Impacts of Hurricanes Katrina and Rita on the microbial landscape of the New Orleans area

Assessment of pathogens in flood waters in coastal rural regions: Case study after Hurricane Michael and Florence

The severity of hurricanes, and thus the associated impacts, is changing over time. One of the understudied threats from damage caused by hurricanes is the potential for cross-contamination of water bodies with pathogens in coastal agricultural regions. Using microbiological data collected after hurricanes Florence and Michael, this study shows a dichotomy in the presence of pathogens in coastal North Carolina and Florida. Salmonella typhimurium was abundant in water samples collected in the regions dominated by swine farms. A drastic decrease in Enterococcus spp. in Carolinas is indicative of pathogen removal with flooding waters. Except for the abundance presence of Salmonella typhimurium, no significant changes in pathogens were observed after Hurricane Michael in the Florida panhandle. We argue that a comprehensive assessment of pathogens must be included in decision-making activities in the immediate aftermath of hurricanes to build resilience against risks of pathogenic exposure in rural agricultural and human populations in vulnerable locations.

Coastal Microbial Communities Disrupted During the 2018 Hurricane Season in Outer Banks, North Carolina

Hurricane frequencies and intensities are expected to increase under warming climate scenarios, increasing potential to disrupt microbial communities from steady-state conditions and alter ecosystem function. This study shows the impact of hurricane season on microbial community dynamics within the barrier island system of Outer Banks, North Carolina. We found that the passage of two sequential energetic hurricanes in 2018 (Florence and Michael) were correlated with shifts in total and active (DNA and RNA) portions of bacterial communities but not in archaeal communities, and within surface waters but not within the sediment. These microbial community shifts were distinct from non-hurricane season conditions, suggesting significant implications for nutrient cycling in nearshore and offshore environments. Hurricane-influenced marine sites in the coastal North Atlantic region had lower microbial community evenness and Shannon diversity, in addition to increased relative abundance of copiotrophic microbes compared to non-hurricane conditions. The abundance of functional genes associated with carbon and nitrogen cycling pathways were also correlated with the storm season, potentially shifting microbial communities at offshore sites from autotroph-dominated to heterotroph-dominated and leading to impacts on local carbon budgets. Understanding the geographic- and system-dependent responses of coastal microbial communities to extreme storm disturbances is critical for predicting impacts to nutrient cycling and ecosystem stability in current and future climate scenarios.

The effect of seasonal and extreme floods on hospitalizations for Legionnaires' disease in the United States, 2000-2011

BACKGROUND

An increasing severity of extreme storms and more intense seasonal flooding are projected consequences of climate change in the United States. In addition to the immediate destruction caused by storm surges and catastrophic flooding, these events may also increase the risk of infectious disease transmission. We aimed to determine the association between extreme and seasonal floods and hospitalizations for Legionnaires' disease in 25 US states during 2000-2011.

METHODS

We used a nonparametric bootstrap approach to examine the association between Legionnaires' disease hospitalizations and extreme floods, defined by multiple hydrometeorological variables. We also assessed the effect of extreme flooding associated with named cyclonic storms on hospitalizations in a generalized linear mixed model (GLMM) framework. To quantify the effect of seasonal floods, we used multi-model inference to identify the most highly weighted flood-indicator variables and evaluated their effects on hospitalizations in a GLMM.

RESULTS

We found a 32% increase in monthly hospitalizations at sites that experienced cyclonic storms, compared to sites in months without storms. Hospitalizations in months with extreme precipitation were in the 89^th percentile of the bootstrapped distribution of monthly hospitalizations. Soil moisture and precipitation were the most highly weighted variables identified by multi-model inference and were included in the final model. A 1-standard deviation (SD) increase in average monthly soil moisture was associated with a 49% increase in hospitalizations; in the same model, a 1-SD increase in precipitation was associated with a 26% increase in hospitalizations.

CONCLUSIONS

This analysis is the first to examine the effects of flooding on hospitalizations for Legionnaires' disease in the United States using a range of flood-indicator variables and flood definitions. We found evidence that extreme and seasonal flooding is associated with increased hospitalizations; further research is required to mechanistically establish whether floodwaters contaminated with Legionella bacteria drive transmission.

Legionella Occurrence beyond Cooling Towers and Premise Plumbing

Legionella is an environmental pathogen that is responsible for respiratory disease and is a common causative agent of water-related outbreaks. Due to their ability to survive in a broad range of environments, transmission of legionellosis is possible from a variety of sources. Unfortunately, a disproportionate amount of research that is devoted to studying the occurrence of Legionella in environmental reservoirs is aimed toward cooling towers and premise plumbing. As confirmed transmission of Legionella has been linked to many other sources, an over-emphasis on the most common sources may be detrimental to increasing understanding of the spread of legionellosis. This review aims to address this issue by cataloguing studies which have examined the occurrence of Legionella in less commonly investigated environments. By summarizing and discussing reports of Legionella in fresh water, ground water, saltwater, and distribution system drinking water, future environmental and public health researchers will have a resource to aid in investigating these pathogens in relevant sources.

Diversity and health risk potentials of the Enterococcus population in tropical coastal water impacted by Hurricane Lane

Hurricane-caused stormwater runoffs transport diverse terrestrial pollutants, adversely impact microbiological water quality, and introduce fecal and other pathogens to coastal water environments. This study investigated the genotypic diversity, phylogenetic composition, antibiotic resistance patterns, and virulence gene repertoire of the Enterococcus population in the Hilo Bay coastal water after the immediate impact of Hurricane Lane. DNA fingerprinting of Enterococcus isolates exhibited large genotypic diversity, while 16S rRNA gene sequencing identified four major species, including E. faecalis (34.7%), E. faecium (22.4%), E. hirae (22.4%), and E. durans (18.4%). Four common enterococcal virulence genes (cylA, esp, asa1, and gelE) were detected in the Enterococcus population, with significant portions of E. durans (33.3%), E. faecalis (41.2%), E. faecium (36.4%), and E. hirae (27.3%) isolates possessing two or more virulence genes. Considerable antibiotic resistance to rifampin, erythromycin, tetracycline, and nitrofurantoin was detected in the Enterococcus population, with one E. durans isolate showing vancomycin resistance. The results indicate considerable health implications associated with Enterococcus spp. in the hurricane-impacted tropical coastal water, illustrating the needs for more comprehensive understanding of the microbiological risks associated with storm-impacted coastal water.

Resident perspectives of environmental health risk exposures after Hurricane Harvey

This study examines what visitors to urban parks in Houston, TX, know about environmental health risks resulting from Hurricane Harvey, a category 4 storm that made landfall in August 2017 and dropped over 60 in. of rain in 8 days making it the most significant rainfall event in US history. Interviews were conducted with adult Houstonians using purposive sampling. In total, 27 interviews were conducted with 36 different participants. Interviews were audio-recorded, transcribed verbatim, and analyzed qualitatively using a phronetic iterative approach. This study found that park visitors lack sufficient knowledge about environmental health risks, yet they have strong desires to learn more about such risks. In particular, participants have clear opinions on what the content of the messages (i.e., concise, manageable, not fear-inducing) should be and how they would like to receive the information (i.e., conveniently accessible, from trusted local sources). Implications for health campaign interventions utilizing uncertainty theories are discussed.

Fecal indicators, pathogens, antibiotic resistance genes, and ecotoxicity in Galveston Bay after Hurricane Harvey

Unprecedented rainfall after Hurricane Harvey caused a catastrophic flood in the southern coast of Texas, and flushed significant floodwater and sediments into Galveston Bay, the largest estuary along the Texas Gulf Coast. This study investigated the immediate and long-term (6 months post-Harvey) fecal indicators, pathogenic bacteria, antibiotic resistance genes (ARGs), and ecotoxicity in the Galveston Bay. Dramatic decrease of salinity profile to zero, increased levels of fecal indicator bacteria and pathogenic bacteria, and detection of various ARGs were observed in the water and sediment samples collected 2 weeks post-Harvey. High levels of Bla_TEM and cytotoxicity measured by yeast bioluminescent assay (BLYR) were also observed especially near the river mouths. While Vibrio spp. was dominant in water, much higher abundance of fecal indicator bacteria and pathogen were detected in the sediments. A decreasing trend of Bla_TEM and cytotoxicity was observed in March 2018 samples, suggesting the Bay has returned to its pre-hurricane conditions 6 months post-Harvey. Interestingly, the abundance of fecal indicator bacteria and pathogens were shifted dramatically according to high-streamflow and low-streamflow seasons in the Bay. The data are useful to construct the model of risk assessment in coastal estuaries system and predict the effects of extreme flooding events in the future.

Impact of wastewater infrastructure improvements on beach water fecal indicator bacteria levels in Monroe County, Florida

The effects of wastewater infrastructure construction on regional and local environments is unknown. This project evaluated the effects of such projects in Monroe County, Florida, an area that had undergone regional wastewater infrastructure improvements. We used fecal indicator bacteria (FIB) (fecal coliform and enterococci), as a proxy indicator of beach water quality for an 18-year period of record. At the highest level of aggregation, FIBs for all 17 beaches within the county were combined to evaluate trends on a yearly basis. At the lower level, yearly FIB trends were evaluated for each beach separately. FIB data on infrastructure project period (categorical variables: before, during, and after construction), and the influences of environmental conditions (quantitative variables of rainfall and temperature) were also evaluated. In the multiple regression models, enterococci and fecal coliform were significantly associated with rainfall (24 h, p < 0.0001) and water temperature (p < 0.0001) when only the quantitative variables were considered. When both categorical and quantitative variables were considered, project period was significant for enterococci (p < 0.0001) and fecal coliform (p < 0.0001), as was 24 h lagged rainfall. Overall, the most significant factors for both fecal coliform and enterococci were rainfall and project period. Considering all beaches, infrastructure projects seem to have the collective desired effects in the years following construction, as there were decreased FIBs measured at beach sites. Only through the aggregation of all projects and measurements at all beach sites could the decreases in FIB levels be observed. Local analysis is needed to explain anomalies from these general trends for specific beaches. This understanding of FIBs, their responses to environmental and project factors, and the need for aggregated and local site analysis can provide guidance to managers at other locations with similar issues of failing wastewater infrastructure and frequent FIB exceedances.

Demonstrating an Integrated Antibiotic Resistance Gene Surveillance Approach in Puerto Rican Watersheds Post-Hurricane Maria

Comprehensive surveillance approaches are needed to assess sources, clinical relevance, and mobility of antibiotic resistance genes (ARGs) in watersheds. Here, we examined metrics derived from shotgun metagenomic sequencing and relationship to human fecal markers (HFMs; crAssphage, enterococci) and anthropogenic antibiotic resistance markers (AARMs; intI1, sul1) in three distinct Puerto Rican watersheds as a function of adjacent land use and wastewater treatment plant (WWTP) input 6 months after Hurricane Maria, a category V storm. Relative abundance and diversity of total ARGs increased markedly downstream of WWTP inputs, with ARGs unique to WWTP and WWTP-impacted river samples predominantly belonging to the aminoglycoside and β-lactam resistance classes. WWTP and other anthropogenic inputs were similarly associated with elevated resistome risk scores and mobility incidence (M%). Contig analysis indicated a wide variety of mobile β-lactam ARGs associated with pathogens downstream of WWTP discharge that were consistent with regional clinical concern, e.g., Klebsiella pneumoniae contigs containing KPC-2 within an ISKpn6-like transposase. HFMs and AARMs correlated strongly with the absolute abundance of total ARGs, but AARMs better predicted the majority of ARGs in general (85.4 versus <2%) and β-lactam ARGs in particular. This study reveals sensitive, quantitative, mobile, clinically relevant, and comprehensive targets for antibiotic resistance surveillance in watersheds.

Untreated sewage contamination of beach sand from a leaking underground sewage system

Thirty people (mostly children) experienced an episode of skin rash days after a sand sifting beach operation at Porto Pim Beach in Faial, Azores during June 2019. An environmental and epidemiologic investigation was conducted to identify the cause of the outbreak of skin rash. The epidemiologic investigation found that some of the patients experiencing symptoms had never entered the beach water. During the pollution period and throughout the epidemiologic investigation, faecal indicator bacteria levels (94 CFU/100 ml for intestinal enterococci and 61 CFU/100 ml for Escherichia coli) in water remained under the limits used for the ninety-five percentile calculation of an Excellent coastal and transitional bathing water defined in the Portuguese Legislation (100 CFU/100 ml for intestinal enterococci and 250 CFU/100 ml for Escherichia coli). Thus sand contact was considered as a likely primary exposure route. Sand microbiological analysis for faecal indicator organisms and electron microscopy strongly suggested faecal contamination. Chemical analysis of the sand also revealed a concomitant substance compatible with sodium-hypochlorite as analysed using gas chromatography and subsequently confirmed by free chlorine analysis. Inspection of the toilet facilities and sewage disposal system revealed a leaking sewage distribution box. Collectively, results suggest that the cause of the outbreak was the leaking underground sewage distribution box that serviced the beach toilet facilities (40 m from beach), where sodium-hypochlorite was used for cleaning and disinfection. This sewage then contaminated the surficial sands to which beach goers were exposed. Chlorine being an irritant substance, was believed to have been the cause of the symptoms given the sudden presentation and dissipation of skin rashes. No gastro-intestinal illness was reported during this episode and during the following 30 days. Like water, beach sand should also be monitored for safety, especially for areas serviced by aged infrastructure.

Search for Campylobacter spp. Reveals High Prevalence and Pronounced Genetic Diversity of Arcobacter butzleri in Floodwater Samples Associated with Hurricane Florence in North Carolina, USA

Climate change and associated extreme weather events can have massive impacts on the prevalence of microbial pathogens in floodwaters. However, limited data are available on foodborne zoonotic pathogens such as Campylobacter or Arcobacter in hurricane-associated floodwaters in rural regions with intensive animal production. With a high density of intensive animal production as well as pronounced vulnerability to hurricanes, eastern North Carolina presents unique opportunities in this regard. Our findings revealed widespread incidence of the emerging zoonotic pathogen Arcobacter butzleri in floodwaters from Hurricane Florence. We encountered high and largely unexplored diversity while also noting the potential for regionally abundant and persistent clones. We noted pronounced partitioning of the floodwater genotypes into two source-associated clades. The data will contribute to elucidating the poorly understood ecology of this emerging pathogen and highlight the importance of surveillance of floodwaters associated with hurricanes and other extreme weather events for Arcobacter and other zoonotic pathogens.

In September 2018, Hurricane Florence caused extreme flooding in eastern North Carolina, USA, a region highly dense in concentrated animal production, especially swine and poultry. In this study, floodwater samples (n = 96) were collected as promptly post-hurricane as possible and for up to approximately 30 days and selectively enriched for Campylobacter using Bolton broth enrichment and isolation on modified charcoal cefoperazone deoxycholate agar (mCCDA) microaerobically at 42°C. Only one sample yielded Campylobacter, which was found to be Campylobacter jejuni with the novel sequence type 2866 (ST-2866). However, the methods employed to isolate Campylobacter readily yielded Arcobacter from 73.5% of the floodwater samples. The Arcobacter isolates failed to grow on Mueller-Hinton agar at 25, 30, 37, or 42°C microaerobically or aerobically but could be readily subcultured on mCCDA at 42°C microaerobically. Multilocus sequence typing of 112 isolates indicated that all were Arcobacter butzleri. The majority (85.7%) of the isolates exhibited novel sequence types (STs), with 66 novel STs identified. Several STs, including certain novel ones, were detected in diverse waterbody types (channel, isolated ephemeral pools, floodplain) and from multiple watersheds, suggesting the potential for regionally dominant strains. The genotypes were clearly partitioned into two major clades, one with high representation of human and ruminant isolates and another with an abundance of swine and poultry isolates. Surveillance of environmental waters and food animal production systems in this animal agriculture-dense region is needed to assess potential regional prevalence and temporal stability of the observed A. butzleri strains as well as their potential association with specific types of food animal production.

IMPORTANCE Climate change and associated extreme weather events can have massive impacts on the prevalence of microbial pathogens in floodwaters. However, limited data are available on foodborne zoonotic pathogens such as Campylobacter or Arcobacter in hurricane-associated floodwaters in rural regions with intensive animal production. With a high density of intensive animal production as well as pronounced vulnerability to hurricanes, eastern North Carolina presents unique opportunities in this regard. Our findings revealed widespread incidence of the emerging zoonotic pathogen Arcobacter butzleri in floodwaters from Hurricane Florence. We encountered high and largely unexplored diversity while also noting the potential for regionally abundant and persistent clones. We noted pronounced partitioning of the floodwater genotypes into two source-associated clades. The data will contribute to elucidating the poorly understood ecology of this emerging pathogen and highlight the importance of surveillance of floodwaters associated with hurricanes and other extreme weather events for Arcobacter and other zoonotic pathogens.

Characterizing a riverine microbiome impacted by extreme disturbance caused by a mining sludge tsunami

Studies on disturbance events in riverine systems caused by environmental disasters and their effects on microbial diversity are scarce. Here, we evaluated the impact of the collapse of an iron ore dam holding approximately 50 million cubic meters of waste on both water and sediment microbiomes by deeply sequencing the 16S rRNA gene. Samples were taken from two impacted rivers and one reference river 7, 30 and 150 days postdisturbance. The impacted community structure changed greatly over spatiotemporal scales, being less diverse and more uneven, particularly on day 7 for the do Carmo River (the closest to the dam). However, the reference community structure remained similar between sampling events. Moreover, the impacted sediments were positively correlated with metals. The taxa abundance varied greatly over spatiotemporal scales, allowing for the identification of several potential bioindicators, e.g., Comamonadaceae, Novosphingobium, Sediminibacterium and Bacteriovorax. Our results showed that the impacted communities consisted mostly of Fe(II) oxidizers and Fe(III) reducers, aromatic compound degraders and predator bacteria. Network analysis showed a highly interconnected microbiome whose interactions switched from positive to negative or vice versa between the impacted and reference communities. This work revealed potential molecular signatures associated with the rivers heavily impacted by metals that might be useful sentinels for predicting riverine health.

Interactions between Environmental Exposures and the Microbiome: Implications for Fetal Programming

Decades of population-based health outcomes data highlight the importance of understanding how environmental exposures in pregnancy affect maternal and neonatal outcomes. Animal model research and epidemiological studies have revealed that such exposures are able to alter fetal programming through stable changes in the epigenome, including altered DNA methylation patterns and histone modifications in the developing fetus and infant. It is similarly known that while microbes can biotransform environmental chemicals via conjugation and de-conjugation, specific exposures can also alter the community profile and function of the human microbiome. In this review, we consider how alterations to the maternal and or fetal/infant microbiome through environmental exposures could directly and indirectly alter fetal programming. We highlight two specific environmental exposures, cadmium (Cd) and polycyclic aromatic hydrocarbons (PAHs), and outline their effects on the developing fetus and the perinatal (maternal and fetal/infant) microbiome. We further consider how chemical exposures in the setting of natural disasters may be of particular importance to environmental health.

Identifying the primary sources of fecal contamination along the beaches and rivers of Trinidad

The aim of this study was to identify the main sources of fecal pollution at popular beaches and rivers in the island of Trinidad. Escherichia coli enumeration and microbial source tracking (MST) were used to identify the primary sources of fecal bacteria contamination at the sites. Nineteen sites exceeded USEPA water quality standards for safe recreational use. Highest levels of fecal contamination were recorded on the central and west coasts of the island and included Brickfield River (4,839 MPN 100 ml^-1), Orange Valley Bay (2,406.6 MPN 100 ml^-1) and Chaguaramas Bay (1,921.2 MPN 100 ml^-1). MST detected human (HF183) fecal pollution at ∼63%, birds at ∼67%, chicken at ∼36% and cattle (BacCow) at ∼34% of the sites. MST is a useful and rapid method for identifying major sources of fecal pollution in rivers and beaches. In Trinidad water bodies, the main sources of fecal pollution were humans and birds. The large number of sites with elevated levels of fecal pollution detected is particularly alarming and represents a serious public health risk.

Proliferation of microalgae and enterococci in the Lake Okeechobee, St. Lucie, and Loxahatchee watersheds

This study is an analysis of relationships between microalgae (measured as chlorophyll a) and the fecal indicator bacteria enterococci. Microalgae blooms and enterococci exceedances have been occurring in Florida's recreational waterways for years. More recently, this has become a management concern as microalgae blooms have been attributed to potentially toxic cyanobacteria, and enterococci exceedances link to human infection/illness. Since both the microalgal blooms and bacterial exceedances occur in regions that receive managed freshwater releases from Lake Okeechobee, we hypothesized that both the blooms and exceedances are related to excess nutrients from the lake. Two experimental sites, on Lake Okeechobee and the St. Lucie River (downstream of the lake), plus a control site on the Loxahatchee River (which does not receive lake flow) were evaluated. The hypothesis was evaluated through three study components: 1) analysis of available long-term data from local environmental databases, 2) a year-long monthly sampling and analysis of chlorophyll a, enterococci, nutrients, and physical-chemical data, and 3) microcosm experiments with altered water/sediment conditions. Results support the hypothesis that excess nutrients play a role in both chlorophyll a and enterococci levels. For the St. Lucie River, analyses indicate that chlorophyll a correlated significantly with total Kjeldahl nitrogen (TKN) (R² = 0.30, p = 0.008) and the strongest model for enterococci included nitrate-nitrite, TKN, total phosphorus, orthophosphorus, and turbidity in our long-term analysis (n = 39, R² = 0.83, p ≤ 0.001). The microcosm results indicated that chlorophyll a and enterococci only persisted for 36 h in water from all sources, and that sediments from Lake Okeechobee may have allowed for sustained levels of chlorophyll a and enterococci levels. Overall similarities were observed in chlorophyll a and enterococci relationships with nutrient concentrations regardless of a Lake Okeechobee connection, as underscored by a study of flow out of the lake and downstream areas. This suggests that both nutrient-rich lake water and untreated surface water runoff contribute to microalgae blooms and enterococci exceedances in southeast Florida.

In hot water: effects of climate change on Vibrio-human interactions

Sea level rise and the anthropogenic warming of the world's oceans is not only an environmental tragedy, but these changes also result in a significant threat to public health. Along with coastal flooding and the encroachment of saltwater farther inland comes an increased risk of human interaction with pathogenic Vibrio species, such as Vibrio cholerae, V. vulnificus and V. parahaemolyticus. This minireview examines the current literature for updates on the climatic changes and practices that impact the location and duration of the presence of Vibrio spp., as well as the infection routes, trends and virulence factors of these highly successful pathogens. Finally, an overview of current treatments and methods for the mitigation of both oral and cutaneous exposures are presented.

Microbiological Assessment of Tap Water Following the 2016 Louisiana Flooding

Floods are a prominent risk factor in the world of public health, as there is a risk of dispersal of harmful biological and chemical contaminants in floodwater. As climate change increases, the occurrence of natural disasters and risk of adverse health outcomes due to flash flooding also increases. Fecal indicator bacteria, such as Escherichia coli and Enterococci, are often encountered in contaminated floodwater and can cause gastrointestinal illnesses as well as a variety of infections. In August 2016, East Baton Rouge and surrounding parishes in Louisiana suffered heavy floods due to intense rainfall. No study of water quality during flooding has been conducted previously in Baton Rouge, Louisiana. Twenty-three pre-flush and post-flush water samples were collected immediately from accessible homes that had been affected by the floods in order to quantify concentrations of fecal indicator bacteria. These samples were analyzed for the presence of E. coli and Enterococci through both quantitative polymerase chain reaction (qPCR) and the IDEXX enzyme substrate method. The qPCR results indicated that 30% of the samples contained Enterococci and 61% of the samples contained E. coli, with the highest concentrations found in the pre-flush outdoor hose and the pre-flush kitchen tap. The IDEXX method yielded total coliforms in 65% of the samples, E. coli in 4%, and Enterococci in 35%, with the highest concentrations in the pre-flush outdoor faucet and the pre-flush post-filtration kitchen tap. Physical parameters including temperature, barometer pressure, dissolved oxygen, oxidation reduction potential, pH, conductivity, and salinity of these samples were also recorded. Of these parameters, conductivity and salinity were significant, suggesting they may positively influence E. coli and Enterococci growth.

Bacterial Community Dynamics in an Oyster Hatchery in Response to Probiotic Treatment

Larval oysters in hatcheries are susceptible to diseases caused by bacterial pathogens, including Vibrio spp. Previous studies have shown that daily addition of the probiotic Bacillus pumilus RI06-95 to water in rearing tanks increases larval survival when challenged with the pathogen Vibrio coralliilyticus. We propose that the presence of probiotics causes shifts in bacterial community structure in rearing tanks, leading to a net decrease in the relative abundance of potential pathogens. During three trials spanning the 2012-2015 hatchery seasons, larvae, tank biofilm, and rearing water samples were collected from control and probiotic-treated tanks in an oyster hatchery over a 12-day period after spawning. Samples were analyzed by 16S rRNA sequencing of the V4 or V6 regions followed by taxonomic classification, in order to determine bacterial community structures. There were significant differences in bacterial composition over time and between sample types, but no major effect of probiotics on the structure and diversity of bacterial communities (phylum level, Bray-Curtis k = 2, 95% confidence). Probiotic treatment, however, led to a higher relative percent abundance of Oceanospirillales and Bacillus spp. in water and oyster larvae. In the water, an increase in Vibrio spp. diversity in the absence of a net increase in relative read abundance suggests a likely decrease in the abundance of specific pathogenic Vibrio spp., and therefore lower chances of a disease outbreak. Co-occurrence network analysis also suggests that probiotic treatment had a systemic effect on targeted members of the bacterial community, leading to a net decrease in potentially pathogenic species.

Possible impacts of sea level rise on disease transmission and potential adaptation strategies, a review

Sea levels are projected to rise in response to climate change, causing the intrusion of sea water into land. In flat coastal regions, this would generate an increase in shallow water covered areas with limited circulation. This scenario raises a concern about the consequences it could have on human health, specifically the possible impacts on disease transmission. In this review paper we identified three categories of diseases which are associated with water and whose transmission can be affected by sea level rise. These categories include: mosquitoborne diseases, naturalized organisms (Vibrio spp. and toxic algae), and fecal-oral diseases. For each disease category, we propose comprehensive adaptation strategies that would help minimize possible health risks. Finally, the City of Key West, Florida is analyzed as a case study, due to its inherent vulnerability to sea level rise. Current and projected adaptation techniques are discussed as well as the integration of additional recommendations, focused on disease transmission control. Given that sea level rise will likely continue into the future, the promotion and implementation of positive adaptation strategies is necessary to ensure community resilience.

Physicochemical Factors Influence the Abundance and Culturability of Human Enteric Pathogens and Fecal Indicator Organisms in Estuarine Water and Sediment

To assess fecal pollution in coastal waters, current monitoring is reliant on culture-based enumeration of bacterial indicators, which does not account for the presence of viable but non-culturable or sediment-associated micro-organisms, preventing effective quantitative microbial risk assessment (QMRA). Seasonal variability in viable but non-culturable or sediment-associated bacteria challenge the use of fecal indicator organisms (FIOs) for water monitoring. We evaluated seasonal changes in FIOs and human enteric pathogen abundance in water and sediments from the Ribble and Conwy estuaries in the UK. Sediments possessed greater bacterial abundance than the overlying water column, however, key pathogenic species (Shigella spp., Campylobacter jejuni, Salmonella spp., hepatitis A virus, hepatitis E virus and norovirus GI and GII) were not detected in sediments. Salmonella was detected in low levels in the Conwy water in spring/summer and norovirus GII was detected in the Ribble water in winter. The abundance of E. coli and Enterococcus spp. quantified by culture-based methods, rarely matched the abundance of these species when measured by qPCR. The discrepancy between these methods was greatest in winter at both estuaries, due to low CFU's, coupled with higher gene copies (GC). Temperature accounted for 60% the variability in bacterial abundance in water in autumn, whilst in winter salinity explained 15% of the variance. Relationships between bacterial indicators/pathogens and physicochemical variables were inconsistent in sediments, no single indicator adequately described occurrence of all bacterial indicators/pathogens. However, important variables included grain size, porosity, clay content and concentrations of Zn, K, and Al. Sediments with greater organic matter content and lower porosity harbored a greater proportion of non-culturable bacteria (including dead cells and extracellular DNA) in winter. Here, we show the link between physicochemical variables and season which govern culturability of human enteric pathogens and FIOs. Therefore, knowledge of these factors is critical for accurate microbial risk assessment. Future water quality management strategies could be improved through monitoring sediment-associated bacteria and non-culturable bacteria. This could facilitate source apportionment of human enteric pathogens and FIOs and direct remedial action to improve water quality.

Seasonal Succession and Spatial Patterns of Synechococcus Microdiversity in a Salt Marsh Estuary Revealed through 16S rRNA Gene Oligotyping

Synechococcus are ubiquitous and cosmopolitan cyanobacteria that play important roles in global productivity and biogeochemical cycles. This study investigated the fine scale microdiversity, seasonal patterns, and spatial distributions of Synechococcus in estuarine waters of Little Sippewissett salt marsh (LSM) on Cape Cod, MA. The proportion of Synechococcus reads was higher in the summer than winter, and higher in coastal waters than within the estuary. Variations in the V4-V6 region of the bacterial 16S rRNA gene revealed 12 unique Synechococcus oligotypes. Two distinct communities emerged in early and late summer, each comprising a different set of statistically co-occurring Synechococcus oligotypes from different clades. The early summer community included clades I and IV, which correlated with lower temperature and higher dissolved oxygen levels. The late summer community included clades CB5, I, IV, and VI, which correlated with higher temperatures and higher salinity levels. Four rare oligotypes occurred in the late summer community, and their relative abundances more strongly correlated with high salinity than did other co-occurring oligotypes. The analysis revealed that multiple, closely related oligotypes comprised certain abundant clades (e.g., clade 1 in the early summer and clade CB5 in the late summer), but the correlations between these oligotypes varied from pair to pair, suggesting they had slightly different niches despite being closely related at the clade level. Lack of tidal water exchange between sampling stations gave rise to a unique oligotype not abundant at other locations in the estuary, suggesting physical isolation plays a role in generating additional microdiversity within the community. Together, these results contribute to our understanding of the environmental and ecological factors that influence patterns of Synechococcus microbial community composition over space and time in salt marsh estuarine waters.

Riverine Bacterial Communities Reveal Environmental Disturbance Signatures within the Betaproteobacteria and Verrucomicrobia

Riverine bacterial communities play an essential role in the biogeochemical coupling of terrestrial and marine environments, transforming elements and organic matter in their journey from land to sea. However, precisely due to the fact that rivers receive significant terrestrial input, the distinction between resident freshwater taxa vs. land-derived microbes can often become ambiguous. Furthermore, ecosystem perturbations could introduce allochthonous microbial groups and reshape riverine bacterial communities. Using full- and partial-length 16S ribosomal RNA gene sequences, we analyzed the composition of bacterial communities in the Tar River of North Carolina from November 2010 to November 2011, during which a natural perturbation occurred: the inundation of the lower reaches of an otherwise drought-stricken river associated with Hurricane Irene, which passed over eastern North Carolina in late August 2011. This event provided the opportunity to examine the microbiological, hydrological, and geochemical impacts of a disturbance, defined here as the large freshwater influx into the Tar River, superimposed on seasonal changes or other ecosystem variability independent of the hurricane. Our findings demonstrate that downstream communities are more taxonomically diverse and temporally variable than their upstream counterparts. More importantly, pre- vs. post-disturbance taxonomic comparison of the freshwater-dominant Betaproteobacteria class and the phylum Verrucomicrobia reveal a disturbance signature of previously undetected taxa of diverse origins. We use known traits of closely-related taxa to interpret the ecological function of disturbance-associated bacteria, and hypothesize that carbon cycling was enhanced post-disturbance in the Tar River, likely due to the flux of organic carbon into the system associated with the large freshwater pulse. Our analyses demonstrate the importance of geochemical and hydrological alterations in structuring bacterial communities, and illustrate the response of temperate riverine bacteria on fine taxonomic scales to a disturbance.

Spatiotemporal Analysis of Microbiological Contamination in New York State Produce Fields following Extensive Flooding from Hurricane Irene, August 2011

Although flooding introduces microbiological, chemical, and physical hazards onto croplands, few data are available on the spatial extent, patterns, and development of contamination over time postflooding. To address this paucity of information, we conducted a spatially explicit study of Escherichia coli and Salmonella contamination prevalence and genetic diversity in produce fields after the catastrophic flooding that occurred in New England during 2011. Although no significant differences were detected between the two participating farms, both random forest and logistic regression revealed changes in the spatial pattern of E. coli contamination in drag swab samples over time. Analyses also indicated that E. coli detection was associated with changes in farm management to remediate the land after flooding. In particular, E. coli was widespread in drag swab samples at 21 days postflooding, but the spatial pattern changed by 238 days postflooding such that E. coli was then most prevalent in close proximity to surface water features. The combined results of several population genetics analyses indicated that over time postflooding E. coli populations on the farms (i) changed in composition and (ii) declined overall. Salmonella was primarily detected in surface water features, but some Salmonella strains were isolated from soil and drag swab samples at 21 and 44 days postflooding. Although postflood contamination and land management responses should always be evaluated in the context of each unique farm landscape, our results provide quantitative data on the general patterns of contamination after flooding and support the practice of establishing buffer zones between flood-contaminated cropland and harvestable crops in produce fields.

Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea, Antarctica

Antarctica polynyas support intense phytoplankton blooms, impacting their environment by a substantial depletion of inorganic carbon and nutrients. These blooms are dominated by the colony-forming haptophyte Phaeocystis antarctica and they are accompanied by a distinct bacterial population. Yet, the ecological role these bacteria may play in P. antarctica blooms awaits elucidation of their functional gene pool and of the geochemical activities they support. Here, we report on a metagenome (~160 million reads) analysis of the microbial community associated with a P. antarctica bloom event in the Amundsen Sea polynya (West Antarctica). Genomes of the most abundant Bacteroidetes and Proteobacteria populations have been reconstructed and a network analysis indicates a strong functional partitioning of these bacterial taxa. Three of them (SAR92, and members of the Oceanospirillaceae and Cryomorphaceae) are found in close association with P. antarctica colonies. Distinct features of their carbohydrate, nitrogen, sulfur and iron metabolisms may serve to support mutualistic relationships with P. antarctica. The SAR92 genome indicates a specialization in the degradation of fatty acids and dimethylsulfoniopropionate (compounds released by P. antarctica) into dimethyl sulfide, an aerosol precursor. The Oceanospirillaceae genome carries genes that may enhance algal physiology (cobalamin synthesis). Finally, the Cryomorphaceae genome is enriched in genes that function in cell or colony invasion. A novel pico-eukaryote, Micromonas related genome (19.6 Mb, ~94% completion) was also recovered. It contains the gene for an anti-freeze protein, which is lacking in Micromonas at lower latitudes. These draft genomes are representative for abundant microbial taxa across the Southern Ocean surface.

Bedforms as Biocatalytic Filters: A Pumping and Streamline Segregation Model for Nitrate Removal in Permeable Sediments

Bedforms are a focal point of carbon and nitrogen cycling in streams and coastal marine ecosystems. In this paper, we develop and test a mechanistic model, the "pumping and streamline segregation" or PASS model, for nitrate removal in bedforms. The PASS model dramatically reduces computational overhead associated with modeling nitrogen transformations in bedforms and reproduces (within a factor of 2 or better) previously published measurements and models of biogeochemical reaction rates, benthic fluxes, and in-sediment nutrient and oxygen concentrations. Application of the PASS model to a diverse set of marine and freshwater environments indicates that (1) physical controls on nitrate removal in a bedform include the pore water flushing rate, residence time distribution, and relative rates of respiration and transport (as represented by the Damkohler number); (2) the biogeochemical pathway for nitrate removal is an environment-specific combination of direct denitrification of stream nitrate and coupled nitrification-denitrification of stream and/or sediment ammonium; and (3) permeable sediments are almost always a net source of dissolved inorganic nitrogen. The PASS model also provides a mechanistic explanation for previously published empirical correlations showing denitrification velocity (N2 flux divided by nitrate concentration) declines as a power law of nitrate concentration in a stream (Mulholland et al. Nature, 2008, 452, 202-205).

Diverse, rare microbial taxa responded to the Deepwater Horizon deep-sea hydrocarbon plume

The Deepwater Horizon (DWH) oil well blowout generated an enormous plume of dispersed hydrocarbons that substantially altered the Gulf of Mexico's deep-sea microbial community. A significant enrichment of distinct microbial populations was observed, yet, little is known about the abundance and richness of specific microbial ecotypes involved in gas, oil and dispersant biodegradation in the wake of oil spills. Here, we document a previously unrecognized diversity of closely related taxa affiliating with Cycloclasticus, Colwellia and Oceanospirillaceae and describe their spatio-temporal distribution in the Gulf's deepwater, in close proximity to the discharge site and at increasing distance from it, before, during and after the discharge. A highly sensitive, computational method (oligotyping) applied to a data set generated from 454-tag pyrosequencing of bacterial 16S ribosomal RNA gene V4-V6 regions, enabled the detection of population dynamics at the sub-operational taxonomic unit level (0.2% sequence similarity). The biogeochemical signature of the deep-sea samples was assessed via total cell counts, concentrations of short-chain alkanes (C1-C5), nutrients, (colored) dissolved organic and inorganic carbon, as well as methane oxidation rates. Statistical analysis elucidated environmental factors that shaped ecologically relevant dynamics of oligotypes, which likely represent distinct ecotypes. Major hydrocarbon degraders, adapted to the slow-diffusive natural hydrocarbon seepage in the Gulf of Mexico, appeared unable to cope with the conditions encountered during the DWH spill or were outcompeted. In contrast, diverse, rare taxa increased rapidly in abundance, underscoring the importance of specialized sub-populations and potential ecotypes during massive deep-sea oil discharges and perhaps other large-scale perturbations.

Confirmed and Potential Sources of Legionella Reviewed

Legionella bacteria are ubiquitous in natural matrices and man-made systems. However, it is not always clear if these reservoirs can act as source of infection resulting in cases of Legionnaires' disease. This review provides an overview of reservoirs of Legionella reported in the literature, other than drinking water distribution systems. Levels of evidence were developed to discriminate between potential and confirmed sources of Legionella. A total of 17 systems and matrices could be classified as confirmed sources of Legionella. Many other man-made systems or natural matrices were not classified as a confirmed source, since either no patients were linked to these reservoirs or the supporting evidence was weak. However, these systems or matrices could play an important role in the transmission of infectious Legionella bacteria; they might not yet be considered in source investigations, resulting in an underestimation of their importance. To optimize source investigations it is important to have knowledge about all the (potential) sources of Legionella. Further research is needed to unravel what the contribution is of each confirmed source, and possibly also potential sources, to the LD disease burden.

Differential specificity of selective culture media for enumeration of pathogenic vibrios: advantages and limitations of multi-plating methods

Plating environmental samples on vibrio-selective chromogenic media is a commonly used technique that allows one to quickly estimate concentrations of putative vibrio pathogens or to isolate them for further study. Although this approach is convenient, its usefulness depends directly on how well the procedure selects against false positives. We tested whether a chromogenic medium, CHROMagar Vibrio (CaV), used alone (single-plating) or in combination (double-plating) with a traditional medium thiosulfate-citrate-bile-salts (TCBS), could improve the discrimination among three pathogenic vibrio species (Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus) and thereby decrease the number of false-positive colonies that must be screened by molecular methods. Assays were conducted on water samples from two estuarine environments (one subtropical, one tropical) in a variety of seasonal conditions. The results of the double-plating method were confirmed by PCR and 16S rRNA sequencing. Our data indicate that there is no significant difference in the false-positive rate between CaV and TCBS when using a single-plating technique, but determining color changes on the two media sequentially (double-plating) reduced the rate of false positive identification in most cases. The improvement achieved was about two-fold on average, but varied greatly (from 0- to 5-fold) and depended on the sampling time and location. The double-plating method was most effective for V. vulnificus in warm months, when overall V. vulnificus abundance is high (false positive rates as low as 2%, n=178). Similar results were obtained for V. cholerae (minimum false positive rate of 16%, n=146). In contrast, the false positive rate for V. parahaemolyticus was always high (minimum of 59%, n=109). Sequence analysis of false-positive isolates indicated that the majority of confounding isolates are from the Vibrionaceae family, however, members of distantly related bacterial groups were also able to grow on vibrio-selective media, even when using the double-plating method. In conclusion, the double-plating assay is a simple means to increase the efficiency of identifying pathogenic vibrios in aquatic environments and to reduce the number of molecular assays required for identity confirmation. However, the high spatial and temporal variability in the performance of the media mean that molecular approaches are still essential to obtain the most accurate vibrio abundance estimates from environmental samples.

Phaeocystis antarctica blooms strongly influence bacterial community structures in the Amundsen Sea polynya

Rising temperatures and changing winds drive the expansion of the highly productive polynyas (open water areas surrounded by sea ice) abutting the Antarctic continent. Phytoplankton blooms in polynyas are often dominated by the haptophyte Phaeocystis antarctica, and they generate the organic carbon that enters the resident microbial food web. Yet, little is known about how Phaeocystis blooms shape bacterial community structures and carbon fluxes in these systems. We identified the bacterial communities that accompanied a Phaeocystis bloom in the Amundsen Sea polynya during the austral summers of 2007–2008 and 2010–2011. These communities are distinct from those determined for the Antarctic Circumpolar Current (ACC) and off the Palmer Peninsula. Diversity patterns for most microbial taxa in the Amundsen Sea depended on location (e.g., waters abutting the pack ice near the shelf break and at the edge of the Dotson glacier) and depth, reflecting different niche adaptations within the confines of this isolated ecosystem. Inside the polynya, P. antarctica coexisted with the bacterial taxa Polaribacter sensu lato, a cryptic Oceanospirillum, SAR92 and Pelagibacter. These taxa were dominated by a single oligotype (genotypes partitioned by Shannon entropy analysis) and together contributed up to 73% of the bacterial community. Size fractionation of the bacterial community [<3 μm (free-living bacteria) vs. >3 μm (particle-associated bacteria)] identified several taxa (especially SAR92) that were preferentially associated with Phaeocystis colonies, indicative of a distinct role in Phaeocystis bloom ecology. In contrast, particle-associated bacteria at 250 m depth were enriched in Colwellia and members of the Cryomorphaceae suggesting that they play important roles in the decay of Phaeocystis blooms.

Microbes in Beach Sands: Integrating Environment, Ecology and Public Health

Beach sand is a habitat that supports many microbes, including viruses, bacteria, fungi and protozoa (micropsammon). The apparently inhospitable conditions of beach sand environments belie the thriving communities found there. Physical factors, such as water availability and protection from insolation; biological factors, such as competition, predation, and biofilm formation; and nutrient availability all contribute to the characteristics of the micropsammon. Sand microbial communities include autochthonous species/phylotypes indigenous to the environment. Allochthonous microbes, including fecal indicator bacteria (FIB) and waterborne pathogens, are deposited via waves, runoff, air, or animals. The fate of these microbes ranges from death, to transient persistence and/or replication, to establishment of thriving populations (naturalization) and integration in the autochthonous community. Transport of the micropsammon within the habitat occurs both horizontally across the beach, and vertically from the sand surface and ground water table, as well as at various scales including interstitial flow within sand pores, sediment transport for particle-associated microbes, and the large-scale processes of wave action and terrestrial runoff. The concept of beach sand as a microbial habitat and reservoir of FIB and pathogens has begun to influence our thinking about human health effects associated with sand exposure and recreational water use. A variety of pathogens have been reported from beach sands, and recent epidemiology studies have found some evidence of health risks associated with sand exposure. Persistent or replicating populations of FIB and enteric pathogens have consequences for watershed/beach management strategies and regulatory standards for safe beaches. This review summarizes our understanding of the community structure, ecology, fate, transport, and public health implications of microbes in beach sand. It concludes with recommendations for future work in this vastly under-studied area.

Quantitative assessment of infection risk from exposure to waterborne pathogens in urban floodwater

Flooding and heavy rainfall have been associated with waterborne infectious disease outbreaks, however, it is unclear to which extent they pose a risk for public health. Here, risks of infection from exposure to urban floodwater were assessed using quantitative microbial risk assessment (QMRA). To that aim, urban floodwaters were sampled in the Netherlands during 23 events in 2011 and 2012. The water contained Campylobacter jejuni (prevalence 61%, range 14- >10(3) MPN/l), Giardia spp. (35%, 0.1-142 cysts/l), Cryptosporidium (30%, 0.1-9.8 oocysts/l), noroviruses (29%, 10(2)-10(4) pdu/l) and enteroviruses (35%, 10(3)-10(4) pdu/l). Exposure data collected by questionnaire, revealed that children swallowed 1.7 ml (mean, 95% Confidence Interval 0-4.6 ml) per exposure event and adults swallowed 0.016 ml (mean, 95% CI 0-0.068 ml) due to hand-mouth contact. The mean risk of infection per event for children, who were exposed to floodwater originating from combined sewers, storm sewers and rainfall generated surface runoff was 33%, 23% and 3.5%, respectively, and for adults it was 3.9%, 0.58% and 0.039%. The annual risk of infection was calculated to compare flooding from different urban drainage systems. An exposure frequency of once every 10 years to flooding originating from combined sewers resulted in an annual risk of infection of 8%, which was equal to the risk of infection of flooding originating from rainfall generated surface runoff 2.3 times per year. However, these annual infection risks will increase with a higher frequency of urban flooding due to heavy rainfall as foreseen in climate change projections.

Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data

Bacteria comprise the most diverse domain of life on Earth, where they occupy nearly every possible ecological niche and play key roles in biological and chemical processes. Studying the composition and ecology of bacterial ecosystems and understanding their function are of prime importance. High-throughput sequencing technologies enable nearly comprehensive descriptions of bacterial diversity through 16S ribosomal RNA gene amplicons. Analyses of these communities generally rely upon taxonomic assignments through reference data bases or clustering approaches using de facto sequence similarity thresholds to identify operational taxonomic units. However, these methods often fail to resolve ecologically meaningful differences between closely related organisms in complex microbial data sets.

In this paper, we describe oligotyping, a novel supervised computational method that allows researchers to investigate the diversity of closely related but distinct bacterial organisms in final operational taxonomic units identified in environmental data sets through 16S ribosomal RNA gene data by the canonical approaches.

Our analysis of two data sets from two different environments demonstrates the capacity of oligotyping at discriminating distinct microbial populations of ecological importance.

Oligotyping can resolve the distribution of closely related organisms across environments and unveil previously overlooked ecological patterns for microbial communities. The URL http://oligotyping.org offers an open-source software pipeline for oligotyping.

A perspective on the history and evolution of an Oceans and Human Health "metadiscipline" in the USA

We review recent history and evolution of Oceans and Human Health programs and related activities in the USA from a perspective within the Federal government. As a result of about a decade of support by the US Congress and through a few Federal agencies, notably the National Science Foundation, National Institute of Environmental Health Sciences, and National Ocean and Atmospheric Administration, robust Oceans and Human Health (OHH) research and application activities are now relatively widespread, although still small, in a number of agencies and academic institutions. OHH themes and issues have been incorporated into comprehensive federal ocean research plans and are reflected in the new National Ocean Policy enunciated by Executive Order 13547. In just a decade, OHH has matured into a recognized "metadiscipline," with development of a small, but robust and diverse community of science and practice, incorporation into academic educational programs, regular participation in ocean and coastal science and public health societies, and active engagement with public health decision makers. In addition to substantial increases in scientific information, the OHH community has demonstrated ability to respond rapidly and effectively to emergency situations such as those associated with extreme weather events (e.g., hurricanes, floods) and human-caused disasters (e.g., the Deep Water Horizon oil spill). Among many other things, next steps include development and implementation of agency health strategies and provision of specific services, such as ecological forecasts to provide routine early warnings for ocean health threats and opportunities for prevention and mitigation of these risks.

Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities

Ruminants rely on a complex rumen microbial community to convert dietary plant material to energy-yielding products. Here we developed a method to simultaneously analyze the community's bacterial and archaeal 16S rRNA genes, ciliate 18S rRNA genes and anaerobic fungal internal transcribed spacer 1 genes using 12 DNA samples derived from 11 different rumen samples from three host species (Ovis aries, Bos taurus, Cervus elephas) and multiplex 454 Titanium pyrosequencing. We show that the mixing ratio of the group-specific DNA templates before emulsion PCR is crucial to compensate for differences in amplicon length. This method, in contrast to using a non-specific universal primer pair, avoids sequencing non-targeted DNA, such as plant- or endophyte-derived rRNA genes, and allows increased or decreased levels of community structure resolution for each microbial group as needed. Communities analyzed with different primers always grouped by sample origin rather than by the primers used. However, primer choice had a greater impact on apparent archaeal community structure than on bacterial community structure, and biases for certain methanogen groups were detected. Co-occurrence analysis of microbial taxa from all three domains of life suggested strong within- and between-domain correlations between different groups of microorganisms within the rumen. The approach used to simultaneously characterize bacterial, archaeal and eukaryotic components of a microbiota should be applicable to other communities occupying diverse habitats.

23S rRNA gene-based enterococci community signatures in Lake Pontchartrain, Louisiana, USA, following urban runoff inputs after Hurricane Katrina

Little is known about the impacts of fecal polluted urban runoff inputs on the structure of enterococci communities in estuarine waters. This study employed a 23S rRNA gene-based polymerase chain reaction (PCR) assay with newly designed genus-specific primers, Ent127F-Ent907R, to determine the possible impacts of Hurricane Katrina floodwaters via the 17th Street Canal discharge on the community structure of enterococci in Lake Pontchartrain. A total of 94 phylotypes were identified through the restriction fragment length polymorphism (RFLP) screening of 494 clones while only 8 phylotypes occurred among 88 cultivated isolates. Sequence analyses of representative phylotypes and their temporal and spatial distribution in the lake and the canal indicated the Katrina floodwater input introduced a large portion of Enterococcus flavescens, Enterococcus casseliflavus, and Enterococcus dispar into the lake; typical fecal groups Enterococcus faecium, Enterococcus durans, Enterococcus hirae, and Enterococcus mundtii were detected primarily in the floodwater-impacted waters. This study provides a global picture of enterococci in estuarine waters impacted by Hurricane Katrina-derived urban runoff. It also demonstrates the culture-independent PCR approach using 23S rRNA gene as a molecular marker could be a good alternative in ecological studies of enterococci in natural environments to overcome the limitation of conventional cultivation methods.

Impact of xynthia tempest on viral contamination of shellfish

Viral contamination in oyster and mussel samples was evaluated after a massive storm with hurricane wind named "Xynthia tempest" destroyed a number of sewage treatment plants in an area harboring many shellfish farms. Although up to 90% of samples were found to be contaminated 2 days after the disaster, detected viral concentrations were low. A 1-month follow-up showed a rapid decrease in the number of positive samples, even for norovirus.

Risk factors for colonization of E. coli in Atlantic Bottlenose Dolphins (Tursiops truncatus) in the Indian River Lagoon, Florida

Opportunistic pathogens related to degradation in water quality are of concern to both wildlife and public health. The objective of this study was to identify spatial, temporal, and environmental risk factors for E. coli colonization among Atlantic bottlenose dolphins (Tursiops truncatus) inhabiting the Indian River Lagoon (IRL), FL between 2003 and 2007. Age, gender, capture location, coastal human population density, proximity of sewage treatment plants, number of septic tanks, cumulative precipitation 48 hrs and 30 days prior to capture, salinity, and water temperature were analyzed as potential risk factors. Highest E. coli colonization rates occurred in the northern segments of the IRL. The risk of E. coli colonization was the highest among the youngest individuals, in counties with the highest cumulative rainfall 48 hrs and in counties with the highest number of septic systems during the year of capture. The prevalence of colonization was the highest during 2004, a year during which multiple hurricanes hit the coast of Florida. Septic tanks, in combination with weather-related events suggest a possible pathway for introduction of fecal coliforms into estuarine ecosystems. The ability of E. coli and related bacteria to act as primary pathogens or cause opportunistic infections adds importance of these findings.

Evaluation of microbiological water quality in the Pettaquamscutt River (Rhode Island, USA) using chemical, molecular and culture-dependent methods

We evaluated microbiological water quality in the Pettaquamscutt River (Rhode Island, USA), an estuarine river. Fecal coliform (FC) and enterococci (FE) bacteria, presence of Bifidobacterium adolescentis DNA (indicating human fecal contamination), and optical brightener (OB) fluorescence (associated with laundry detergents) were determined for 14 stations from May to September 2010. Six stations had high counts of FE and FC, and the presence of B. adolescentis DNA and high OB fluorescence indicated human fecal contamination - four had septic systems as likely sources of contamination; the others were in sewered areas. The ability of FC and FE to indicate human fecal contamination was assessed against a positive B. adolescentis test. FC and FE had false positive rates of 25% and 17%, respectively, and false negatives of 44% for FC and 63% for FE. Inclusion of molecular and chemical indicators should improve tracking of human fecal contamination sources in the river.

Temporal and spatial variability in culturable pathogenic Vibrio spp. in Lake Pontchartrain, Louisiana, following hurricanes Katrina and Rita

We investigated the abundance, distribution, and virulence gene content of Vibrio cholerae, V. parahaemolyticus, and V. vulnificus in the waters of southern Lake Pontchartrain in Louisiana on four occasions from October 2005 to September 2006, using selective cultivation and molecular assays. The three targeted pathogenic vibrios were generally below the detection level in January 2006, when the water was cold (13°C), and most abundant in September 2006, when the lake water was warmest (30°C). The maximum values for these species were higher than reported previously for the lake by severalfold to orders of magnitude. The only variable consistently correlated with total vibrio abundance within a single sampling was distance from shore (P = 0.000). Multiple linear regression of the entire data set revealed that distance from shore, temperature, and turbidity together explained 82.1% of the variability in total vibrio CFU. The log-transformed mean abundance of V. vulnificus CFU in the lake was significantly correlated with temperature (P = 0.014), but not salinity (P = 0.625). Virulence-associated genes of V. cholerae (ctx) and V. parahaemolyticus (trh and tdh) were not detected in any isolates of these species (n = 128 and n = 20, respectively). In contrast, 16S rRNA typing of V. vulnificus (n = 298) revealed the presence of both environmental (type A) and clinical (type B) strains. The percentage of the B-type V. vulnificus was significantly higher in the lake in October 2005 (35.8% of the total) than at other sampling times (P ≤ 0.004), consistent with the view that these strains represent distinct ecotypes.

Indicator microbes correlate with pathogenic bacteria, yeasts and helminthes in sand at a subtropical recreational beach site

AIMS

Research into the relationship between pathogens, faecal indicator microbes and environmental factors in beach sand has been limited, yet vital to the understanding of the microbial relationship between sand and the water column and to the improvement of criteria for better human health protection at beaches. The objectives of this study were to evaluate the presence and distribution of pathogens in various zones of beach sand (subtidal, intertidal and supratidal) and to assess their relationship with environmental parameters and indicator microbes at a non-point source subtropical marine beach.

METHODS AND RESULTS

In this exploratory study in subtropical Miami (Florida, USA), beach sand samples were collected and analysed over the course of 6 days for several pathogens, microbial source tracking markers and indicator microbes. An inverse correlation between moisture content and most indicator microbes was found. Significant associations were identified between some indicator microbes and pathogens (such as nematode larvae and yeasts in the genus Candida), which are from classes of microbes that are rarely evaluated in the context of recreational beach use.

CONCLUSIONS

Results indicate that indicator microbes may predict the presence of some of the pathogens, in particular helminthes, yeasts and the bacterial pathogen Staphylococcus aureus including methicillin-resistant forms. Indicator microbes may thus be useful for monitoring beach sand and water quality at non-point source beaches.

SIGNIFICANCE AND IMPACT OF THE STUDY

The presence of both indicator microbes and pathogens in beach sand provides one possible explanation for human health effects reported at non-point sources beaches.

Amoebae and Legionella pneumophila in saline environments

Amoeboid protists that harbor bacterial pathogens are of significant interest as potential reservoirs of disease-causing organisms in the environment, but little is known about them in marine and other saline environments. We enriched amoeba cultures from sediments from four sites in the New England estuarine system of Mt. Hope Bay, Massachusetts and from sediments from six sites in the Great Salt Lake, Utah. Cultures of amoebae were enriched using both minimal- and non-nutrient agar plates, made with fresh water, brackish water or saltwater. Recovered amoeba cultures were assayed for the presence of Legionella species using nested polymerase chain reactions (PCR) and primers specific for the genus. Positive samples were then screened with nested amplification using primers specific for the macrophage infectivity potentiator surface protein (mip) gene from L. pneumophila. Forty-eight percent (185 out of 388) of isolated amoeba cultures were positive for the presence of Legionella species. Legionella pneumophila was detected by PCR in 4% of the amoeba cultures (17 out of 388), and most of these amoebae were growing on marine media. Our results show that amoebae capable of growing in saline environments may harbor not only a diverse collection of Legionella species, but also species potentially pathogenic to humans.

Evaluation of physical, chemical and microbiological parameters of water quality in the Harris Neck estuarine marshes along the Georgia coast

Analysis of the physical, chemical and biological parameters assessing water quality in Harris Neck estuary indicated that the average dissolved oxygen level was 8.6 mg/L, it maintained moderate levels of total dissolved nitrogen (2.7-4.6 mg/L) and total dissolved phosphorous (<0.05 mg/L), chlorophyll a was above 5.0 μg/L and it is contaminated with low levels of fecal bacteria. Bifidobacterium adolescentis, a putative marker of human fecal pollution, was detected once at stations 3 and 5. Overall the Harris Neck water quality analyses indicated a relatively pristine and a healthy functioning marine environment.

Beach boundary layer: a framework for addressing recreational water quality impairment at enclosed beaches

Nearshore waters in bays, harbors, and estuaries are frequently contaminated with human pathogens and fecal indicator bacteria. Tracking down and mitigating this contamination is complicated by the many point and nonpoint sources of fecal pollution that can degrade water quality along the shore. From a survey of the published literature, we propose a conceptual and mathematical framework, the "beach boundary layer model", for understanding and quantifying the relative impact of beach-side and bay-side sources of fecal pollution on nearshore water quality. In the model, bacterial concentration in ankle depth water C(ankle) [bacteria L(-3)] depends on the flux m'' [bacteria L(-2) T(-1)] of fecal bacteria from beach-side sources (bather shedding, bird and dog feces, tidal washing of sediments, decaying vegetation, runoff from small drains, and shallow groundwater discharge), a cross-shore mass transfer velocity k [L T(-1)] that accounts for the physics of nearshore transport and mixing, and a background concentration C(bay) [bacteria L(-3)] attributable to bay-side sources of pollution that impact water quality over large regions (sewage outfalls, creeks and rivers): C(ankle) = m''/k + C(bay). We demonstrate the utility of the model for identifying risk factors and pollution sources likely to impact shoreline water quality, and evaluate the model's underlying assumptions using computational fluid dynamic simulations of flow, turbulence, and mass transport in a trapezoidal channel.

Prominent human health impacts from several marine microbes: history, ecology, and public health implications

This paper overviews several examples of important public health impacts by marine microbes and directs readers to the extensive literature germane to these maladies. These examples include three types of dinoflagellates (Gambierdiscus spp., Karenia brevis, and Alexandrium fundyense), BMAA-producing cyanobacteria, and infectious microbes. The dinoflagellates are responsible for ciguatera fish poisoning, neurotoxic shellfish poisoning, and paralytic shellfish poisoning, respectively, that have plagued coastal populations over time. Research interest on the potential for marine cyanobacteria to contribute BMAA into human food supplies has been derived by BMAA's discovery in cycad seeds and subsequent implication as the putative cause of amyotrophic lateral sclerosis/parkinsonism dementia complex among the Chamorro people of Guam. Recent UPLC/MS analyses indicate that recent reports that BMAA is prolifically distributed among marine cyanobacteria at high concentrations may be due to analyte misidentification in the analytical protocols being applied for BMAA. Common infectious microbes (including enterovirus, norovirus, Salmonella, Campylobacter, Shigella, Staphylococcus aureus, Cryptosporidium, and Giardia) cause gastrointestinal and skin-related illness. These microbes can be introduced from external human and animal sources, or they can be indigenous to the marine environment.

Evidence-based point-of-care tests and device designs for disaster preparedness

OBJECTIVES

To define pathogen tests and device specifications needed for emerging point-of-care (POC) technologies used in disasters.

DESIGN

Surveys included multiple-choice and ranking questions. Multiple-choice questions were analyzed with the chi2 test for goodness-of-fit and the binomial distribution test. Rankings were scored and compared using analysis of variance and Tukey's multiple comparison test.

PARTICIPANTS

Disaster care experts on the editorial boards of the American Journal of Disaster Medicine and the Disaster Medicine and Public Health Preparedness, and the readers of the POC Journal.

RESULTS

Vibrio cholera and Staphylococcus aureus were top-ranked pathogens for testing in disaster settings. Respondents felt that disaster response teams should be equipped with pandemic infectious disease tests for novel 2009 H1N1 and avian H5N1 influenza (disaster care, p < 0.05; POC, p < 0.01). In disaster settings, respondents preferred self-contained test cassettes (disaster care, p < 0.05; POC, p < 0.001) for direct blood sampling (POC, p < 0.01) and disposal of biological waste (disaster care, p < 0.05; POC, p < 0.001). Multiplex testing performed at the POC was preferred in urgent care and emergency room settings.

CONCLUSIONS

Evidence-based needs assessment identifies pathogen detection priorities in disaster care scenarios, in which Vibrio cholera, methicillin-sensitive and methicillin-resistant Staphylococcus aureus, and Escherichia coli ranked the highest. POC testing should incorporate setting-specific design criteria such as safe disposable cassettes and direct blood sampling at the site of care.

Comparison of four polymerase chain reaction methods for the rapid detection of human fecal pollution in marine and inland waters

We compared the effectiveness of three PCR protocols for the detection of Bifidobacterium adolescentis and one PCR protocol for detecting Bacteroidales as indicators of human fecal pollution in environmental samples. Quantitative PCR indicated that a higher concentration of B. adolescentis DNA was recovered from sewage samples on the 0.2 μm filters compared to the 0.45 μm filters, and there was no evidence of qPCR inhibitors in the DNA extracts. With the Matsuki method (1999), B. adolescentis was detected only in undiluted sewage samples. The King method (2007) performed well and detected B. adolescentis in all of the sewage dilutions (from undiluted to 10⁻⁴). In contrast, the Bonjoch approach (2004) was effective at detecting B. adolescentis at lower dilutions (10⁻³) of sewage samples and it gave false positive results with some (3/8) pig fecal samples. Human-specific Bacteroidales (HuBacs) were detected in the lower diluents of sewage samples but was positive in pig (6/8) and cattle fecal samples. PCR detection of B. adolescentis in marine samples from Puerto Rico and freshwater samples from Georgia indicated that the PCR method of King et al. (2007) and the modified Layton method for HuBac were in agreement in detecting human fecal pollution in most sites.

Microbial community structure across the tree of life in the extreme Río Tinto

Understanding biotic versus abiotic forces that shape community structure is a fundamental aim of microbial ecology. The acidic and heavy metal extreme Río Tinto (RT) in southwestern Spain provides a rare opportunity to conduct an ecosystem-wide biodiversity inventory at the level of all three domains of life, because diversity there is low and almost exclusively microbial. Despite improvements in high-throughput DNA sequencing, environmental biodiversity studies that use molecular metrics and consider entire ecosystems are rare. These studies can be prohibitively expensive if domains are considered separately, and differences in copy number of eukaryotic ribosomal RNA genes can bias estimates of relative abundances of phylotypes recovered. In this study we have overcome these barriers (1) by targeting all three domains in a single polymerase chain reaction amplification and (2) by using a replicated sampling design that allows for incidence-based methods to extract measures of richness and carry out downstream analyses that address community structuring effects. Our work showed that combined bacterial and archaeal richness is an order of magnitude higher than eukaryotic richness. We also found that eukaryotic richness was highest at the most extreme sites, whereas combined bacterial and archaeal richness was highest at less extreme sites. Quantitative community phylogenetics showed abiotic forces to be primarily responsible for shaping the RT community structure. Canonical correspondence analysis revealed co-occurrence of obligate symbionts and their putative hosts that may contribute to biotic forces shaping community structure and may further provide a possible mechanism for persistence of certain low-abundance bacteria encountered in the RT.

Air quality during demolition and recovery activities in post-Katrina New Orleans

Air samples were collected during demolition and cleanup operations in the Lakeview district of New Orleans, Louisiana, USA, in late 2005 during the period immediately after Hurricane Katrina. Three different high-volume air samples were collected around waste collection areas that were created to temporarily hold the debris from the cleanup of residential properties in the area. Particulate concentrations were elevated and included crystalline fibers associated with asbestos. Metal concentrations on particulate matter resembled those measured in sediments deposited by floodwaters with the exception of Ba, which was elevated at all three locations. The highest organic contaminant concentration measured on particulates was the pesticide Ziram (Zinc, bis[diethylcarbamodithioato-S,S']-, [T-4]-) at 2,200 microg/g of particulate matter during sampling period 2. Ziram is used in latex paint, adhesives, caulking, and wallboard as a preservative. Fungal isolates developed from particulate air samples included species associated with disease including Aspergillus and Penicillium species. These data represent the most comprehensive assessment of demolition activities during the period immediately after Hurricane Katrina.