Association between submerged aquatic vegetation and elevated levels of Escherichia coli and potential bacterial pathogens in freshwater lakes

Microbe-sediment interactions in Great Lakes recreational waters: Implications for human health risk

Microbial assessments of recreational water have traditionally focused on culturing or DNA-based approaches of the planktonic water column, omitting influence from microbe-sediment relationships. Sediment (bed and suspended) has been shown to often harbour levels of bacteria higher than the planktonic phase. The fate of suspended sediment (SS) bacteria is extensively related to transport dynamics (e.g., deposition) of the associated sediment/floc. When hydraulic energy allows, SS will settle, introducing new (potentially pathogenic) organisms to the bed. With turbulence, including waves, currents and swimmers, the risk of human ingestion is elevated due to resuspension of bed sediment and associated microbes. This research used multiplex nanofluidic reverse transcriptase quantitative PCR on RNA of bacteria associated with bed and SS to explore the active bacteria in freshwater shorelines. Bacterial genes of human health concern regarding recreational water use were targeted, such as faecal indicator bacteria (FIB), microbial source tracking genes and virulence factors from waterborne pathogens. Results indicate avian sources (i.e., gulls, geese) to be the largest nonpoint source of FIB associated with sediment in Great Lakes shorelines. This research introduces a novel approach to microbial water quality assessments and enhances our understanding of microbe-sediment dynamics and the quality of freshwater beaches.

Influence of Water Hyacinth (Eichhornia crassipes) on Concentration and Distribution of Escherichia coli in Water Surrounding an Informal Floating Community in Iquitos, Peru

Floating communities exist throughout the world. Many live on water with a high pathogen load due to difficulties associated with sewage management. In Claverito, an informal floating community in Iquitos, Peru, we conducted a controlled experiment to test the ability of water hyacinth (Eichhornia crassipes) to remove Escherichia coli from water. When river E. coli concentrations were at or below ∼1,500 CFU 100 mL^-1, water hyacinth reduced shallow concentrations (8 cm depth) down to levels deemed safe by U.S. EPA for recreational use. Above this threshold, plants were able to reduce E. coli levels within shallow water, but not down to "safe" levels. At deeper depths (>25 cm), there was evidence that plants increased E. coli concentrations. Water hyacinth removed E. coli from shallow water by providing a surface (i.e., submerged roots) onto which E. coli sorbed and by protecting organisms that can potentially consume E. coli. Unfortunately, because of root association, the total E. coli load within the water column was greater with water hyacinth present. The use of water hyacinth to keep surface water around floating communities low in E. coli could be beneficial as this is the water layer with which people most likely interact. Aquatic vegetation naturally proliferates in and around Claverito. While this study was based on curating aquatic plants in order to achieve a water-quality outcome, it nonetheless supports concrete actions for Claverito residents under non-curated conditions, which are outlined at the end of the manuscript.

Combined hydrothermal and biological treatments for valorization of fruit and vegetable waste into liquid organic fertilizer

This study investigated the effects of hydrothermal treatment, biological treatment and their combination on nutrients recovery from fruit and vegetable waste (FVW) and evaluated the feasibility of fruit and vegetable waste juice (FVWJ) from the combined treatment as liquid organic fertilizer. In this study, following conditions were determined suitable for FVW treatment: the temperature of 165 °C and retention time of 45 min for hydrothermal treatment, 20 h for biological treatment, and Weissella, as the dominant microbial genus present in FVW, was suggested as inoculum for biological treatment. In the combined treatment, based on the above conditions of hydrothermal and biological treatments, the yield of FVWJ was 93.03 g out of 100 g FVW, and concentrations of organic matter (1.45%, w/w), primary nutrients (0.51%, w/w), and toxic components in the FVWJ complied with the requirements for use concentration in both Chinese and European standards for liquid organic fertilizer. The economic analysis showed the net saving of 13.60 USD per ton FVW, indicating that it is an economical approach to valorize fruit and vegetable waste into liquid organic fertilizer through the combined treatment.

Modelling the transport of sloughed cladophora in the nearshore zone of Lake Michigan

The invasion of dreissenid mussels has profoundly altered benthic physical environments and whole-lake nutrient cycling in the Great Lakes over the past several decades. The resurgence of the filamentous green alga Cladophora appears to be one of the consequences of this invasion. Sloughed Cladophora deteriorates water quality, fouls recreational beaches, and may contribute to outbreaks of avian botulism, which have been especially severe in the Sleeping Bear Dunes National Lakeshore (SLBE) region of Lake Michigan. To help determine the fate of sloughed Cladophora, a Lagrangian particle trajectory model was developed to track the transport of Cladophora fragments in the nearshore zone based upon a physical transport-mixing model. The model results demonstrate that the primary deposition sites of sloughed Cladophora within the SLBE region are mid-depth sites not far away from their initial growth area. Because of high algae production in the nearshore waters and limited exchange between the inner and outer bay, the shoreline beach of Platte Bay appears to be particularly vulnerable to fouling, with overall three times as many accumulated particles as those along the Sleeping Bear Bay and Good Harbor Bay. The results of this model may be used to guide regional environmental management initiatives and provide insights into the mechanisms responsible for avian botulism outbreaks. This model may also inform the development of whole-lake ecosystem models that account for nearshore-offshore interactions.

Biogeographic patterns of potential pathogenic bacteria in the middle and lower reaches of the Yangtze River as well as its two adjoining lakes, China

Understanding the distribution patterns and shaping factors of bacterial pathogens in aquatic ecosystems, especially in natural waters, are critical to the control of pathogen transmission. In this study, using 16S rRNA gene amplicon sequencing, we explored the composition and biogeographic dynamics of potential bacterial pathogens in the middle and lower reaches of the Yangtze River, as well as its two vast adjoining lakes (Dongting Lake and Poyang Lake). The pathogen community belonged to 12 potential pathogenic groups, with “intracellular parasites,” “animal parasites or symbionts” and “human pathogens all” occupying 97.5% in total. The potential pathogen community covered seven phyla with Proteobacteria (69.8%) and Bacteroidetes (13.5%) the most predominant. In addition, 53 genera were identified with Legionella (15.2%) and Roseomonas (14.2%) the most dominant. The average relative abundance, alpha diversity and microbial composition of the potential bacterial pathogens exhibited significant biogeographical variations among the different sections. An in-depth analysis reflected that environmental variables significantly structured the potential bacterial pathogens, including water physiochemical properties (i.e., chlorophyll-a, total nitrogen and transparency), heavy metals (i.e., As and Ni), climate (i.e., air temperature) and land use type (i.e., waters). Compared to the overall bacterial community which was composed of both pathogenic and non-pathogenic bacteria, the pathogen community exhibited distinct microbial diversity patterns and shaping factors. This signifies the importance of different variables for shaping the pathogen community. This study represents one attempt to explore pathogen diversity patterns and their underlying drivers in the Yangtze River, which provides a foundation for the management of pathogenic bacteria.

A preliminary evaluation of microbial water quality in the irrigation pond

This study aimed to determine the microbial water quality of Imrahor Pond by enumerating the coliform bacteria levels in the area. Water samples were collected biweekly from the surface and bottom waters at seven points in the pond. Samples were analyzed for total coliforms, Escherichia coli, physicochemical parameters (water temperature, conductivity, pH, turbidity, dissolved oxygen, nitrate) and 1-day rainfall. The average values of TC and E. coli were 1487.4 and 36.3 MPN/100 ml, respectively. TC concentrations/physicochemical parameters were met at least 2nd class water quality class and E. coli results were met "guideline value" (E. coli < 250 MPN/100 ml) of national regulation. Overall, among measured physicochemical parameters, rainfall had the strongest positive correlation (r = 0.377 for total coliforms and r = 0.466 for E. coli, p < 0.05) with both indicators, indicted that surface runoff due to rainfall is the main factor which effects microbial water quality in the study area. This study demonstrated the preliminary microbial water quality results (TC and E. coli) in the Imrahor Pond and can serve as a basis for developing more precise water quality monitoring and management studies in the future. PRACTITIONER POINTS: Prevalence of TC and E. coli in the surface and bottom waters of Imrahor Pond were investigated for the first time. Imrahor Pond was met guideline value of national regulations based on E. coli concentrations, in the study period. Surface runoff after rainfall was the main environmental factor which influenced the microbial water quality of the pond.

Interactions of E. coli with algae and aquatic vegetation in natural waters

Both algae and bacteria are essential inhabitants of surface waters. Their presence is of ecological significance and sometimes of public health concern triggering various control actions. Interactions of microalgae, macroalgae, submerged aquatic vegetation, and bacteria appear to be important phenomena necessitating a deeper understanding by those involved in research and management of microbial water quality. Given the long-standing reliance on Escherichia coli as an indicator of the potential presence of pathogens in natural waters, understanding its biology in aquatic systems is necessary. The major effects of algae and aquatic vegetation on E. coli growth and survival, including changes in the nutrient supply, modification of water properties and constituents, impact on sunlight radiation penetration, survival as related to substrate attachment, algal mediation of secondary habitats, and survival inhibition due to the release of toxic substances and antibiotics, are discussed in this review. An examination of horizontal gene transfer and antibiotic resistance potential, strain-specific interactions, effects on the microbial, microalgae, and grazer community structure, and hydrodynamic controls is given. Outlooks due to existing and expected consequences of climate change and advances in observation technologies via high-resolution satellite imaging, unmanned aerial vehicles (drones), and mathematical modeling are additionally covered. The multiplicity of interactions among bacteria, algae, and aquatic vegetation as well as multifaceted impacts of these interactions, create a wide spectrum of research opportunities and technology developments.

Sediment-associated microbial community profiling: sample pre-processing through sequential membrane filtration for 16S rRNA amplicon sequencing

BACKGROUND

Sequential membrane filtration as a pre-processing step for capturing sediment-associated microorganisms could provide good quality and integrity DNA that can be preserved and kept at ambient temperatures before community profiling through culture-independent molecular techniques. However, the effects of sample pre-processing via filtration on DNA-based profiling of sediment-associated microbial community diversity and composition are poorly understood. Specifically, the influences of pre-processing on the quality and quantity of extracted DNA, high-throughput DNA sequencing reads, and detected microbial taxa need further evaluation.

RESULTS

We assessed the impact of pre-processing freshwater sediment samples by sequential membrane filtration (from 10, 5 to 0.22 μm pore size) for 16S rRNA-based community profiling of sediment-associated microorganisms. Specifically, we examined if there would be method-driven differences between non- and pre-processed sediment samples regarding the quality and quantity of extracted DNA, PCR amplicon, resulting high-throughput sequencing reads, microbial diversity, and community composition. We found no significant difference in the qualities and quantities of extracted DNA and PCR amplicons, and the read abundance after bioinformatics processing (i.e., denoising and chimeric-read filtering steps) between the two methods. Although the non- and pre-processed sediment samples had more unique than shared amplicon sequence variants (ASVs), we report that their shared ASVs accounted for 74% of both methods' absolute read abundance. More so, at the genus level, the final collection filter identified most of the genera (95% of the reads) captured from the non-processed samples, with a total of 51 false-negative (2%) and 59 false-positive genera (3%). We demonstrate that while there were differences in shared and unique taxa, both methods revealed comparable microbial diversity and community composition.

CONCLUSIONS

Our observations highlight the feasibility of pre-processing sediment samples for community analysis and the need to further assess sampling strategies to help conceptualize appropriate study designs for sediment-associated microbial community profiling.

Variability of the structure of winter microbial communities in Chelyabinsk lakes

Microorganisms form complex and dynamic communities that play a key role in the biogeochemical cycles of lakes. A high level of urbanization is currently a serious threat to bacterial communities and the ecosystem of freshwater bodies. To assess the contribution of anthropogenic load to variations in the structure of winter microbial communities in lakes, microorganisms of four water bodies of Chelyabinsk region were studied for the first time. We used cultural, chromatography-mass spectrometric, and modern methods of statistical data processing (particularly, multivariate exploratory analysis and canonical analysis of correspondences). The research showed that the composition of winter microbial communities in lakes Chebarkul’, Smolino, Pervoye, and Shershenevskoye Reservoir did not differ significantly between the main phyla of microorganisms. The dominant microorganisms were found to be of the Firmicutes phylum and Actinobacteria phylum. The structure of bacterial communities had special features depending on the characteristics of the water body and the sampling depths. Thus, in the lakes Smolino, Pervoye, and Shershenevskoye Reservoir, an important role was played by associations between microorganisms – indicators of fecal contamination: coliform bacteria and Enterococcus. On the contrary, in Chebarkul’ Lake, members of the genus Bacillus, which are natural bioremediators, formed stable winter associations. However, the differences between water bodies and sampling depths reflected 28.1% and 9.8% of the variability of the winter microbial communities, respectively. The largest contribution (about 60%) to the variability of the structure was made by intra-water processes, which determined the high heterogeneity of samples from different water areas. We assume that an important role in this variability was played by the high anthropogenic impact in a large industrial metropolis. In our opinion, this line of research is very promising for addressing key environmental issues.

Variability of the structure of winter microbial communities in Chelyabinsk lakes

Microorganisms form complex and dynamic communities that play a key role in the biogeochemical cycles of lakes. A high level of urbanization is currently a serious threat to bacterial communities and the ecosystem of freshwater bodies. To assess the contribution of anthropogenic load to variations in the structure of winter microbial communities in lakes, microorganisms of four water bodies of Chelyabinsk region were studied for the first time. We used cultural, chromatography-mass spectrometric, and modern methods of statistical data processing (particularly, multivariate exploratory analysis and canonical analysis of correspondences). The research showed that the composition of winter microbial communities in lakes Chebarkul’, Smolino, Pervoye, and Shershenevskoye Reservoir did not differ significantly between the main phyla of microorganisms. The dominant microorganisms were found to be of the Firmicutes phylum and Actinobacteria phylum. The structure of bacterial communities had special features depending on the characteristics of the water body and the sampling depths. Thus, in the lakes Smolino, Pervoye, and Shershenevskoye Reservoir, an important role was played by associations between microorganisms – indicators of fecal contamination: coliform bacteria and Enterococcus. On the contrary, in Chebarkul’ Lake, members of the genus Bacillus, which are natural bioremediators, formed stable winter associations. However, the differences between water bodies and sampling depths reflected 28.1% and 9.8% of the variability of the winter microbial communities, respectively. The largest contribution (about 60%) to the variability of the structure was made by intra-water processes, which determined the high heterogeneity of samples from different water areas. We assume that an important role in this variability was played by the high anthropogenic impact in a large industrial metropolis. In our opinion, this line of research is very promising for addressing key environmental issues.

Leptospirosis and Coinfection: Should We Be Concerned?

Pathogenic Leptospira is the causative agent of leptospirosis, an emerging zoonotic disease affecting animals and humans worldwide. The risk of host infection following interaction with environmental sources depends on the ability of Leptospira to persist, survive, and infect the new host to continue the transmission chain. Leptospira may coexist with other pathogens, thus providing a suitable condition for the development of other pathogens, resulting in multi-pathogen infection in humans. Therefore, it is important to better understand the dynamics of transmission by these pathogens. We conducted Boolean searches of several databases, including Google Scholar, PubMed, SciELO, and ScienceDirect, to identify relevant published data on Leptospira and coinfection with other pathogenic bacteria. We review the role of the host-microbiota in determining the synanthropic interaction of Leptospira sp. with other bacteria, thus creating a suitable condition for the leptospira to survive and persist successfully. We also discuss the biotic and abiotic factors that amplify the viability of Leptospira in the environment. The coinfection of leptospira with pathogenic bacteria has rarely been reported, potentially contributing to a lack of awareness. Therefore, the occurrence of leptospirosis coinfection may complicate diagnosis, long-lasting examination, and mistreatment that could lead to mortality. Identifying the presence of leptospirosis with other bacteria through metagenomic analysis could reveal possible coinfection. In conclusion, the occurrence of leptospirosis with other diseases should be of concern and may depend on the success of the transmission and severity of individual infections. Medical practitioners may misdiagnose the presence of multiple infections and should be made aware of and receive adequate training on appropriate treatment for leptospirosis patients. Physicians could undertake a more targeted approach for leptospirosis diagnosis by considering other symptoms caused by the coinfected bacteria; thus, more specific treatment could be given.

The Changing Face of the Family Enterobacteriaceae (Order: "Enterobacterales"): New Members, Taxonomic Issues, Geographic Expansion, and New Diseases and Disease Syndromes

The family Enterobacteriaceae has undergone significant morphogenetic changes in its more than 85-year history, particularly during the past 2 decades (2000 to 2020). The development and introduction of new and novel molecular methods coupled with innovative laboratory techniques have led to many advances. We now know that the global range of enterobacteria is much more expansive than previously recognized, as they play important roles in the environment in vegetative processes and through widespread environmental distribution through insect vectors. In humans, many new species have been described, some associated with specific disease processes. Some established species are now observed in new infectious disease settings and syndromes. The results of molecular taxonomic and phylogenetics studies suggest that the current family Enterobacteriaceae should possibly be divided into seven or more separate families. The logarithmic explosion in the number of enterobacterial species described brings into question the relevancy, need, and mechanisms to potentially identify these taxa. This review covers the progression, transformation, and morphogenesis of the family from the seminal Centers for Disease Control and Prevention publication (J. J. Farmer III, B. R. Davis, F. W. Hickman-Brenner, A. McWhorter, et al., J Clin Microbiol 21:46-76, 1985, https://doi.org/10.1128/JCM.21.1.46-76.1985) to the present.

Fecal indicator bacteria from environmental sources; strategies for identification to improve water quality monitoring

In tropical to temperate environments, fecal indicator bacteria (FIB), such as enterococci and Escherichia coli, can persist and potentially multiply, far removed from their natural reservoir of the animal gut. FIB isolated from environmental reservoirs such as stream sediments, beach sand and vegetation have been termed "naturalized" FIB. In addition, recent research suggests that the intestines of poikilothermic animals such as fish may be colonized by enterococci and E. coli, and therefore, these animals may contribute to FIB concentrations in the aquatic environment. Naturalized FIB that are derived from fecal inputs into the environment, and subsequently adapted to maintain their population within the non-host environment are termed "naturalized enteric FIB". In contrast, an additional theory suggests that some "naturalized" FIB diverged from enteric FIB many millions of years ago and are now normal inhabitants of the environment where they are referred to as "naturalized non-enteric FIB". In the case of the Escherichia genus, the naturalized non-enteric members are identified as E. coli during routine water quality monitoring. An over-estimation of the health risk could result when these naturalized, non-enteric FIB, (that is, not derived from avian or mammalian fecal contamination), contribute to water quality monitoring results. It has been postulated that these environmental FIB belonging to the genera Escherichia and Enterococcus can be differentiated from enteric FIB by genetic methods because they lack some of the genes required for colonization of the host intestine, and have acquired genes that aid survival in the environment. Advances in molecular tools such as next generation sequencing will aid the identification of genes peculiar or "enriched" in particular habitats to discriminate between enteric and environmental FIB. In this appraisal, we have reviewed the research studying "naturalized" FIB, and discussed the techniques for their differentiation from enteric FIB. This differentiation includes the important distinction between enteric FIB derived from fresh and non-recent fecal inputs, and those truly non-enteric environmental microbes, which are currently identified as FIB during routine water quality monitoring. The inclusion of tools for the identification of naturalized FIB (enteric or environmental) would be a valuable resource for future studies assessing water quality.

Fecal pollution source characterization at non-point source impacted beaches under dry and wet weather conditions

Though Lake Michigan beaches in Chicago are not impacted by stormwater or wastewater outfalls, several of those beaches often exceed USEPA Beach Action Values (BAVs). We investigated the role of microbial source tracking (MST) as a complement to routine beach monitoring at Chicago beaches. In summer 2016, water samples from nine Chicago beaches were analyzed for E. coli by culture and enterococci by qPCR. A total of 195 archived samples were then tested for human (HF183/BacR287, HumM2), canine (DG3, DG37), and avian (GFD) microbial source tracking (MST) markers. Associations between MST and general fecal indicator bacteria (FIB) measures were evaluated and stratified based on wet and dry weather definitions. Among the 195 samples, HF183/BacR287 was quantifiable in 4%, HumM2 in 1%, DG3 in 6%, DG37 in 2%, and GFD in 23%. The one beach with a dog area was far more likely to have DG3 present in the quantifiable range than other beaches. Exceedance of general FIB BAVs increased the odds of human, dog and avian marker detection. MST marker weighted-average fecal scores for DG3 was 2.4 times, DG37 was 2.1 times, and GFD was 1.6 times higher during wet compared to dry weather conditions. HF183/BacR287 weighted-average fecal scores were not associated with precipitation. Associations between FIB BAV exceedance and MST marker detection were generally stronger in wet weather. Incorporating MST testing into routine beach water monitoring can provide information that beach managers can use when developing protection plans for beaches not impacted by point sources.

Children's Abrasions in Recreational Beach Areas and a Review of Possible Wound Infections

The Beach Exposure and Child Health Study (BEACHES) quantified the behavior of children at recreational beach areas to evaluate how various behaviors might affect their exposure to environmental contaminants such as bacteria and chemicals. Due to limited information in the study about abrasions, we conducted a literature review to examine how marine bacteria cause infections in open wounds. The literature review revealed possible adverse health effects from the bacterium Vibrio vulnificus due to its increasing prevalence and the severity of infection. We used data from the BEACHES study to review children's behavior and their susceptibility to abrasions. Children six years of age and younger were evaluated before and after 1 hour of play for open or healing abrasions at two beaches in Miami-Dade County, Florida (Crandon and Haulover), and two beaches in Galveston County, Texas (Stewart and Seawall). The children were videotaped to monitor their activities and to determine the behavior that would increase their susceptibility to obtaining abrasions. Overall, 58.2% of the children had at least one existing abrasion before playing at the beach, while 8.2% of the children acquired a new abrasion during their time at the beach. Children who acquired new abrasions most often played in the sea water, with new abrasions most frequently occurring on exposed skin surfaces such as the knees. Proper wound care before and after visiting the beach should be encouraged to minimize the risk of bacterial infection, especially considering the possible detrimental impacts that can be caused by some bacterial pathogens through wound exposures.