Diverse reductive dehalogenases are associated with Clostridiales-enriched microcosms dechlorinating 1,2-dichloroethane

The achievement of successful biostimulation of active microbiomes for the cleanup of a polluted site is strictly dependent on the knowledge of the key microorganisms equipped with the relevant catabolic genes responsible for the degradation process. In this work, we present the characterization of the bacterial community developed in anaerobic microcosms after biostimulation with the electron donor lactate of groundwater polluted with 1,2-dichloroethane (1,2-DCA). Through a multilevel analysis, we have assessed (i) the structural analysis of the bacterial community; (ii) the identification of putative dehalorespiring bacteria; (iii) the characterization of functional genes encoding for putative 1,2-DCA reductive dehalogenases (RDs). Following the biostimulation treatment, the structure of the bacterial community underwent a notable change of the main phylotypes, with the enrichment of representatives of the order Clostridiales. Through PCR targeting conserved regions within known RD genes, four novel variants of RDs previously associated with the reductive dechlorination of 1,2-DCA were identified in the metagenome of the Clostridiales-dominated bacterial community

Biodegradation of microcystin-LR using acclimatized bacteria isolated from different units of the drinking water treatment plant

Bacterial community isolated from different units of a Drinking Water Treatment Plant (DWTP) including pre-ozonation unit (POU), the effluent-sludge mixture of the sedimentation unit (ESSU) and top-sand layer water sample from the filtration unit (TSFU) were acclimatized separately in the microcystin-leucine arginine (MC-LR)-rich environment to evaluate MC-LR biodegradation. Maximum biodegradation efficiency of 97.2 ± 8.7% was achieved by the acclimatized-TSFU bacterial community followed by 72.1 ± 6.4% and 86.2 ± 7.3% by acclimatized-POU and acclimatized-ESSU bacterial community, respectively. Likewise, the non-acclimatized bacterial community showed similar biodegradation efficiency of 71.1 ± 7.37%, 86.7 ± 3.19% and 94.35 ± 10.63% for TSFU, ESSU and POU, respectively, when compared to the acclimatized ones. However, the biodegradation rate increased 1.5-folds for acclimatized versus non-acclimatized conditions. The mass spectrometry studies on MC-LR degradation depicted hydrolytic linearization of cyclic MC-LR along with the formation of small peptide fragments including Adda molecule that is linked to the reduced toxicity (qualitative toxicity analysis). This was further confirmed quantitatively by using Rhizobium meliloti as a bioindicator. The acclimatized-TSFU bacterial community comprised of novel MC-LR degrading strains, Chryseobacterium sp. and Pseudomonas fragi as confirmed by 16S rRNA sequencing. Biodegradation of microcystin-LR by in-situ bacterial community present in the drinking water treatment plant without formation of toxic by-product.Fil: Kumar, Pratik. Université du Québec a Montreal; CanadáFil: Hegde, Krishnamoorthy. Université du Québec a Montreal; CanadáFil: Brar, Satinder Kaur. Université du Québec a Montreal; CanadáFil: Cledón, Maximiliano. Universidad Nacional del Comahue; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Kermanshahi-pour, Azadeh. Dalhousie University Halifax; CanadáFil: Roy-Lachapelle, Audrey. University of Montreal; CanadáFil: Galvez-Cloutier, Rosa. Laval University; Canad

Statistics of correlated percolation in a bacterial community

Signal propagation over long distances is a ubiquitous feature of multicellular communities, but cell-to-cell variability can cause propagation to be highly heterogeneous. Simple models of signal propagation in heterogenous media, such as percolation theory, can potentially provide a quantitative understanding of these processes, but it is unclear whether these simple models properly capture the complexities of multicellular systems. We recently discovered that in biofilms of the bacterium Bacillus subtilis, the propagation of an electrical signal is statistically consistent with percolation theory, and yet it is reasonable to suspect that key features of this system go beyond the simple assumptions of basic percolation theory. Indeed, we find here that the probability for a cell to signal is not independent from other cells as assumed in percolation theory, but instead is correlated with its nearby neighbors. We develop a mechanistic model, in which correlated signaling emerges from cell division, phenotypic inheritance, and cell displacement, that reproduces the experimentally observed correlations. We find that the correlations do not significantly affect the spatial statistics, which we rationalize using a renormalization argument. Moreover, the fraction of signaling cells is not constant in space, as assumed in percolation theory, but instead varies within and across biofilms. We find that this feature lowers the fraction of signaling cells at which one observes the characteristic power-law statistics of cluster sizes, consistent with our experimental results. We validate the model using a mutant biofilm whose signaling probability decays along the propagation direction. Our results reveal key statistical features of a correlated signaling process in a multicellular community. More broadly, our results identify extensions to percolation theory that do or do not alter its predictions and may be more appropriate for biological systems.P50 GM085764 - NIGMS NIH HHS; Howard Hughes Medical Institute; R01 GM121888 - NIGMS NIH HHSPublished versio

Bacterial Community Reconstruction Using A Single Sequencing Reaction

Bacteria are the unseen majority on our planet, with millions of species and comprising most of the living protoplasm. While current methods enable in-depth study of a small number of communities, a simple tool for breadth studies of bacterial population composition in a large number of samples is lacking. We propose a novel approach for reconstruction of the composition of an unknown mixture of bacteria using a single Sanger-sequencing reaction of the mixture. This method is based on compressive sensing theory, which deals with reconstruction of a sparse signal using a small number of measurements. Utilizing the fact that in many cases each bacterial community is comprised of a small subset of the known bacterial species, we show the feasibility of this approach for determining the composition of a bacterial mixture. Using simulations, we show that sequencing a few hundred base-pairs of the 16S rRNA gene sequence may provide enough information for reconstruction of mixtures containing tens of species, out of tens of thousands, even in the presence of realistic measurement noise. Finally, we show initial promising results when applying our method for the reconstruction of a toy experimental mixture with five species. Our approach may have a potential for a practical and efficient way for identifying bacterial species compositions in biological samples.Comment: 28 pages, 12 figure

From high throughput 454 GS FLX data analysis process of 16S RNA gene sequences using barcoding to bacterial community exploration

From high throughput 454 GS FLX data analysis process of 16S RNA gene sequences using barcoding to bacterial community exploratio

Resolving environmental drivers of microbial community structure in Antarctic soils

Antarctic soils are extremely cold, dry, and oligotrophic, yet harbour surprisingly high bacterial diversity. The severity of environmental conditions has constrained the development of multi-trophic communities, and species richness and distribution is thought to be driven primarily by abiotic factors. Sites in northern and southern Victoria Land were sampled for bacterial community structure and soil physicochemical properties in conjunction with the US and New Zealand Latitudinal Gradient Project. Bacterial community structure was determined using a high-resolution molecular fingerprinting method for 80 soil samples from Taylor Valley and Cape Hallett sites which are separated by five degrees of latitude and have distinct soil chemistry. Taylor Valley is part of the McMurdo Dry Valleys, while Cape Hallett is the site of a penguin rookery and contains ornithogenic soils. The influence of soil moisture, pH, conductivity, ammonia, nitrate, total nitrogen and organic carbon on community structure was revealed using Spearman rank correlation, Mantel test, and principal components analysis. High spatial variability was detected in bacterial communities and community structure was correlated with soil moisture and pH. Both unique and shared bacterial community members were detected at Taylor Valley and Cape Hallett despite the considerable distance between the sites

Responses in bacterial community structure to waste nutrients from aquaculture: an in situ microcosm experiment in a Chilean fjord

Indexación: Web of Science; Scopus.Chilean salmon farms release inorganic nutrients excreted by the fish into the surrounding water in Patagonian fjords. The objective of this experiment from the Comau Fjord (42.2 degrees S) in southern Chile was to study how increased input of ammonium (NH4) and phosphate (PO4) from salmon farms might affect the community structure of bacteria in surface waters where fish farms are located. We used microcosms (35 l) with NH4-N and PO4-P added to the natural seawater in a gradient of nutrient-loading rates, with the same N: P ratio as in salmon aquaculture effluents. Additionally, we measured bacterial community structure at different depths in the Comau Fjord to assess the natural variation to compare with our experiment. We used denaturing gradient gel electrophoresis (DGGE) to create 16S rDNA fingerprints of the bacterial communities and monitored biological and environmental variables (chlorophyll a, inorganic nutrients, pH, microbial abundance). The nutrient- loading rate had a significant impact on the bacterial community structure, and the community dissimilarity between low and high nutrient additions was up to 78%. Of the measured environmental variables, phytoplankton abundance and increased pH from photosynthesis had a significant effect. We observed no significant changes in bacterial diversity, which remained at the same level as in the unmanipulated community. Thus, the bacterial community of the fjord was not resistant, but resilient within the time frame and nutrient gradient of our experiment.http://www.int-res.com/abstracts/aei/v9/p21-32

Are Bursaphelenchus xylophilus-associated bacteria playing a role in pine wilt disease?

Pine wilt disease (PWD), presently the most severe coniferous disease worldwide, is caused by the plant parasitic nematode Bursaphelenchus xylophilus, the pinewood nematode (PWN). Although PWN is considered the major pathogenic factor in PWD, its associated bacterial community is not ruled out as potential helpers in this complex and still little understood disease. This work presents the characterization of PWN-associated bacteria and plant pathogenicity trials in the pine host Pinus pinaster. The 16S rRNA gene sequencing of PWN-associated bacteria revealed the presence of bacteria from two phyla Proteobacteria (Burkholderiales, Pseudomonadales, Enterobacteriales and Xanthomonadales) and Firmicutes (Lactobacillales and Bacilalles). Phenotypic characterization revealed the presence of a heterogeneous bacterial community associated with PWN, exhibiting plant pathogenic traits common in wilting diseases. Our results suggest the intriguing possibility that some PWN-associated bacteria may play a significant role in the development of PWD

Acidification increases abundances of Vibrionales and Planctomycetia associated to a seaweed-grazer system: potential consequences for disease and prey digestion efficiency

Ocean acidification significantly affects marine organisms in several ways, with complex interactions. Seaweeds might benefit from rising CO2 through increased photosynthesis and carbon acquisition, with subsequent higher growth rates. However, changes in seaweed chemistry due to increased CO2 may change the nutritional quality of tissue for grazers. In addition, organisms live in close association with a diverse microbiota, which can also be influenced by environmental changes, with feedback effects. As gut microbiomes are often linked to diet, changes in seaweed characteristics and associated microbiome can affect the gut microbiome of the grazer, with possible fitness consequences. In this study, we experimentally investigated the effects of acidification on the microbiome of the invasive brown seaweed Sargassum muticum and a native isopod consumer Synisoma nadejda. Both were exposed to ambient CO2 conditions (380 ppm, pH 8.16) and an acidification treatment (1,000 ppm, pH 7.86) for three weeks. Microbiome diversity and composition were determined using high-throughput sequencing of the variable regions V5-7 of 16S rRNA. We anticipated that as a result of acidification, the seaweed-associated bacterial community would change, leading to further changes in the gut microbiome of grazers. However, no significant effects of elevated CO2 on the overall bacterial community structure and composition were revealed in the seaweed. In contrast, significant changes were observed in the bacterial community of the grazer gut. Although the bacterial community of S. muticum as whole did not change, Oceanospirillales and Vibrionales (mainly Pseudoalteromonas) significantly increased their abundance in acidified conditions. The former, which uses organic matter compounds as its main source, may have opportunistically taken advantage of the possible increase of the C/N ratio in the seaweed under acidified conditions. Pseudoalteromonas, commonly associated to diseased seaweeds, suggesting that acidification may facilitate opportunistic/pathogenic bacteria. In the gut of S. nadejda, the bacterial genus Planctomycetia increased abundance under elevated CO2. This shift might be associated to changes in food (S. muticum) quality under acidification. Planctomycetia are slow-acting decomposers of algal polymers that could be providing the isopod with an elevated algal digestion and availability of inorganic compounds to compensate the shifted C/N ratio under acidification in their food. In conclusion, our results indicate that even after only three weeks of acidified conditions, bacterial communities associated to ungrazed seaweed and to an isopod grazer show specific, differential shifts in associated bacterial community. These have potential consequences for seaweed health (as shown in corals) and isopod food digestion. The observed changes in the gut microbiome of the grazer seem to reflect changes in the seaweed chemistry rather than its microbial composition.Erasmus Mundus Doctoral Programme MARES on Marine Ecosystem Health Conservation [MARES_13_08]; FCT (Foundation for Science and Technology, Portugal) [SFRH/BPD/63703/2009, SFRH/BPD/107878/2015, SFRH/BPD/116774/2016]; EU SEAS-ERA project INVASIVES [SEAS-ERA/0001/2012]; [CCMAR/Multi/04326/2013