Metagenomic and metatranscriptomic analyses reveal that biobed systems can enrich for antibiotic resistance and genetic mobility genes.

Antibiotic resistance gene pollution in the environment has been identified as a potential contributor to the global issue of antibiotic resistance prevalence, creating a need to identify and characterize environmental reservoirs for antibiotic resistance genes. Because many polluted environments have been shown to contain elevated levels of antibiotic resistance genes, agriculturally based pesticide bioremediation systems called 'biobeds' could serve as environmental reservoirs for antibiotic resistance genes, although this has never been extensively explored. Metagenomic and metatranscriptomic analyses of an on-farm biobed system sampled before and after a season of pesticide use demonstrated that in situ pesticide applications applied to biobeds can enrich for multidrug, sulphonamide, aminoglycoside and beta-lactam resistance genes. Additionally, this study demonstrated an enrichment for genes associated with gene mobilization, such as genes involved in horizontal gene transfer and plasmid mobility, as well as transposons and integrases.

Identifying the core bacterial and fungal communities within four agricultural biobeds used for the treatment of pesticide rinsates.

AIMS: This study evaluated the variability of bacterial and fungal communities within unique pesticide remediation biobeds. METHODS AND RESULTS: Four biobeds receiving different applied pesticide rinsates, were sampled throughout an operational season to determine pesticide removal efficacy and microbial communities. Biomixture samples collected from different biobed depths, were subjected to Illumina sequencing of the 16S rRNA (bacteria) and ITS2 (fungi) genes. Pesticide removal rates for all biobeds averaged 99%, with microbial community analysis revealing biobeds shared 60-70% of the most abundant bacterial and fungal orders, respectively. Though biobed depth did not greatly impact microbial community profile or diversity, bacterial and fungal taxa profiles between biobeds notably diverge at levels of genera and OTU. Biobed bacterial communities exhibited greater diversity than fungal communities between and within all biobeds. CONCLUSIONS: Biobeds receiving variable pesticide rinsates share a 'core' microbial community, exhibiting greater bacterial diversity relative to fungal diversity. Pesticide exposure increased bacterial diversity throughout the biobeds, while fungal diversity was variable, meriting further understanding of fungicide application to biobed fungal community stability. SIGNIFICANCE AND IMPACT OF THE STUDY: Biobeds achieve high treatment efficacy of unique pesticide rinsates, regardless of differentiation of specific genera in response to specific compounds; supporting biobeds as a robust engineered system for pesticide rinsates bioremediation.

Baseline and storm event monitoring of Bacteroidales marker concentrations and enteric pathogen presence in a rural Canadian watershed.

Bacteroidales 16S rRNA gene markers were evaluated for their use as a microbial source tracking tool in a well characterized 750 ha agricultural watershed in Nova Scotia, Canada. Water quality monitoring was conducted following the validation of host-specific and universal Bacteroidales (AllBac) markers for their proficiency in this particular geographic region, which provided further evidence that these markers are geographically stable. Increasing Escherichia coli concentrations were positively correlated (p < 0.01) with concentrations of the AllBac marker in water samples, suggesting that this universal marker is more suited as a positive DNA control rather than as an indicator of recent fecal contamination. Ruminant (BacR) and bovine (CowM2) specific marker detection was associated with increased runoff due to precipitation in sub-watersheds putatively impacted by cattle farming, demonstrating that the BacR and CowM2 markers can be used to detect the recent introduction of fecal matter from cattle farming activities during rainfall events. However, the human associated marker (BacH) was only detected once in spite of numerous on-site residential wastewater treatment systems in the watershed, suggesting that this assay is not sensitive enough to detect this type of human sewage source. E. coli O157:H7 and Salmonella spp. DNA was not detected in any of the 149 watershed samples; however, 114 (76.5%) of those samples tested positive for Campylobacter spp. No significant correlation (p > 0.05) was found between Campylobacter spp. presence and either E. coli or AllBac marker levels. Further studies should be conducted to assess the origins of Campylobacter spp. in these types of watersheds, and to quantify pathogen cell numbers to allow for a human health risk assessment.

Characterization of a mobile and multiple resistance plasmid isolated from swine manure and its detection in soil after manure application.

AIMS: To isolate and characterize multiple antibiotic resistance plasmids found in swine manure and test for plasmid-associated genetic markers in soil following manure application to an agricultural field. METHODS AND RESULTS: Plasmids were isolated from an erythromycin enrichment culture that used liquid swine manure as an inoculant. Plasmids were transformed into Escherichia coli DH10ß for subsequent characterization. We isolated and DNA sequenced a 22 102-bp plasmid (pMC2) that confers macrolide, and tetracycline resistances, and carries genes predicted to code for mercury and chromium resistance. Conjugation experiments using an pRP4 derivative as a helper plasmid confirm that pMC2 has a functional mobilization unit. PCR was used to detect genetic elements found on pMC2 in DNA extracted from manure amended soil. CONCLUSIONS: The pMC2 plasmid has a tetracycline-resistant core and has acquired additional resistance genes by insertion of an accessory region (12 762 bp) containing macrolide, mercury and chromium resistance genes, which was inserted between the truncated DDE motifs within the Tn903/IS102 mobile element. SIGNIFICANCE AND IMPACT OF THE STUDY: Liquid swine manure used for manure spreading contains multiple antibiotic resistance plasmids that can be detected in soil following manure application.

Quantitative real-time PCR assays for sensitive detection of Canada goose-specific fecal pollution in water sources.

Canada geese (Branta canadensis) are prevalent in North America and may contribute to fecal pollution of water systems where they congregate. This work provides two novel real-time PCR assays (CGOF1-Bac and CGOF2-Bac) allowing for the specific and sensitive detection of Bacteroides 16S rRNA gene markers present within Canada goose feces.

Evaluation of host-specific Bacteroidales 16S rRNA gene markers as a complementary tool for detecting fecal pollution in a prairie watershed.

Our ability to identify and eliminate fecal contamination of water, now and in the future, is essential to reduce incidences of waterborne disease. Bacterial source tracking is a recently developed approach for identifying sources of fecal pollution. PCR primers designed by Bernhard and Field [Bernhard, A.E., Field, K.G., 2000a. A PCR assay to discriminate human and ruminant feces on the basis of host differences in Bacteroides-Prevotella genes encoding 16S rRNA. Appl. Environ. Microbiol. 66(10), 4571-4574] and Dick et al. [Dick, L.K., Bernhard, A.E., Brodeur, T.J., Santo Domingo, J.W., Simpson, J.M., Walters, S.P., Field, K.G., 2005. Host distributions of uncultivated fecal Bacteroidales bacteria reveal genetic markers for fecal source identification. Appl. Environ. Microbiol. 71(6), 3184-3191] for the detection of human (HF183), pig (PF163) and ruminant (CF128) specific Bacteroidales 16s rRNA genetic markers were tested for their suitability in detecting fecal pollution in Saskatchewan, Canada. The sensitivity and specificity of these primers were assessed by testing eight raw human sewage samples and 265 feces from 12 different species in Saskatchewan. The specificity of each primer set was > or =94%. The accuracy of HF183 and PF163 to distinguish between the different species was 100%, whereas CF128 cross-reacted with 22% of the pig feces. Occurrence of the host-specific Bacteroidales markers and the conventional indicator Escherichia coli in relation to several enteropathogens was investigated in 70 water samples collected from different sites along the Qu'Appelle River (Saskatchewan, Canada). Human and ruminant fecal markers were identified in 41 and 14% of the water samples, respectively, whereas the pig marker was never detected in the river water. The largest concentrations in E. coli counts were concomitant to the simultaneous detection of HF183 and CF128. Thermotolerant Campylobacter spp., Salmonella spp. and Shiga toxin genes (stx1 and stx2)-positive E. coli (STEC) were detected in 6, 7 and 63% of the water samples, respectively. However, none of the stx positive water samples were positive for the E. coli O157:H7 gene marker (uidA). Odds ratios analysis suggests that CF128 may be predictive for the presence of Salmonella spp. in the river investigated. None of the fecal indicators were able to confidently predict the presence of thermotolerant Campylobacter spp. and STEC.

Evaluation of the ability of lysozyme and nisin to control meat spoilage bacteria.

The antimicrobials lysozyme, nisin, and mixtures of the two were studied to ascertain their abilities to control the growth of the meat-borne spoilage bacteria, Brochothrix thermosphacta B2 and Carnobacterium sp. 845. The goal was to optimize an antimicrobial for potential use in preservation of fresh meats. Their efficacies were evaluated in APT broth, in a meat juice extract and on cores of lean and fat pork tissue. Both lysozyme and nisin alone as well as mixtures of the two effectively inhibited B. thermosphacta B2 at 250 microg/ml in APT broth, the lowest concentration evaluated, for 10 days at 2 degrees C. In the presence of 500 microg/ml lysozyme, B. thermosphacta B2 grew after 12 days incubation. Only 125 microg of antimicrobial/ml was required to inhibit B. thermosphacta B2 for 27 days at 2 degrees C in pork juice. An estimated surface concentration of 130 microg/cm2 of each of the antimicrobials effectively inhibited B. thermosphacta B2 on inoculated cores of fat and lean pork tissue when the cores were incubated in vacuum packages for 6 weeks at 2 degrees C. In APT broth and in pork juice, lysozyme showed no antimicrobial activity against Carnobacterium sp. 845 at concentrations of 500 and 1000 microg/ml, respectively. Nisin and mixtures of the two antimicrobials inhibited Carnobacterium sp. 845 so that its numbers were at least 3 log units lower than untreated samples after 26 and 27 days incubation for APT and pork juice, respectively. The antimicrobial effect was concentration dependent. On lean pork tissue, numbers of Carnobacterium sp. 845 were significantly lower than untreated samples or samples treated with 195 microg/cm2 lysozyme when 260 microg/cm2 of a 1:3 (w/w) ratio of nisin to lysozyme was introduced to the cores. The inhibitory effect lasted for 14 of 42 days incubation in vacuum at 2 degrees C. On fat tissue, both lysozyme alone and the 1:3 nisin/lysozyme mixture inhibited Carnobacterium sp. 845 for 21 days storage in vacuum at 2 degrees C. On fat and lean tissue, mixtures of nisin and lysozyme would be more effective antimicrobials than either nisin or lysozyme alone.

The use of multiplex PCR reactions to characterize populations of lactic acid bacteria associated with meat spoilage.

A rapid, systematic and reliable approach for identifying lactic acid bacteria associated with meat was developed, allowing for detection of Carnobacterium spp., Lactobacillus curvatus, Lact. sakei and Leuconostoc spp. Polymerase chain reaction primers specific for Carnobacterium and Leuconostoc were created from 16S rRNA oligonucleotide probes and used in combination with species-specific primers for the 16S/23S rRNA spacer region of Lact. curvatus and Lact. sakei in multiplex PCR reactions. The method was used successfully to characterize lactic acid bacteria isolated from a vacuum-packaged pork loin stored at 2 degrees C. Seventy isolates were selected for identification and 52 were determined to be Lact. sakei, while the remaining 18 isolates were identified as Leuconostoc spp.

Megaplasmid pRme2011a of Sinorhizobium meliloti is not required for viability.

We report the curing of the 1,360-kb megaplasmid pRme2011a from Sinorhizobium meliloti strain Rm2011. With a positive selection strategy that utilized Tn5B12-S containing the sacB gene, we were able to cure this replicon by successive rounds of selecting for deletion formation in vivo. Subsequent Southern blot, Eckhardt gel, and pulsed-field gel electrophoresis analyses were consistent with the hypothesis that the resultant strain was indeed missing pRme2011a. The cured derivative grew as well as the wild-type strain in both complex and defined media but was unable to use a number of substrates as a sole source of carbon on defined media.

Rhizobium leguminosarum as a plant growth-promoting rhizobacterium: direct growth promotion of canola and lettuce.

Early seedling root growth of the nonlegumes canola (Brassica campestris cv. Tobin, Brassica napus cv. Westar) and lettuce (Lactuca sativa cv. Grand Rapids) was significantly promoted by inoculation of seeds with certain strains of Rhizobium leguminosarum, including nitrogen- and nonnitrogen-fixing derivatives under gnotobiotic conditions. The growth-promotive effect appears to be direct, with possible involvement of the plant growth regulators indole-3-acetic acid and cytokinin. Auxotrophic Rhizobium mutants requiring tryptophan or adenosine (precursors for indole-3-acetic acid and demonstrate a new facet of the Rhizobium-plant relationship and that Rhizobium leguminosarum can be considered a plant growth-promoting rhizobacterium (PGPR).