Mangrove microniches determine the structural and functional diversity of enriched petroleum hydrocarbon-degrading consortia

In this study, the combination of culture enrichments and molecular tools was used to identify bacterial guilds, plasmids and functional genes potentially important in the process of petroleum hydrocarbon (PH) decontamination in mangrove microniches (rhizospheres and bulk sediment). In addition, we aimed to recover PH-degrading consortia (PHDC) for future use in remediation strategies. The PHDC were enriched with petroleum from rhizosphere and bulk sediment samples taken from a mangrove chronically polluted with oil hydrocarbons. Southern blot hybridization (SBH) assays of PCR amplicons from environmental DNA before enrichments resulted in weak positive signals for the functional gene types targeted, suggesting that PH-degrading genotypes and plasmids were in low abundance in the rhizosphere and bulk sediments. However, after enrichment, these genes were detected and strong microniche-dependent differences in the abundance and composition of hydrocarbonoclastic bacterial populations, plasmids (IncP-1 alpha, IncP-1 beta, IncP-7 and IncP-9) and functional genes (naphthalene, extradiol and intradiol dioxygenases) were revealed by in-depth molecular analyses [PCR-denaturing gradient gel electrophoresis and hybridization (SBH and microarray)]. Our results suggest that, despite the low abundance of PH-degrading genes and plasmids in the environmental samples, the original bacterial composition of the mangrove microniches determined the structural and functional diversity of the PHDC enriched.Deutsche Forschungsgemeinschaft [SM59/4-1, 4-2]; FAPERJ-Brazil; European Commission [003998, 211684]; Alexander-von-Humboldt-Stiftung; CONICET (Argentina)info:eu-repo/semantics/publishedVersio

Investigating exudate- and habitat-mediated effects of phytoplankton on lake bacterial community dynamics

Correlated patterns of abundance, activity, and composition are commonly observed between phytoplankton and bacterial communities. There are a number of potential explanations for correlated dynamics. Recent observations of temporal succession in lake microbial communities provide evidence for phytoplankton populations acting as biological drivers structuring bacterial communities. The following thesis addresses two potentially important connections between phytoplankton and bacteria: resource-mediated linkage through production of labile carbon exudates and habitat-mediated linkage. To investigate phytoplankton exudates as a potential linkage, the first investigation focused on bacteria able to use the photorespiration-specific exudate glycolate. Diversity and dynamics of glycolate-utilizing bacteria were characterized in six lakes using functional gene glycolate oxidase subunit D (glcD). Freshwater glycolate-utilizing populations exhibited a range of taxonomic diversity and contained many sequences clustering with a glcD sequence from the cosmopolitan freshwater Polynucleobacter genus. Glycolate-utilizing and total bacterial community-level variation was largely explained by dynamics of phytoplankton populations (35-40%) and the interaction between these phytoplankton populations and the environment (17-18%). Population-level correlations between specific phytoplankton and glycolate-utilizing bacteria were also detected. These observations support the hypothesis that algal exudates are resource-based drivers of bacterial community composition and identify bacterial taxonomic groups with members capable of responding directly to a specific exudate. Contribution of epiphytic bacteria inhabiting algal cells to correlated community dynamics was investigated by comparing temporal community patterns in the particle-associated bacteria to those of whole bacteria and phytoplankton in Crystal and South Sparkling Bogs. Regular patterns of succession, in addition to correlations between phytoplankton and whole bacterial communities (ρ=0.514, p=0.001) and phytoplankton and particle-associated bacterial communities (ρ=0.739, p=0.001), were detected in Crystal, but not South Sparkling Bog (ρ=0.265, p=0.038; ρ=0.167, p=0.103, respectively). Attached and free-living bacterial assemblages were compared to classify bacterial taxa based on presence in attached and/ or free-living fractions. Despite mixed results for community-level correlations, bacterial populations were positively correlated to abundance of specific phytoplankton in both lakes. Algal-correlated bacteria ranged from primarily particle-associated bacteria in Crystal Bog to a mix of particle-associated and free-living bacteria in South Sparkling Bog. These observations provide support for habitat-mediated linkages, while also indicating the importance of other mechanisms that affect free-living and habitat generalist populations. Taken together, these investigations contribute to a growing body of research demonstrating the importance of biological interactions in shaping microbial community structure. Microbial community composition and function have implications for energy flow, carbon flux, and biogeochemical transformations with ecosystem-level consequences. Understanding biological interactions that structure bacterial communities may facilitate the building of a predictive framework for understanding compositional and functional responses of bacteria and microbially-mediated processes to changing environmental conditions

Contrasting Microbial Community Assembly Hypotheses: A Reconciling Tale from the Río Tinto

The Río Tinto (RT) is distinguished from other acid mine drainage systems by its natural and ancient origins. Microbial life from all three domains flourishes in this ecosystem, but bacteria dominate metabolic processes that perpetuate environmental extremes. While the patchy geochemistry of the RT likely influences the dynamics of bacterial populations, demonstrating which environmental variables shape microbial diversity and unveiling the mechanisms underlying observed patterns, remain major challenges in microbial ecology whose answers rely upon detailed assessments of community structures coupled with fine-scale measurements of physico-chemical parameters.By using high-throughput environmental tag sequencing we achieved saturation of richness estimators for the first time in the RT. We found that environmental factors dictate the distribution of the most abundant taxa in this system, but stochastic niche differentiation processes, such as mutation and dispersal, also contribute to observed diversity patterns.We predict that studies providing clues to the evolutionary and ecological processes underlying microbial distributions will reconcile the ongoing debate between the Baas Becking vs. Hubbell community assembly hypotheses

Role of environmental factors for the vertical distribution (0–1000 m) of marine bacterial communities in the NW Mediterranean Sea

Bacterioplankton plays a central role in energy and matter fluxes in the sea, yet the factors that constrain its variation in marine systems are still poorly understood. Here we use the explanatory power of direct multivariate gradient analysis to evaluate the driving forces exerted by environmental parameters on bacterial community distribution in the water column. We gathered and analysed data from a one month sampling period from the surface to 1000 m depth at the JGOFS-DYFAMED station (NW Mediterranean Sea). This station is characterized by very poor horizontal advection currents which makes it an ideal model to test hypotheses on the causes of vertical stratification of bacterial communities. Capillary electrophoresis single strand conformation polymorphism (CE-SSCP) fingerprinting profiles analyzed using multivariate statistical methods demonstrated a vertical zonation of bacterial assemblages in three layers, above, in or just below the chlorophyll maximum and deeper, that remained stable during the entire sampling period. Through the use of direct gradient multivariate ordination analyses we demonstrate that a complex array of biogeochemical parameters is the driving force behind bacterial community structure shifts in the water column. Physico-chemical parameters such as phosphate, nitrate, salinity and to a lesser extent temperature, oxygen, dissolved organic carbon and photosynthetically active radiation acted in synergy to explain bacterial assemblages changes with depth. Analysis of lipid biomarkers of organic matter sources and fates suggested that bacterial community structure in the surface layers was in part explained by lipids of chloroplast origin. Further detailed analysis of pigment-based phytoplankton diversity gave evidence of a compartmentalized influence of several phytoplankton groups on bacterial community structure in the first 150 m depth

Tailings microbial community profile and prediction of its functionality in basins of tungsten mine

In a circular economy concept, where more than 300 million tons of mining and quarrying wastes are produced annually, those are valuable resources, supplying metals that are extracted today by other processes, if innovative methods and processes for efficient extraction of these elements are applied. This work aims to assess microbiological and chemical spatial distribution within two tailing basins from a tungsten mine, using a MiSeq approach targeting the 16S rRNA gene, to relate microbial composition and function with chemical variability, thus, providing information to enhance the efficiency of the exploitation of these secondary sources. The tailings sediments core microbiome comprised members of family Anaerolineacea and genera Acinetobacter, Bacillus, Cellulomonas, Pseudomonas, Streptococcus and Rothia, despite marked differences in tailings physicochemical properties. The higher contents of Al and K shaped the community of Basin 1, while As-S-Fe contents were correlated with the microbiome composition of Basin 2. The predicted metabolic functions of the microbiome were rich in genes related to metabolism pathways and environmental information processing pathways. An in-depth understanding of the tailings microbiome and its metabolic capabilities can provide a direction for the management of tailings disposal sites and maximize their potential as secondary resources

Microbiome

BackgroundInfant botulism is the most prevalent form of botulism in the USA, representing 68.5\uc2\ua0% of cases reported from 2001\ue2\u20ac\u201c2012. Infant botulism results when botulinum toxin-producing clostridia (BTPC) colonize the infant gut with concomitant in vivo production of the highly potent botulinum neurotoxin (BoNT). The gut microbiota of infants with botulism is largely uncharacterized; therefore, it remains unclear whether the microbiota profile of these patients are distinct in composition, abundance, or diversity. To address this uncertainty, we employed 16S rRNA gene profiling to characterize the fecal microbiota in 14 stool samples among laboratory-confirmed and non-confirmed infant botulism cases.ResultsSeven bacterial phyla were identified among all 14 infant stool samples examined. Compared to samples from non-confirmed cases, the fecal microbiota of infant botulism patients displayed significantly higher Proteobacteria abundance. Of the 20 bacterial families identified, Enterobacteriaceae was significantly more abundant in samples from infants with botulism. Firmicutes abundance and the abundance ratio of Firmicutes/Proteobacteria was significantly lower in samples from infants with botulism. Lactobacillus spp. abundance was notably reduced in 12 of the 14 samples. Clostridium botulinum and Clostridium baratii were identified in low relative abundances in confirmed and non-confirmed samples based on their 16S rRNA gene profiles, although their toxigenicity remained undetermined. No significant differences were observed in the number of operational taxonomic units (OTUs) observed or in fecal microbiota diversity between laboratory-confirmed and non-confirmed samples. Correlations between individual phylum abundances and infant age were variable, and no significant differences were shown in number of OTUs observed or in fecal microbiota diversity between samples delineated by overall mean age.ConclusionsSignificant differences in Proteobacteria, Firmicutes, and Enterobacteriaceae abundances were identified in the fecal microbiota of infants with botulism when compared to samples from non-confirmed cases. Fecal microbiota diversity was not significantly altered in infants with botulism, and a limited presence of BTPC was shown. It could not be determined whether the fecal microbiota profiles shown here were comparable prior to patient illness, or whether they were the direct result of infant botulism. The results of this study do, however, provide a detailed and descriptive observation into the infant gut microbiota after intestinal colonization by BTPC.2015-11-23T00:00:00Z26593441PMC465545