MethodsTo understand bacterial genetic diversity during SAB more broadly, we applied whole genome sequencing to a large collection of sequential isolates obtained from patients with persistent or relapsing bacteraemia. After excluding genetically unrelated isolates, we performed an in-depth genomic analysis of point mutations and chromosome structural variants arising within individual SAB episodes.ResultsWe show that, while adaptation pathways are heterogenous and episode-specific, isolates from persistent bacteraemia have a distinctive molecular signature, characterised by a low mutation frequency and high proportion of non-silent mutations. Analysis of structural genomic variants revealed that these often overlooked genetic events are commonly acquired during SAB. We discovered that IS256 insertion may represent the most effective driver of within-host microevolution in selected lineages, with up to three new insertion events per isolate even in the absence of other mutations. Genetic mechanisms resulting in significant phenotypic changes, such as increases in vancomycin resistance, development of small colony phenotypes, and decreases in cytotoxicity, included mutations in key genes (rpoB, stp, agrA) and an IS256 insertion upstream of the walKR operon.ConclusionsThis study provides for the first time a large-scale analysis of within-host genomic changes during invasive S. aureus infection and describes specific patterns of adaptation that will be informative for both understanding S. aureus pathoadaptation and utilising genomics for management of complicated S. aureus infections.

The Structure and Diversity of Bacterial Communities in Differently Managed Soils Studied by Molecular Fingerprinting Methods

The soil bacterial community structure is sensitive to different agricultural management practices and changes in the soil community composition can affect ecosystem sustainability and ecosystem stability. The basic idea of reduced and conservation soil tillage technologies is to preserve favorable soil parameters and also to enhance soil fertility and to reduce the negative impacts on the soil. Four soil tillage treatments—conventional, reduced, mulch-till, and no-till—were studied for their bacterial communities at a soil depth of 10 cm in September 2013 and April 2014 using the automated ribosomal intergenic spacer analysis (ARISA) and the terminal restriction fragment length polymorphism (T-RFLP) methods. The total microbial biomass was statistically higher in April 2014 than in September 2013 in all tillage treatments. On the other hand, no statistical differences were detected in the bacterial richness between the sampling dates in all tillage treatments. Only one statistical difference regarding the bacterial richness was detected between the conventional and reduced tillage in September 2013 by using ARISA. Bacterial genetic diversity measured by the Gini–Simpson, Shannon, and Pielou indices did not indicate differences among the four types of soil management systems. Additionally, no substantial variation in the composition of bacterial communities under different treatments was observed based on the principal component analysis and cluster analysis. Additionally, the changes in bacterial community composition between both sampling dates have not occurred overall or within the individual agricultural management systems.

Strategies used by helicobacter pylori to establish persistent infection.

Helicobacter pylori (H. pylori) is a Gram-negative and motile bacterium that colonizes the hostile microniche of the human stomach, then persists for the host’s entire life, if not effectively treated. Clinically, H. pylori plays a causative role in the development of a wide spectrum of diseases including chronic active gastritis, peptic ulceration, gastric adenocarcinoma, and gastric mucosa-associated lymphoid tissue lymphoma. Due to the global distribution of H. pylori, it is no exaggeration to conclude that smart strategies are contributing to adaptation of the bacterium to its permanent host. Thirty-four years after the discovery of this bacterium, there are still many unanswered questions. For example, which strategies help the bacterium to survive in this inhospitable microniche? This question is slightly easier to answer if we presume the same clinical concept for both persistent infection and disease. Understanding the mechanisms governing H. pylori persistence will improve identification of the increased risk of diseases such as gastric cancer in patients infected with this bacterium. A well-defined and long-term equilibrium between the human host and H. pylori allows bacterial persistence in the gastric microniche; although this coexistence leads to a high risk of severe diseases such as gastric cancer. To escape the bactericidal activity of stomach acid, H. pylori secretes large amounts of surface-associated and cytosolic urease. The potential to avoid acidic conditions and immune evasion are discussed in order to explain the persistence of H. pylori colonization in the gastric mucosa, and data on bacterial genetic diversity are included. Information on the mechanisms related to H. pylori persistence can also provide the direction for future research concerning effective therapy and management of gastroduodenal disorders. The topics presented in the current review are important for elucidating the strategies used by H. pylori to help the bacterium persist in relation to the immune system and the many unfavorable features of living in the gastric microniche.

Monitoring of Rhizosphere Bacterial Communities in Soil with Sewage Sludge Addition Using Two Molecular Fingerprinting Methods: Do These Methods Give Similar Results?

Abstract In this study, bacterial genetic diversity from the rhizosphere of barley and wheat were studied. The plants were sown in pots with aliquot amount of 15 t/ha concentration of soil additive derived from sewage sludge and agricultural by-products represented by wastes from grain mill industry and crushed corn cobs. The plants sown in pots without the addition of soil additive represented control samples. The rhizosphere samples were collected on two dates (plant flowering and maturity) and the composition of bacterial communities were detected using two molecular fingerprinting methods – automated ribosomal intergenic spacer analysis (ARISA) and terminal restriction fragment length polymorphism (T-RFLP). Microbial biomass expressed as the amount of metagenomics DNA was higher in soils with addition of soil additive, except during maturity stage in barley rhizosphere. Nevertheless, statistically significant differences between control and sludge samples were not detected in any case. Similarly, no changes were detected in the composition of bacterial community between control and sludge samples in barley and wheat rhizosphere by using cluster analysis. Only minor temporal changes in the composition of bacterial community between flowering and maturity periods were observed. These changes were related to the samples collected in the plant maturity stage. In this stage, plants were completely mature and their impact on the rhizosphere bacterial communities in the form of root exudates was limited. Statistically significant differences between ARISA and T-RFLP methods were detected in all measured values of diversity indices. Despite these differences, both methods gave results leading to similar conclusions.

The genetic diversity of soil bacteria affected by phytoremediation in a typical barren rare earth mined site of South China.

The soil bacterial diversity is one of the most important indicators to evaluate the effect of phytoremediation. In this study, the technologies of Sequence-Related Amplified Polymorphism (SRAP) and 16S rRNA gene sequence analysis were used to evaluate the soil bacterial diversity after phytoremediation in a barren rare earth mined area. The results showed that the plant density was remarkably increased after the phytoremediation. The SRAP analysis suggested that the soil bacterial diversity declined dramatically after mining, while increased significantly in second and third year of the phytoremediation. A total of eight bacterial genera were identified by using 16S rRNA gene sequence analysis, with Arthrobacter and Bacillus as the dominant species before the mining, and Brevibacillus as the dominant species after the mining and during the first year of the phytoremediation. The Bacillus, which was a dominant type of bacteria before the mining, disappeared after mining and appeared again in the second and third years of the phytoremediation, other bacterial genera present. Principal component analysis and 16S rRNA gene analysis revealed a new bacterial type after phytoremediation that was not existed in the original mined area. The results of the present study indicated that the soil bacterial richness and genetic diversity significantly increased after the phytoremediation in the mined site.

Role of bacteria in the production and degradation of Microcystis cyanopeptides.

The freshwater cyanobacteria, Microcystis sp., commonly form large colonies with bacteria embedded in their mucilage. Positive and negative interactions between Microcystis species and their associated bacteria have been reported. However, the potential role of bacteria in the production and degradation of cyanobacterial secondary metabolites has not been investigated. In this study, a Microcystis‐associated bacterial community was isolated and added to the axenic M. aeruginosa PCC7806 liquid culture. After 3 years of cocultivation, we studied the bacterial genetic diversity adapted to the PCC7806 strain and compared the intra‐ and extracellular concentration of major cyanopeptides produced by the cyanobacterial strain under xenic and axenic conditions. Mass spectrometric analyses showed that the intracellular concentration of peptides was not affected by the presence of bacteria. Interestingly, the produced peptides were detected in the axenic media but could not be found in the xenic media. This investigation revealed that a natural bacterial community, dominated by Alpha‐proteobacteria, was able to degrade a wide panel of structurally varying cyclic cyanopeptides.

Malagasy bats shelter a considerable genetic diversity of pathogenic Leptospira suggesting notable host-specificity patterns.

Pathogenic Leptospira are the causative agents of leptospirosis, a disease of global concern with major impact in tropical regions. Despite the importance of this zoonosis for human health, the evolutionary and ecological drivers shaping bacterial communities in host reservoirs remain poorly investigated. Here, we describe Leptospira communities hosted by Malagasy bats, composed of mostly endemic species, in order to characterize host-pathogen associations and investigate their evolutionary histories. We screened 947 individual bats (representing 31 species, 18 genera and seven families) for Leptospira infection and subsequently genotyped positive samples using three different bacterial loci. Molecular identification showed that these Leptospira are notably diverse and include several distinct lineages mostly belonging to Leptospira borgpetersenii and L. kirschneri. The exploration of the most probable host-pathogen evolutionary scenarios suggests that bacterial genetic diversity results from a combination of events related to the ecology and the evolutionary history of their hosts. Importantly, based on the data set presented herein, the notable host-specificity we have uncovered, together with a lack of geographical structuration of bacterial genetic diversity, indicates that the Leptospira community at a given site depends on the co-occurring bat species assemblage. The implications of such tight host-specificity on the epidemiology of leptospirosis are discussed.

Stimulation of bacteria and protists in rhizosphere of glyphosate-treated barley

Glyphosate is extensively used for weed control and to ripen crops. Despite a number of studies on the direct effect of glyphosate on plants and soil organisms, only little is known about indirect effect of glyphosate on rhizosphere microbial communities, following the accelerated turnover of the fast-dying root biomass. In microcosms we studied the indirect effect of glyphosate on the microbial community in the rhizosphere of barley with phyllosphere application of glyphosate in comparison to leaving the plant intact or cutting off the shoot. Attempting to link the response of bacterial and protist communities to foliar application of glyphosate, we measured bacterial and protist abundance, diversity and physiological status, as well as soil organic carbon. Foliar application of glyphosate doubled bacterial abundance of the culturable fraction present in the rhizosphere compared to the other treatments with no effect on total abundance. Also the abundance of culturable protists increased as an effect of glyphosate and the bacterial genetic diversity as revealed by 16S rDNA DGGE analysis was affected. Overall, the results indicate that when barley leaves are treated with glyphosate, the availability of organic carbon in the rhizosphere of the dying roots is altered, which in turn may alter the bacterial and protist communities and their interactions. This can have implications for general soil carbon turnover processes and CO2 release in arable systems.

Assessment of a metaviromic dataset generated from nearshore Lake Michigan

Bacteriophages are powerful ecosystem engineers. They drive bacterial mortality rates and genetic diversity, and affect microbially mediated biogeochemical processes on a global scale. This has been demonstrated in marine environments; however, phage communities have been less studied in freshwaters, despite representing a potentially more diverse environment. Lake Michigan is one of the largest bodies of freshwater on the planet, yet to date the diversity of its phages has yet to be examined. Here, we present a composite survey of viral ecology in the nearshore waters of Lake Michigan. Sequence analysis was performed using a web server previously used to analyse similar data. Our results revealed a diverse community of DNA phages, largely comprising the order Caudovirales. Within the scope of the current study, the Lake Michigan virome demonstrates a distinct community. Although several phages appeared to hold dominance, further examination highlighted the importance of interrogating metagenomic data at the genome level. We present our study as baseline information for further examination of the ecology of the lake. In the current study we discuss our results and highlight issues of data analysis which may be important for freshwater studies particularly, in light of the complexities associated with examining phage ecology generally.