Using E. coli and Bacteroides distribution and abundance in a eutrophic lake as a tracer for nutrient inputs, Wilgreen Lake, Madison County, Kentucky

Wilgreen Lake is a eutrophic lake that has been listed on the EPA’s 303d list as nutrient impaired. Potential sources of this impairment are likely from humans, cattle manure, and fertilizers. We suspect that the majority of nutrients originate from human sources, namely from septic tank effluent emanating from key housing developments ringing the lakeshore. We test our hypothesis with conventional microbial assays (Escherichia coli) and RT-PCR techniques (Bacteroides). We took water samples at 19 sampling locations on 4 occasions, and measured the abundance of Escherichia coli using IDEXX methods. Corresponding sub-samples slated for potential PCR analysis were stored at -40oC. We chose PCR assay candidates on the basis of elevated E. coli levels, and the probability of differing source contributions. There is a systematic decline in E. coli microbial abundance distal to developments with closely-spaced septic units. This suggests that the principal source of microbial input is from septic systems; however, we cannot eliminate the possibility that fecal microbes are introduced into the lake via inflows. We used quantitative PCR analysis to measure Bacteroides abundance, and to distinguish between human and cattle sources. We measured 14 samples and found total fecal microbe concentrations in all samples targeting all Bacteroides species ranged from 45 mg/L to 142 mg/L. Unlike other studies, there was no apparent relationship between the concentration of all Bacteroides species and that of E. coli. We also attempted to quantitatively determine the proportion of Bacteroides contributions from specific sources, namely human and bovine fecal matter. Although fecal contamination was measured in all 14 samples, only 1 sample had significant amounts of human fecal contamination (21%) as measured by the human-associated Bacteroides assay. None of the samples had significant amounts bovine fecal concentration as measured by the bovine-associated Bacteroides assay. These inconclusive results suggest that either there are other unidentified sources of fecal contamination by Bacteroides and/or E. coli, or that the prevailing drought conditions skewed our results by not capturing fecal transport effects due to lack of surface and/or groundwater flow

Research Notes : United States : Genes for resistance to Phytophthora megasperma f. sp. glycinea in PI 273483D, PI 64747, PI 274212, PI 82312N, and PI 340046

Several years ago, we identified seven plant introductions resistant to the 16 races of Phytophthora megasperma f. sp. glycinea Kuan and Erwin (Pmg) known at that time. Each of these was crossed to the eight cultivars in Table 1 to determine how resistance was controlled. They were not crossed to cultivars that contained Rps2 or Rps5 because Rps2 was found using root inoculation in a liquid culture solution, and Rps5 was described after this study was started

Genome sequence of the Bacteroides fragilis phage ATCC 51477-B1

The genome of a fecal pollution indicator phage, Bacteroides fragilis ATCC 51477-B1, was sequenced and consisted of 44,929 bases with a G+C content of 38.7%. Forty-six putative open reading frames were identified and genes were organized into functional clusters for host specificity, lysis, replication and regulation, and packaging and structural proteins

Draft Genome Sequences of 10 Strains of the Genus Exiguobacterium

High-quality draft genome sequences were determined for 10 Exiguobacterium strains in order to provide insight into their evolutionary strategies for speciation and environmental adaptation. The selected genomes include psychrotrophic and thermophilic species from a range of habitats, which will allow for a comparison of metabolic pathways and stress response genes

Fecal Contamination of Shallow Tubewells in Bangladesh Inversely Related to Arsenic

The health risks of As exposure due to the installation of millions of shallow tubewells in the Bengal Basin are known, but fecal contamination of shallow aquifers has not systematically been examined. This could be a source of concern in densely populated areas with poor sanitation because the hydraulic travel time from surface water bodies to shallow wells that are low in As was previously shown to be considerably shorter than for shallow wells that are high in As. In this study, 125 tubewells 6−36 m deep were sampled in duplicate for 18 months to quantify the presence of the fecal indicator Escherichia coli. On any given month, E. coli was detected at levels exceeding 1 most probable number per 100 mL in 19−64% of all shallow tubewells, with a higher proportion typically following periods of heavy rainfall. The frequency of E. coli detection averaged over a year was found to increase with population surrounding a well and decrease with the As content of a well, most likely because of downward transport of E. coli associated with local recharge. The health implications of higher fecal contamination of shallow tubewells, to which millions of households in Bangladesh have switched in order to reduce their exposure to As, need to be evaluated

Comparison of fecal indicators with pathogenic bacteria and rotavirus in groundwater

Groundwater is routinely analyzed for fecal indicators but direct comparisons of fecal indicators to the presence of bacterial and viral pathogens are rare. This study was conducted in rural Bangladesh where the human population density is high, sanitation is poor, and groundwater pumped from shallow tubewells is often contaminated with fecal bacteria. Five indicator microorganisms (E. coli, total coliform, F+RNA coliphage, Bacteroides and human-associated Bacteroides) and various environmental parameters were compared to the direct detection of waterborne pathogens by quantitative PCR in groundwater pumped from 50 tubewells. Rotavirus was detected in groundwater filtrate from the largest proportion of tubewells (40%), followed by Shigella (10%), Vibrio (10%), and pathogenic E. coli (8%). Spearman rank correlations and sensitivity-specificity calculations indicate that some, but not all, combinations of indicators and environmental parameters can predict the presence of pathogens. Culture-dependent fecal indicator bacteria measured on a single date did not predict total bacterial pathogens, but annually averaged monthly measurements of culturable E. coli did improve prediction for total bacterial pathogens. A qPCR-based E. coli assay was the best indicator for the bacterial pathogens. F+RNA coliphage were neither correlated nor sufficiently sensitive towards rotavirus, but were predictive of bacterial pathogens. Since groundwater cannot be excluded as a significant source of diarrheal disease in Bangladesh and neighboring countries with similar characteristics, the need to develop more effective methods for screening tubewells with respect to microbial contamination is necessary

How genomics can help biodiversity conservation

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.info:eu-repo/semantics/publishedVersio

The era of reference genomes in conservation genomics

info:eu-repo/semantics/publishedVersio

The era of reference genomes in conservation genomics

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics

The era of reference genomes in conservation genomics

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics