Application of molecular source tracking and mass balance approach to identify potential sources of fecal indicator bacteria in a tropical river.

Microbial source tracking and a mass balance approach were used to identify sources of fecal indicator bacteria (FIB) in the Hanalei River, Kaua'i, Hawai'i. Historically, concentrations enterococci and Clostridium perfringens were significantly higher during storm flows compared to non-storm flows in the Hanalei River, and correlated to total suspended solids in the river. During targeted dry weather studies, the Hanalei River bed sediments and streambank soils were documented to harbor E. coli, enterococci, and the human- and pig-specific fecal markers in Bacteroidales, suggesting that sediments and soils may be potential sources of these microorganisms to the Hanalei river. The human-specific marker in Bacteroidales was four times as likely to be detected in sediment and soil samples as in water samples. Furthermore, the occurrence of host-specific source tracking markers is indicative that a portion of FIB present in the Hanalei River are of fecal origin. A mass balance approach was used to explore causes of observed FIB loadings and losses along different reaches of the river. Resuspension or deposition of FIB-laden river sediments cannot account for changes in E. coli and enterococci concentrations along the river during dry weather. Additionally, losses due to bacterial inactivation were insignificant. Groundwater and ditches draining agricultural and urban lands were shown to provide sufficient FIB fluxes to account for the observed loads along some river reaches. The presence of the human-specific Bacteroidales marker in the river water, sediments and adjacent soils, as well as the presence of the human enterovirus marker in the water, suggests that there is widespread human fecal contamination in the Hanalei River that is likely a result of nearby wastewater disposal systems.

Simultaneous adaptation and maladaptation of tree populations to local rhizosphere microbial communities at different taxonomic scales.

Plant populations are often adapted to their local conditions, but the specific selective forces creating this adaptation are often unclear. All plants interact with diverse microbial communities, but we know little about how these microbial communities as a whole shape the evolutionary trajectory of plant populations. We tested whether tree populations were adapted or maladapted to their local rhizosphere microbial communities by growing seedlings sourced from multiple locations with soil microbial communities from all locations in a fully reciprocal design, using seedling growth as a proxy for fitness. In addition, we compared the microbial composition of the experimental inocula with that of the communities we detected associating with naturally occurring trees at the seedling source populations. We found that seedlings grew similarly when inoculated with local vs foreign microbial communities, but this neutral response derived from conflicting patterns - plant populations appeared to be adapted to the presence or absence of whole taxonomic groups in their local microbial community, but were simultaneously maladapted to the particular microbial populations present in their local site. As rapid climate change and other factors push tree populations into new areas, the successful establishment of seedlings may depend critically on the balance between the novelty and familiarity of the microbial communities they encounter.

Ectomycorrhizal fungal richness declines towards the host species' range edge.

Plant range boundaries are generally considered to reflect abiotic conditions; however, a rise in negative or decline in positive species interactions at range margins may contribute to these stable boundaries. While evidence suggests that pollinator mutualisms may decline near range boundaries, little is known about other important plant mutualisms, including microbial root symbionts. Here, we used molecular methods to characterize root-associated fungal communities in populations of two related temperate tree species from across the species' range in the eastern United States. We found that ectomycorrhizal fungal richness on plant roots declined with distance from the centre of the host species range. These patterns were not evident in nonmycorrhizal fungal communities on roots nor in fungal communities in bulk soil. Climatic and soil chemical variables could not explain these biogeographic patterns, although these abiotic gradients affected other components of the bulk soil and rhizosphere fungal community. Depauperate ectomycorrhizal fungal communities may represent an underappreciated challenge to marginal tree populations, especially as rapid climate change pushes these populations outside their current climate niche.

Recombination shapes the structure of an environmental Vibrio cholerae population.

Vibrio cholerae consists of pathogenic strains that cause sporadic gastrointestinal illness or epidemic cholera disease and nonpathogenic strains that grow and persist in coastal aquatic ecosystems. Previous studies of disease-causing strains have shown V. cholerae to be a primarily clonal bacterial species, but isolates analyzed have been strongly biased toward pathogenic genotypes, while representing only a small sample of the vast diversity in environmental strains. In this study, we characterized homologous recombination and structure among 152 environmental V. cholerae isolates and 13 other putative Vibrio isolates from coastal waters and sediments in central California, as well as four clinical V. cholerae isolates, using multilocus sequence analysis of seven housekeeping genes. Recombinant regions were identified by at least three detection methods in 72% of our V. cholerae isolates. Despite frequent recombination, significant linkage disequilibrium was still detected among the V. cholerae sequence types. Incongruent but nonrandom associations were observed for maximum likelihood topologies from the individual loci. Overall, our estimated recombination rate in V. cholerae of 6.5 times the mutation rate is similar to those of other sexual bacteria and appears frequently enough to restrict selection from purging much of the neutral intraspecies diversity. These data suggest that frequent recombination among V. cholerae may hinder the identification of ecotypes in this bacterioplankton population.

Hands, water, and health: fecal contamination in Tanzanian communities with improved, non-networked water supplies.

Almost half of the world's population relies on non-networked water supply services, which necessitates in-home water storage. It has been suggested that dirty hands play a role in microbial contamination of drinking water during collection, transport, and storage. However, little work has been done to evaluate quantitatively the association between hand contamination and stored water quality within households. This study measured levels of E. coli, fecal streptococci, and occurrence of the general Bacteroidales fecal DNA marker in source water, in stored water, and on hands in 334 households among communities in Dar es Salaam, Tanzania, where residents use non-networked water sources. Levels of fecal contamination on hands of mothers and children were positively correlated to fecal contamination in stored drinking water within households. Household characteristics associated with hand contamination included mother's educational attainment, use of an improved toilet, an infant in the household, and dissatisfaction with the quantity of water available for hygiene. In addition, fecal contamination on hands was associated with the prevalence of gastrointestinal and respiratory symptoms within a household. The results suggest that reducing fecal contamination on hands should be investigated as a strategy for improving stored drinking water quality and health among households using non-networked water supplies.

Biogeographic patterns in genomic diversity among a large collection of Vibrio cholerae isolates.

Vibrio cholerae strains are capable of inhabiting multiple niches in the aquatic environment and in some cases cause disease in humans. However, the ecology and biodiversity of these bacteria in environmental settings remains poorly understood. We used the genomic fingerprinting technique enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) to profile 835 environmental isolates from waters and sediments obtained at nine sites along the central California coast. We identified 115 ERIC-PCR genotypes from 998 fingerprints, with a reproducibility of 98.5% and a discriminatory power of 0.971. When the temporal dynamics at a subset of sampling sites were explored, several genotypes provided evidence for cosmopolitan or geographically restricted distributions, and other genotypes displayed nonrandom patterns of cooccurrence. Partial Mantel tests confirmed that genotypic similarity of isolates across all sampling events was correlated with environmental similarity (0.04 < or = r < or = 0.05), temporal proximity (r = 0.09), and geographic distance (r = 0.09). A neutral community model for all sampling events explained 61% of the variation in genotype abundance. Cooccurrence indices (C-score, C-board, and Combo) were significantly different than expected by chance, suggesting that the V. cholerae population may have a competitive structure, especially at the regional scale. Even though stochastic processes are undoubtedly important in generating biogeographic patterns in diversity, deterministic factors appear to play a significant, albeit small, role in shaping the V. cholerae population structure in this system.

Genomic and phenotypic diversity of coastal Vibrio cholerae strains is linked to environmental factors.

Studies of Vibrio cholerae diversity have focused primarily on pathogenic isolates of the O1 and O139 serotypes. However, autochthonous environmental isolates of this species routinely display more extensive genetic diversity than the primarily clonal pathogenic strains. In this study, genomic and metabolic profiles of 41 non-O1/O139 environmental isolates from central California coastal waters and four clinical strains are used to characterize the core genome and metabolome of V. cholerae. Comparative genome hybridization using microarrays constructed from the fully sequenced V. cholerae O1 El Tor N16961 genome identified 2,787 core genes that approximated the projected species core genome within 1.6%. Core genes are almost universally present in strains with widely different niches, suggesting that these genes are essential for persistence in diverse aquatic environments. In contrast, the dispensable genes and phenotypic traits identified in this study should provide increased fitness for certain niche environments. Environmental parameters, measured in situ during sample collection, are correlated to the presence of specific dispensable genes and metabolic capabilities, including utilization of mannose, sialic acid, citrate, and chitosan oligosaccharides. These results identify gene content and metabolic pathways that are likely selected for in certain coastal environments and may influence V. cholerae population structure in aquatic environments.

Detection and transformation of genome segments that differ within a coastal population of Vibrio cholerae strains.

Vibrio cholerae is an autochthonous member of diverse aquatic ecosystems around the globe. Collectively, the genomes of environmental V. cholerae strains comprise a large repository of encoded functions which can be acquired by individual V. cholerae lineages through uptake and recombination. To characterize the genomic diversity of environmental V. cholerae, we used comparative genome hybridization to study 41 environmental strains isolated from diverse habitats along the central California coast, a region free of endemic cholera. These data were used to classify genes of the epidemic V. cholerae O1 sequenced strain N16961 as conserved, variably present, or absent from the isolates. For the most part, absent genes were restricted to large mobile elements and have known functions in pathogenesis. Conversely, genes present in some, but not all, California isolates were in smaller contiguous clusters and were less likely to be near genes with functions in DNA mobility. Two such clusters of variable genes encoding different selectable metabolic phenotypes (mannose and diglucosamine utilization) were transformed into the genomes of environmental isolates by chitin-dependent competence, indicating that this mechanism of general genetic exchange is conserved among V. cholerae. The transformed DNA had an average size of 22.7 kbp, demonstrating that natural competence can mediate the movement of large chromosome fragments. Thus, whether variable genes arise through the acquisition of new sequences by horizontal gene transfer or by the loss of preexisting DNA though deletion, natural transformation provides a mechanism by which V. cholerae clones can gain access to the V. cholerae pan-genome.

An analytical model of enterococci inactivation, grazing, and transport in the surf zone of a marine beach.

An analytical model of enterococci (ENT) concentrations in the surf zone of a long sandy beach is constructed considering the physical processes of dilution by rip currents and alongshore littoral drift, and the biological processes of inactivation and mortality by grazing. The solution is used to construct an expression for the length of shoreline adversely impacted by ENT from a point source. Two non-dimensional parameters are developed whose magnitude can be used to ascertain whether dilution, inactivation, or grazing is the dominant sink for ENT in the surf zone. The model is applied to beaches in southern California, USA. Model input parameters related to physical processes and inactivation are compiled from the literature. Laboratory experiments are conducted to determine grazing mortality rates of ENT (6.5 x 10(-6) s(-1)). Results indicate that at the field sites, between 1000 and 5000 m of shoreline are typically impacted by a continuous point source of ENT. Dilution is the primary cause of decline in ENT concentrations within the surf zone, with inactivation secondary and grazing tertiary. Results recommend strategic positioning of point sources and timing of effluent releases to take advantage of high dilution conditions. Our estimates for grazing mortality rates are within the same order of magnitude as some published inactivation rates, thus we cannot rule out the possibility that grazing is an important sink for ENT, especially in low dilution environments like enclosed bays.