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Escherichia coli contain a high level of genetic diversity and are generally associated with the guts of warm-blooded animals but have also been isolated from secondary habitats outside hosts. We used E. coli isolates from previous in situ microcosm experiments conducted under actual beach conditions and performed population-level genomic analysis to identify accessory genes associated with survival within the beach sand environment. E. coli strains capable of surviving had been selected for by seeding isolates originating from sand, sewage, and gull waste (n = 528; 176 from each source) into sand, which was sealed in microcosm chambers and buried for 45 days in the backshore beach of Lake Michigan. In the current work, survival-associated genes were identified by comparing the pangenome of viable E. coli populations at the end of the microcosm experiment with the original isolate collection and identifying loci enriched in the out put samples. We found that environmental survival was associated with a wide variety of genetic factors, with the majority corresponding to metabolism enzymes and transport proteins. Of the 414 unique functions identified, most were present across E. coli phylogroups, except B2 which is often associated with human pathogens. Gene modules that were enriched in surviving populations included a betaine biosynthesis pathway, which produces an osmoprotectant, and the GABA (gamma-aminobutyrate) biosynthesis pathway, which aids in pH homeostasis and nutrient use versatility. Overall, these results demonstrate that the genetic flexibility within this species allows for survival in the environment for extended periods. [ABSTRACT FROM AUTHOR]

Research has been conducted on the microbial small-subunit rRNAs. The distribution of these rRNAs in Lake Michigan offshore sediments has been investigated via molecular biological methods, and the results indicate that the nitrogen cycling in these sediments may have a seasonal component.

The universal oligonucleotide hybridization probe S-*-Univ-1390-a-A-18 accurately estimates domain-level community composition of microbes in environmental samples, under low-stringency wash conditions. However, the probe overestimates methanogen rRNA concentrations under high-stringency wash conditions. The universal probe S-*-Univ-1392-a-A-15 gives overestimated results with both high- and low-stringency wash conditions. Defined mixtures of rRNAs from pure cultures and anaerobic digester samples are used for the comparison of the two probes.

Extended multilocus sequence typing (MLST) analysis of atypical Escherichia isolates were performed to identify five novel phylogenetic clades (CI to CV) among isolates from environmental, human, and animal sources. The sample data from evaluation of all Escherichia lineages suggested that CIII, CIV, and CV represent environmentally adapted Escherichia lineages might be more abundant outside the host gastrointestinal tract.

A total of 16 different strains of Microbacterium spp. were isolated from contaminated soil and enriched on the carcinogen, hexavalent chromium [Cr(VI)]. The majority of the isolates (11 of the 16) were able to tolerate concentrations (0.1 mM) of cobalt, cadmium, and nickel, in addition to Cr(VI) (0.5-20 mM). Interestingly, these bacteria were also able to tolerate three different antibiotics (ranges: ampicillin 0-16 µg ml-1, chloramphenicol 0-24 µg ml-1, and vancomycin 0-24 µg ml-1). To gain genetic insight into these tolerance pathways, the genomes of these isolates were assembled and annotated. The genomes of these isolates not only have some shared genes (core genome) but also have a large amount of variability. The genomes also contained an annotated Cr(VI) reductase (chrR) that could be related to Cr(VI) reduction. Further, various heavy metal tolerance (e.g., Co/Zn/Cd efflux system) and antibiotic resistance genes were identified, which provide insight into the isolates' ability to tolerate metals and antibiotics. Overall, these isolates showed a wide range of tolerances to heavy metals and antibiotics and genetic diversity, which was likely required of this population to thrive in a contaminated environment. [ABSTRACT FROM AUTHOR]

Contamination of recreational beaches due to fecal waste from gulls complicates beach monitoring and may pose a risk to public health. Gulls that feed at human waste sites may ingest human fecal microorganisms associated with that waste. If these gulls also visit beaches, they may serve as vectors, transporting fecal microorganisms to the beach where they may subsequently contaminate sand and water. In this study, samples collected from landfills, treated wastewater storage lagoons, and public beaches demonstrated a spatial and temporal overlap of markers for gull and human-associated microorganisms. In addition, markers for gull, fecal indicator bacteria, and the human-associated marker, HF183, were detected in gull feces and cloacae samples. Further, HF183 was detected in cloacae samples from gulls that were documented by radio-telemetry traveling between human waste sites and public beaches. This study highlights the potential for gulls that visit human waste sites to disperse human-associated microorganisms in the beach landscape. [ABSTRACT FROM AUTHOR]

Microbial communities within beach sand play a key role in nutrient cycling and are important to the nearshore ecosystem function. Escherichia coli and enterococci, two common indicators of fecal pollution, have been shown to persist in the beach sand, but little is known about how microbial community assemblages are related to these fecal indicator bacteria (FIB) reservoirs. We examined eight beaches across a geographic gradient and range of land use types and characterized the indigenous community structure in the water and the backshore, berm, and submerged sands. FIB were found at similar levels in sand at beaches adjacent to urban, forested, and agricultural land and in both the berm and backshore. However, there were striking differences in the berm and backshore microbial communities, even within the same beach, reflecting the very different environmental conditions in these beach zones in which FIB can survive. In contrast, the microbial communities in a particular beach zone were similar among beaches, including at beaches on opposite shores of Lake Michigan. The differences in the microbial communities that did exist within a beach zone correlated to nutrient levels, which varied among geographic locations. Total organic carbon and total phosphorus were higher in Wisconsin beach sand than in beach sand from Michigan. Within predominate genera, finescale sequence differences could be found that distinguished the populations from the two states, suggesting a biogeographic effect. This work demonstrates that microbial communities are reflective of environmental conditions at freshwater beaches and are able to provide useful information regarding long-term anthropogenic stress. [ABSTRACT FROM AUTHOR]

The article focuses on the issues with environmental occurrence and transport of fecal indicators and pathogens, method's development and application for their detection as well as the source that tracks for their detection. It is being noted that the fecal indicator bacteria (FIB) are bacteria that are commensal in animal intestines, which are shed by feces. Accordingly, their presence in the ecosystem is assumed to indicate that there is a presence of fecal matter and therefore the potential presence of pathogens of intestinal origin. Hence, the author implies that interpretation of the detection of conventional FIB in the environment is sometimes straightforward, though not all the time.

The article presents a study regarding environmental occurrence and transport, detection methods, and source tracking of fecal indicator organisms and pathogens in water and mentions information on detection methods like polymerase chain reaction (PCR) and portable and real time monitoring systems.

Ring-billed Gull (Larus delawarensis) populations have dramatically increased throughout their geographic range with the largest concentrations in the Great Lakes region of Canada and the United States. Large populations of gulls cause conflict with humans at recreational beaches, where their effects on human health and safety include bacteria contamination from gull feces. We used border collies to harass and exclude gulls from beaches in summer 2012 and 2013, then measured gull numbers and Escherichia coli. Dogs were effective at reducing gull numbers by 56–76% during continuous and noncontinuous dog treatment periods. Levels of E. coli were lower on dog-treated beaches, but only during the first half of the summer. Mixed modeling analysis showed presence of dogs was a strong predictor of gull numbers and E. coli levels, with variation among dogs, possibly related to age. Noncontinuous use of dogs, applied within an integrated beach management framework, can provide a nonlethal method for reducing gull use and E. coli levels at recreational beaches. [ABSTRACT FROM AUTHOR]

Introduction: Influenza A viruses have the potential to cause devastating illness in humans and domestic poultry. Wild birds are the natural reservoirs of Influenza A viruses and migratory birds are implicated in their global dissemination. High concentrations of this virus are excreted in the faeces of infected birds and faecal contamination of shared aquatic habitats can lead to indirect transmission among birds via the faecal-oral route. The role of migratory birds in the spread of avian influenza has led to large-scale surveillance efforts of circulating avian influenza viruses through direct sampling of live and dead wild birds. Environmental monitoring of bird habitats using molecular detection methods may provide additional information on the persistence of influenza virus at migratory stopover sites distributed across large spatial scales. Materials and methods: In the current study, faecal and water samples were collected at migratory stopover sites and evaluated for Influenza A by real-time quantitative reverse transcriptase PCR. Results and Discussion: This study found that Influenza A was detected at 53% of the evaluated stopover sites, and 7% and 4.8% of the faecal and water samples, respectively, tested positive for Influenza A virus. Conclusion: Environmental monitoring detected Influenza A at stopover sites used by migratory birds. [ABSTRACT FROM AUTHOR]