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Results for “Research in Microbiology”

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USGS2003

Pathogenic human viruses in coastal waters

This review addresses both historical and recent investigations into viral contamination of marine waters. With the relatively recent emergence of molecular biology-based assays, a number of investigations have shown that pathogenic viruses are prevalent in marine waters being impacted by sewage. Research has shown that this group of fecal-oral viral pathogens (enteroviruses, hepatitis A viruses, Norwalk viruses, reoviruses, adenoviruses, rotaviruses, etc.) can cause a broad range of asymptomatic to severe gastrointestinal, respiratory, and eye, nose, ear, and skin infections in people exposed through recreational use of the water. The viruses and the nucleic acid signature survive for an extended period in the marine environment. One of the primary concerns of public health officials is the relationship between the presence of pathogens and the recreational risk to human health in polluted marine environments. While a number of studies have attempted to address this issue, the relationship is still poorly understood. A contributing factor to our lack of progress in the field has been the lack of sensitive methods to detect the broad range of both bacterial and viral pathogens. The application of new and advanced molecular methods will continue to contribute to our current state of knowledge in this emerging and

Clinical Microbiology Reviews↗

USGS2023

Exchange of carbapenem-resistant Escherichia coli Sequence Type 38 intercontinentally and among wild bird, human, and environmental niches

Carbapenem-resistant Enterobacteriaceae (CRE) are a global threat to human health and are increasingly being isolated from nonclinical settings. OXA-48-producing Escherichia coli sequence type 38 (ST38) is the most frequently reported CRE type in wild birds and has been detected in gulls or storks in North America, Europe, Asia, and Africa. The epidemiology and evolution of CRE in wildlife and human niches, however, remains unclear. We compared wild bird origin E. coli ST38 genome sequences generated by our research group and publicly available genomic data derived from other hosts and environments to (i) understand the frequency of intercontinental dispersal of E. coli ST38 clones isolated from wild birds, (ii) more thoroughly measure the genomic relatedness of carbapenem-resistant isolates from gulls sampled in Turkey and Alaska, USA, using long-read whole-genome sequencing and assess the spatial dissemination of this clone among different hosts, and (iii) determine whether ST38 isolates from humans, environmental water, and wild birds have different core or accessory genomes (e.g., antimicrobial resistance genes, virulence genes, plasmids) which might elucidate bacterial or gene exchange among niches. Our results suggest that E. coli ST38 strains, including those resistant to carbapenems, are exchanged between humans and wild birds, rather than separately maintained populations within each niche. Furthermore, despite close genetic similarity among OXA-48-producing E. coli ST38 clones from gulls in Alaska and Turkey, intercontinental dispersal of ST38 clones among wild birds is uncommon. Interventions to mitigate the dissemination of antimicrobial resistance throughout the environment (e.g., as exemplified by the acquisition of carbapenem resistance by birds) may be warranted.

Applied and Environmental Microbiology↗

USGS2020

Evaluating the impacts of foreshore sand and birds on microbiological contamination at a freshwater beach

Beaches along the Great Lakes shorelines are important recreational and economic resources. However, contamination at the beaches can threaten their usage during the swimming season, potentially resulting in beach closures and/or advisories. Thus, understanding the dynamics that control nearshore water quality is integral to effective beach management. There have been significant improvements in this effort, including incorporating modeling (empirical, mechanistic) in recent years. Mechanistic modeling frameworks can contribute to this understanding of dynamics by determining sources and interactions that substantially impact fecal indicator bacteria concentrations, an index routinely used in water quality monitoring programs. To simulate E. coli concentrations at Jeorse Park beaches in southwest Lake Michigan, a coupled hydrodynamic and wave–current interaction model was developed that progressively added contaminant sources from river inputs, avian presence, bacteria–sediment interactions, and bacteria–sand–sediment interactions. Results indicated that riverine inputs affected E. coli concentrations at Jeorse Park beaches only marginally, while avian, shoreline sand, and sediment sources were much more substantial drivers of E. coli contamination at the beach. By including avian and riverine inputs, as well as bacteria–sand–sediment interactions at the beach, models can reasonably capture the variability in observed E. coli concentrations in nearshore water and bed sediments at Jeorse Park beaches. Consequently, it will be crucial to consider avian contamination sources and water-sand-sediment interactions in effective management of the beach for public health and as a recreational resource and to extend these findings to similar beaches affected by shoreline embayment.

Illlinois↗

USGS2024

Temporally dense monitoring of pathogen occurrence at four drinking-water well sites – Insights and Implications

Yearlong, event based, microbiological and chemical sampling was conducted at four public water supply well sites spanning a range of geologic settings and well depths to look for correlation between precipitation events and microbial occurrence. Near-continuous monitoring using autosamplers occurred just before, during, and after 5–7 sampling events triggered by rainfall and/or snowmelt. Microbial genetic material was noted at all four locations during all but one sampling event, but was exceedingly variable in time, where one sample would have no detections and the next sample could be a relatively high concentration. The highest microbial sums (microbial concentrations summed over an event) were observed during months in which precipitation exceeded historical averages. Extended wet conditions through the spring thaw resulted in the highest percentage of microbial positive samples, though at relatively low concentrations. Sampling events that followed drier than normal periods showed longer lag times between the onset of precipitation and microbial occurrence, as well as lower microbial detection rates. Although a general lag time pattern was observed at each site, the largest offset in time was observed at the site with the greatest depth to water. The study's temporally dense representation of drinking water pathogen characterization suggests that single event or infrequent periodic sampling of a drinking water supply cannot provide a representative characterization of the probability that pathogens are present, which likely has ramifications for calculating health risk assessments.

Minnesota↗

USGS2010

Enumeration of viruses and prokaryotes in deep-sea sediments and cold seeps of the Gulf of Mexico

Little is known about the distribution and abundance of viruses in deep-sea cold-seep environments. Like hydrothermal vents, seeps support communities of macrofauna that are sustained by chemosynthetic bacteria. Sediments close to these communities are hypothesized to be more microbiologically active and therefore to host higher numbers of viruses than non-seep areas. Push cores were taken at five types of Gulf of Mexico habitats at water depths below 1000 m using a remotely operated vehicle (ROV). The habitats included non-seep reference sediment, brine seeps, a microbial mat, an urchin field, and a pogonophoran worm community. Samples were processed immediately for enumeration of viruses and prokaryotes without the addition of a preservative. Prokaryote counts were an order of magnitude lower in sediments directly in contact with macrofauna (urchins, pogonophorans) compared to all other samples (10 7 vs. 10 8 cells g -1 dry weight) and were highest in areas of elevated salinity (brine seeps). Viral-Like Particle (VLP) counts were lowest in the reference sediments and pogonophoran cores (10 8 VLP g -1 dry wt), higher in brine seeps (10 9 VLP g -1 dry wt), and highest in the microbial mats (10 10 VLP g -1 dry wt). Virus-prokaryote ratios (VPR) ranged from <5 in the reference sediment to >30 in the microbial mats and >60 in the urchin field. VLP counts and VPR were all significantly greater than those reported from sediments in the deep Mediterranean Sea and in most cases were higher than recent data from a cold-seep site near Japan. The high VPR suggest that greater microbial activity in or near cold-seep environments results in greater viral production and therefore higher numbers of viruses.

Gulf Of Mexico;Green Canyon;Atwater Valley;Alamino↗

USGS2021

Oil and gas wastewater components alter streambed microbial community structure and function

The widespread application of directional drilling and hydraulic fracturing technologies expanded oil and gas (OG) development to previously inaccessible resources. A single OG well can generate millions of liters of wastewater, which is a mixture of brine produced from the fractured formations and injected hydraulic fracturing fluids (HFFs). With thousands of wells completed each year, safe management of OG wastewaters has become a major challenge to the industry and regulators. OG wastewaters are commonly disposed of by underground injection, and previous research showed that surface activities at an Underground Injection Control (UIC) facility in West Virginia affected stream biogeochemistry and sediment microbial communities immediately downstream from the facility. Because microbially driven processes can control the fate and transport of organic and inorganic components of OG wastewater, we designed a series of aerobic microcosm experiments to assess the influence of high total dissolved solids (TDS) and two common HFF additives—the biocide 2,2-dibromo-3-nitrilopropionamide (DBNPA) and ethylene glycol (an anti-scaling additive)—on microbial community structure and function. Microcosms were constructed with sediment collected upstream (background) or downstream (impacted) from the UIC facility in West Virginia. Exposure to elevated TDS resulted in a significant decrease in aerobic respiration, and microbial community analysis following incubation indicated that elevated TDS could be linked to the majority of change in community structure. Over the course of the incubation, the sediment layer in the microcosms became anoxic, and addition of DBNPA was observed to inhibit iron reduction. In general, disruptions to microbial community structure and function were more pronounced in upstream and background sediment microcosms than in impacted sediment microcosms. These results suggest that the microbial community in impacted sediments had adapted following exposure to OG wastewater releases from the site. Our findings demonstrate the potential for releases from an OG wastewater disposal facility to alter microbial communities and biogeochemical processes. We anticipate that these studies will aid in the development of useful models for the potential impact of UIC disposal facilities on adjoining surface water and shallow groundwater.

Frontiers in Microbiology↗

USGS2006

Examination of the watershed-wide distribution of Escherichia coli along southern Lake Michigan: An integrated approach

Recent research has highlighted the occurrence of Escherichia coli in natural habitats not directly influenced by sewage inputs. Most studies on E. coli in recreational water typically focus on discernible sources (e.g., effluent discharge and runoff) and fall short of integrating riparian, nearshore, onshore, and outfall sources. An integrated “beachshed” approach that links E. coli inputs and interactions would be helpful to understand the difference between background loading and sewage pollution; to develop more accurate predictive models; and to understand the differences between potential, net, and apparent culturable E. coli . The objective of this study was to examine the interrelatedness of E. coli occurrence from various coastal watershed components along southern Lake Michigan. The study shows that once established in forest soil, E. coli can persist throughout the year, potentially acting as a continuous non-point source of E. coli to nearby streams. Year-round background stream loading of E. coli can influence beach water quality. E. coli is present in highly variable counts in beach sand to depths just below the water table and to distances at least 5 m inland from the shore, providing a large potential area of input to beach water. In summary, E. coli in the fluvial-lacustrine system may be stored in forest soils, sediments surrounding springs, bank seeps, stream margins and pools, foreshore sand, and surface groundwater. While rainfall events may increase E. coli counts in the foreshore sand and lake water, concentrations quickly decline to prerain concentrations. Onshore winds cause an increase in E. coli in shallow nearshore water, likely resulting from resuspension of E. coli -laden beach sand. When examining indicator bacteria source, flux, and context, the entire “beachshed” as a dynamic interacting system should be considered.

Applied and Environmental Microbiology↗

USGS2025

Bacterial community diversity and potential eco-physiological roles in toxigenic blooms composed of Microcystis, Aphanizomenon or Planktothrix

Cyanobacterial toxicity, cyanotoxins, and their impact on aquatic ecosystems and human health are well documented. In comparison, less is known about bloom-associated bacterial communities. Co-occurring bacteria can influence bloom development, physiology and collapse, and may also provide a niche for pathogenic bacteria. Existing research focuses on the cyanosphere of Microcystis -dominated blooms, despite the increasing prevalence of filamentous genera ( Aphanizomenon and Planktothrix ). This pilot study aimed to broaden our understanding of the bacterial consortia attached to morphologically distinct cyanobacteria (coccoid and filamentous) dominating phytoplankton communities and to explore their potential roles in amplifying the impacts of cyanobacterial blooms. We investigated four shallow freshwater bodies across three continents and two climate zones: an urban pond in the USA, a dammed reservoir and a natural lake in Poland, and an urban water body in Singapore. Amplicon sequencing (16S rRNA gene) was used to characterize bacterial communities, while shotgun metagenomics identified nitrogen- and phosphorus-cycling genes to infer potential eco-physiological functions. Cyanobacteria dominated bacterioplankton assemblages at all sites (>35.6%), with bloom composition influencing toxigenic profiles. A mixed bloom of Microcystis , Snowella , and Aphanizomenon had the broadest range of cyanotoxin synthetase genes ( mcy E, cyr J, ana F and sxt A). Microcystis blooms correlated with increased Roseomonas , while Planktothrix co-occurred with Flavobacterium – both bacteria likely contribute to nutrient-cycling within blooms and represent potential opportunistic pathogens for aquatic organisms and humans. The Microcystis cyanosphere exhibited the highest number of significant positive correlations with bacteria (19 relations), compared to Planktothrix and Aphanizomenon (11 and 2 relations, respectively). Non-diazotrophic blooms of Microcystis and Planktothrix showed greater abundances of nitrogen – ( ure B, gln A, nar B, and nar HZ) and phosphorus-cycling genes ( pho BHPR and ppk 1), indicating a strong dependence on associated bacteria for nutrient acquisition compared to diazotrophic Aphanizomenon . These findings suggest that Aphanizomenon -dominated blooms may be sustained by simpler microbiomes. Our results provide preliminary evidence of cyanosphere heterogeneity potentially shaped by the dominance or coexistence of three morphologically and eco-physiologically distinct genera of cyanobacteria. A comprehensive knowledge of the taxonomy and functional roles of bloom-associated microbiomes is therefore essential to understand bloom activity, evaluate the environmental threat, and develop effective strategies for prevention and mitigation.

Frontiers in Microbiology↗