An analysis of culture-based methods used for the detection and isolation of Salmonella spp., Escherichia coli, and Enterococcus spp. from surface water: A systematic review

Identification of methods for the standardized assessment of bacterial pathogens and antimicrobial resistance (AMR) in environmental water can improve the quality of monitoring and data collected, support global surveillance efforts, and enhance the understanding of environmental water sources. We conducted a systematic review to assemble and synthesize available literature that identified methods for assessment of prevalence and abundance of bacterial fecal indicators and pathogens in water for the purposes of monitoring bacterial pathogens and AMR. After screening for quality, 175 unique publications were identified from 15 databases, and data were extracted for analysis. This review identifies the most common and robust methods, and media used to isolate target organisms from surface water sources, summarizes methodological trends, and recognizes knowledge gaps. The information presented in this review will be useful when establishing standardized methods for monitoring bacterial pathogens and AMR in water in the United States and globally.

Dissemination of antimicrobial resistance in agricultural ecosystems following irrigation with treated municipal wastewater

The spread of antimicrobial resistance (AMR) in agricultural systems via irrigation water is a serious public health issue as it can be transmitted to humans through the food chain. Therefore, understanding the dissemination routes of antibiotic resistance genes (ARGs) in agricultural systems is crucial for the assessment of health risks associated with eating fresh vegetables such as spinach and radish irrigated with treated municipal wastewater (TMW). In this study, we investigated the bacterial community structure and resistome in the soil-plant-earthworm continuum after irrigation of spinach and radish with TMW containing the antibiotics trimethoprim (TMP), sulfamethoxazole (SMZ), and sulfapyridine (SPD) using 16S rRNA gene sequencing and high throughput quantitative PCR (HT-qPCR). The study was conducted in two phases: Phase I involved eight weeks of spinach and radish production using TMW for irrigation, whereas Phase II entailed three weeks of earthworm exposure to contaminated plant material obtained in Phase I. The 16S data indicated that the rhizosphere bacterial community composition and structure were more resilient to antibiotic residuals in the irrigated water, with radish showing less susceptibility than spinach than those of bulk soils. The HT-qPCR analysis revealed that a total of 271 ARGs (out of 285) and 9 mobile genetic elements (MGEs) (out of 10) were detected in all samples. Higher diversity and abundance of ARGs were observed for samples irrigated with higher concentrations of antibiotics in both spinach and radish treatments. However, compared to spinach, radish ARG dynamics in the soil biome were more stable due to the change of antibiotic introduction to the soil. At the class level, multi-drug resistance (MDR) class was altered significantly by the presence of antibiotics in irrigation water. Compared to earthworm fecal samples, their corresponding soil environments showed a higher number of detected ARGs, suggesting that earthworms could play a role in reducing ARG dissemination in the soil environments. These findings will not only provide insight into the dissemination of ARGs in agricultural environments due to antibiotic residuals in irrigated water but could help understand the potential human health risks associated with ARGs.

Dissemination of antibiotic resistance genes through soil-plant-earthworm continuum in the food production environment

Treated municipal wastewater (TMW) can provide a reliable source of irrigation water for crops, which is especially important in arid areas where water resources are limited or prone to drought. Nonetheless, TMW may contain residual antibiotics, potentially exposing the crops to these substances. The goal of this study was to investigate the dissemination of antibiotics resistance genes (ARGs) in the soil-plant-earthworm continuum after irrigation of spinach and radish plants with TMW containing trimethoprim, sulfamethoxazole, and sulfapyridine in a greenhouse experiment, followed by feeding of earthworms with harvested plant materials. Our results showed that antibiotic resistance genes (ARGs) were enriched in the soil-plant-earthworm microbiomes irrigated with TMW and TMW spiked with higher concentrations of antibiotics. The number of ARGs and antibiotic-resistant bacteria (ARB) enrichment varied with plant type, with spinach harboring a significantly higher amount of ARGs and ARB compared to radish. Our data showed that bulk and rhizosphere soils of spinach and radish plants irrigated with MilliQ water, TMW, TMW10, or TMW100 had significant differences in bacterial community (p < 0.001), ARG (p < 0.001), and virulence factor gene (VFG) (p < 0.001) diversities. The abundance of ARGs significantly decreased from bulk soil to rhizosphere to phyllosphere and endosphere. Using metagenome assembled genomes (MAGs), we recovered many bacterial MAGs and a near complete genome (>90 %) of bacterial MAG of genus Leclercia adecarboxylata B from the fecal microbiome of earthworm that was fed harvested radish tubers and spinach leaves grown on TMW10 irrigated waters, and this bacterium has been shown to be an emerging pathogen causing infection in immunocompromised patients that may lead to health complications and death. Therefore, crops irrigated with TMW containing residual antibiotics and ARGs may lead to increased incidences of enrichment of ARB in the soil-plant-earthworm continuum.

A comparison of methods to detect low levels of Salmonella enterica in surface waters to support antimicrobial resistance surveillance efforts performed in multiple laboratories

Developing effective and sensitive detection methods for antimicrobial resistant Salmonella enterica from surface water is a goal of the National Antimicrobial Resistance Monitoring System (NARMS). There are no specified methods for recovery of S. enterica in surface waters in the U.S. A multi-laboratory evaluation of four methods - bulk water enrichment (BW), vertical Modified Moore Swab (VMMS), modified Standard Method 9260.B2 (SM), and dead-end ultrafiltration (DEUF) - was undertaken to recover S. enterica from surface water. In Phase 1, one-liter volumes of water were collected from the same site on five different dates. Water was shipped and analyzed at four different laboratory locations (A, B, C, and D) for recovery of 1) inoculated fluorescent S. Typhimurium strain (ca. 30 CFU/L) and 2) Salmonella present in the water sampled. At each location, BW, VMMS, or SM recovery was performed on five separate 1 L water samples. Twenty 1 L water samples were subjected to each recovery method, and overall, sixty 1 L samples were assayed for Salmonella. Inoculated, fluorescent Salmonella Typhimurium and environmental Salmonella spp. were recovered from 65 % (39/60) and 45 % (27/60) of water samples, respectively. BW, VMMS, and SM recovered fluorescent S. Typhimurium from 60 %, 60 %, and 75 % of inoculated samples, respectively. Analysis by Chi-squared test determined laboratory location had a significant (p < 0.05) effect on fluorescent S. Typhimurium recovery compared to method or date of water collection. In Phase 2, recovery of inoculated fluorescent S. Typhimurium from 1 L samples by SM and DEUF was compared at laboratory locations B and D. SM and DEUF recovered fluorescent S. Typhimurium from 100 % (20/20) and 95 % (19/20) of inoculated water samples, respectively; laboratory location (p > 0.05) did not affect Salmonella recovery. Uniform laboratory methodology and training should be prioritized in conducting Salmonella recovery from surface water in laboratories.

Potential reservoirs of antimicrobial resistance in livestock waste and treated wastewater that can be disseminated to agricultural land

Livestock manure, dairy lagoon effluent, and treated wastewater are known reservoirs of antibiotic resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and virulence factor genes (VFGs), and their application to agricultural farmland could be a serious public health threat. However, their dissemination to agricultural lands and impact on important geochemical pathways such as the nitrogen (N) cycle have not been jointly explored. In this study, shotgun metagenomic sequencing and analyses were performed to examine the diversity and composition of microbial communities, ARGs, VFGs, and N cycling genes in different livestock manure/lagoon and treated wastewater collected from concentrated animal feeding operations (CAFOs) and a municipal wastewater treatment plant along the west coast of the United States. Multivariate analysis showed that diversity indices of bacterial taxa from the different microbiomes were not significantly different based on InvSimpson (P = 0.05), but differences in ARG mechanisms were observed between swine manure and other microbiome sources. Comparative resistome profiling showed that ARGs in microbiome samples belonged to four core resistance classes: aminoglycosides (40-55 %), tetracyclines (30-45 %), beta-lactam-resistance (20-35 %), macrolides (18-30 %), and >50 % of the VFGs that the 24 microbiomes harbored were phyletically affiliated with two bacteria, Bacteroidetes fragilis and Enterobacter aerogenes. Network analysis based on Spearman correlation showed co-occurrence patterns between several genes such as transporter-gene and regulator, efflux pump and involved-in-polymyxin- resistance, aminoglycoside, beta-lactam, and macrolide with VFGs and bacterial taxa such as Firmicutes, Candidatus Themoplasmatota, Actinobacteria, and Bacteroidetes. Metabolic reconstruction of metagenome-assembled genome (MAGs) analysis showed that the most prevalent drug resistance mechanisms were associated with carbapenem resistance, multidrug resistance (MDR), and efflux pump. Bacteroidales was the main taxa involved in dissimilatory nitrate reduction (DNRA) in dairy lagoon effluent. This study demonstrates that the dissemination of waste from these sources can increase the spread of ARGs, ARB, and VFGs into agricultural lands, negatively impacting both soil and human health.

Dissemination of antibiotics through the wastewater-soil-plant-earthworm continuum

Under the ongoing climate change scenario, treated municipal wastewater (TMW) is a potential candidate for irrigated agriculture but may result in the exposure of agricultural environments to antibiotics. We studied the transfers of trimethoprim, sulfamethoxazole, and sulfapyridine in the TMW-soil-plant-earthworm continuum under greenhouse/laboratory conditions. Irrigation of potted spinach and radish with as-collected TMW resulted in no transfers of antibiotics into soil or plants owing to their low concentrations in the tertiary-treated TMW. However, TMW spiked with higher antibiotic concentrations led to transfers through this continuum. High initial inputs, slow soil degradation, and chemical speciation of the antibiotics, coupled with an extensive plant-root distribution, were important factors enhancing the plant uptake of antibiotics. In microcosm studies, transfers from vegetable materials into earthworms were low but showed potential for bioaccumulation. Such food chain transfers of antibiotics may be a driver for antibiotic resistance in agricultural systems, which is an area worthy of future study. These issues can perhaps be mitigated through high levels of TMW purification to effectively remove antibiotic compounds.

Influence of seasonal changes and salinity on spinach phyllosphere bacterial functional assemblage

The phyllosphere is the aerial part of plants that is exposed to different environmental conditions and is also known to harbor a wide variety of bacteria including both plant and human pathogens. However, studies on phyllosphere bacterial communities have focused on bacterial composition at different stages of plant growth without correlating their functional capabilities to bacterial communities. In this study, we examined the seasonal effects and temporal variabilities driving bacterial community composition and function in spinach phyllosphere due to increasing salinity and season and estimated the functional capacity of bacterial community16S V4 rRNA gene profiles by indirectly inferring the abundance of functional genes based on metagenomics inference tool Piphillin. The experimental design involved three sets of spinach (Spinacia oleracea L., cv. Racoon) grown with saline water during different seasons. Total bacteria DNA from leaf surfaces were sequenced using MiSeq® Illumina platform. About 66.35% of bacteria detected in the phyllosphere were dominated by four phyla- Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Permutational analysis of variance (PERMANOVA) showed that phyllosphere microbiomes were significantly (P < 0.003) affected by season, but not salinity (P = 0.501). The most abundant inferred functional pathways in leaf samples were the amino acids biosynthesis, ABC transporters, ribosome, aminoacyl-tRNA biosynthesis, two-component system, carbon metabolism, purine metabolism, and pyrimidine metabolism. The photosynthesis antenna proteins pathway was significantly enriched in June leaf samples, when compared to March and May. Several genes related to toxin co-regulated pilus biosynthesis proteins were also significantly enriched in June leaf samples, when compared to March and May leaf samples. Therefore, planting and harvesting times must be considered during leafy green production due to the influence of seasons in growth and proliferation of phyllosphere microbial communities.

Tricarboxylic Acid (TCA) Cycle Enzymes and Intermediates Modulate Intracellular Cyclic di-GMP Levels and the Production of Plant Cell Wall-Degrading Enzymes in Soft Rot Pathogen Dickeya dadantii

Dickeya dadantii is a plant-pathogenic bacterium that causes soft-rot in a wide range of plants. Although we have previously demonstrated that cyclic bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP), a bacterial secondary messenger, plays a central role in virulence regulation in D. dadantii, the upstream signals that modulate c-di-GMP remain enigmatic. Using a genome-wide transposon mutagenesis approach of a Δhfq mutant strain that has high c-di-GMP and reduced motility, we uncovered transposon mutants that recovered the c-di-GMP-mediated repression on swimming motility. A number of these mutants harbored transposon insertions in genes encoding tricarboxylic acid (TCA) cycle enzymes. Two of these TCA transposon mutants were studied further by generating chromosomal deletions of the fumA gene (encoding fumarase) and the sdhCDAB operon (encoding succinate dehydrogenase). Disruption of the TCA cycle in these deletion mutants resulted in reduced intracellular c-di-GMP and enhanced production of pectate lyases (Pels), a major plant cell wall-degrading enzyme (PCWDE) known to be transcriptionally repressed by c-di-GMP. Consistent with this result, addition of TCA cycle intermediates such as citrate also resulted in increased c-di-GMP levels and decreased production of Pels. Additionally, we found that a diguanylate cyclase GcpA was solely responsible for the observed citrate-mediated modulation of c-di-GMP. Finally, we demonstrated that addition of citrate induced not only an overproduction of GcpA protein but also a concomitant repression of the c-di-GMP-degrading phosphodiesterase EGcpB which, together, resulted in an increase in the intracellular concentration of c-di-GMP. In summary, our report demonstrates that bacterial respiration and respiration metabolites serve as signals for the regulation of c-di-GMP signaling.

A newly developed Escherichia coli isolate panel from a cross section of U.S. animal production systems reveals geographic and commodity-based differences in antibiotic resistance gene carriage

There are limited numbers of Escherichia coli isolate panels that represent United States food animal production. The majority of existing Escherichia coli isolate panels are typically designed: (i) to optimize genetic and/or phenotypic diversity; or (ii) focus on human isolates. To address this shortfall in agriculturally-related resources, we have assembled a publicly-available isolate panel (AgEc) from the four major animal production commodities in the United States, including beef, dairy, poultry, and swine, as well as isolates from agriculturally-impacted environments, and other commodity groups. Diversity analyses by phylotyping and Pulsed-field Gel Electrophoresis revealed a highly diverse composition, with the 300 isolates clustered into 71 PFGE sub-types based upon an 80% similarity cutoff. To demonstrate the panel's utility, tetracycline and sulfonamide resistance genes were assayed, which identified 131 isolates harboring genes involved in tetracycline resistance, and 41 isolates containing sulfonamide resistance genes. There was strong overlap in the two pools of isolates, 38 of the 41 isolates harboring sulfonamide resistance genes also contained tetracycline resistance genes. Analysis of antimicrobial resistance gene patterns revealed significant differences along commodity and geographical lines. This panel therefore provides the research community an E. coli isolate panel for study of issues pertinent to U.S. food animal production.

A feed-forward signalling circuit controls bacterial virulence through linking cyclic di-GMP and two mechanistically distinct sRNAs, ArcZ and RsmB

Dickeya dadantii is a plant pathogen that causes soft rot disease on vegetable and potato crops. To successfully cause infection, this pathogen needs to coordinately modulate the expression of genes encoding several virulence determinants, including plant cell wall degrading enzymes (PCWDEs), type III secretion system (T3SS) and flagellar motility. Here, we uncover a novel feed-forward signalling circuit for controlling virulence. Global RNA chaperone Hfq interacts with an Hfq-dependent sRNA ArcZ and represses the translation of pecT, encoding a LysR-type transcriptional regulator. We demonstrate that the ability of ArcZ to be processed to a 50 nt 3'- end fragment is essential for its regulation of pecT. PecT down-regulates PCWDE and the T3SS by repressing the expression of a global post-transcriptional regulator- (RsmA-) associated sRNA encoding gene rsmB. In addition, we show that the protein levels of two cyclic di-GMP (c-di-GMP) diguanylate cyclases (DGCs), GcpA and GcpL, are repressed by Hfq. Further studies show that both DGCs are essential for the Hfq-mediated post-transcriptional regulation on RsmB. Overall, our report provides new insights into the interplays between ubiquitous signalling transduction systems that were most studied independently and sheds light on multitiered regulatory mechanisms for a precise disease regulation in bacteria.

Impact of treated wastewater for irrigation on soil microbial communities

The use of treated wastewater (TWW) for irrigation has been suggested as an alternative to use of fresh water because of the increasing scarcity of fresh water in arid and semiarid regions of the world. However, significant barriers exist to widespread adoption due to some potential contaminants that may have adverse effects on soil quality and or public health. In this study, we investigated the abundance and diversity of bacterial communities and the presence of potential pathogenic bacterial sequences in TWW in comparison to synthetic fresh water (SFW) using pyrosequencing. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity and abundance of different bacterial groups in TWW irrigated soils to soils treated with SFW. Shannon diversity index values (H') suggest that microbial diversity was not significantly different (P<0.086) between soils with TWW and SFW. Pyrosequencing detected sequences of 17 bacterial phyla with Proteobacteria (32.1%) followed by Firmicutes (26.5%) and Actinobacteria (14.3%). Most of the sequences associated with nitrifying bacteria, nitrogen-fixing bacteria, carbon degraders, denitrifying bacteria, potential pathogens, and fecal indicator bacteria were more abundant in TWW than in SFW. Therefore, TWW effluent may contain bacterial that may be very active in many soil functions as well as some potential pathogens.

Bacterial community dynamics in surface flow constructed wetlands for the treatment of swine waste

Constructed wetlands are generally used for the removal of waste from contaminated water. In the swine production system, wastes are traditionally flushed into an anaerobic lagoon which is then sprayed on agricultural fields. However, continuous spraying of lagoon wastewater on fields can lead to high N and P accumulations in soil or lead to runoff which may contaminate surface or ground water with pathogens and nutrients. In this study, continuous marsh constructed wetland was used for the removal of contaminants from swine waste. Using pyrosequencing, we assessed bacterial composition within the wetland using principal coordinate analysis (PCoA) which showed that bacterial composition from manure influent and lagoon water were significantly different (P=0.001) from the storage pond to the final effluent. Canonical correspondence analysis (CCA) showed that different bacterial populations were significantly impacted by ammonium--NH4 (P=0.035), phosphate--PO4(3-) (P=0.010), chemical oxygen demand--COD (P=0.0165), total solids--TS (P=0.030), and dissolved solids--DS (P=0.030) removal, with 54% of the removal rate explained by NH4+PO4(3-) according to a partial CCA. Our results showed that different bacterial groups were responsible for the composition of different wetland nutrients and decomposition process. This may be the major reason why most wetlands are very efficient in waste decomposition.

Potential pathogens, antimicrobial patterns and genotypic diversity of Escherichia coli isolates in constructed wetlands treating swine wastewater

Escherichia coli populations originating from swine houses through constructed wetlands were analyzed for potential pathogens, antimicrobial susceptibility patterns, and genotypic diversity. Escherichia coli isolates (n = 493) were screened for the presence of the following virulence genes: stx1, stx2 and eae (Shiga toxin-producing E. coli [STEC]), heat-labile enterotoxin (LT) genes and heat stable toxin STa and STb (enterotoxigenic E. coli (ETEC), cytotoxin necrotizing factors 1 and 2 (cnf1 and cnf2 [necrotoxigenic E. coli- NTEC]), as well as O and H antigens, and the presence of the antibiotic resistance genes blaTEM, blaSHV, blaCMY-2, tet A, tet B, tet C, mph(A), aadA, StrA/B, sul1, sul2 and sul3. The commensal strains were further screened for 16 antimicrobials and characterized by BOX AIR-1 PCR for unique genotypes. The highest antibiotic resistance prevalence was for tetracycline, followed by erythromycin, ampicillin, streptomycin, sulfisoxazole and kanamycin. Our data showed that most of the isolates had high distribution of single or multidrug-resistant (MDR) genotypes. Therefore, the occurrence of MDR E. coli in the wetland is a matter of great concern due to possible transfer of resistance genes from nonpathogenic to pathogenic strains or vice versa in the environment.

Topological data analysis of Escherichia coli O157:H7 and non-O157 survival in soils

Shiga toxin-producing E. coli O157:H7 and non-O157 have been implicated in many foodborne illnesses caused by the consumption of contaminated fresh produce. However, data on their persistence in soils are limited due to the complexity in datasets generated from different environmental variables and bacterial taxa. There is a continuing need to distinguish the various environmental variables and different bacterial groups to understand the relationships among these factors and the pathogen survival. Using an approach called Topological Data Analysis (TDA); we reconstructed the relationship structure of E. coli O157 and non-O157 survival in 32 soils (16 organic and 16 conventionally managed soils) from California (CA) and Arizona (AZ) with a multi-resolution output. In our study, we took a community approach based on total soil microbiome to study community level survival and examining the network of the community as a whole and the relationship between its topology and biological processes. TDA produces a geometric representation of complex data sets. Network analysis showed that Shiga toxin negative strain E. coli O157:H7 4554 survived significantly longer in comparison to E. coli O157:H7 EDL 933, while the survival time of E. coli O157:NM was comparable to that of E. coli O157:H7 EDL 933 in all of the tested soils. Two non-O157 strains, E. coli O26:H11 and E. coli O103:H2 survived much longer than E. coli O91:H21 and the three strains of E. coli O157. We show that there are complex interactions between E. coli strain survival, microbial community structures, and soil parameters.

Influence of fumigants on soil microbial diversity and survival of E. coli O157:H7

The aim of this study was to assess the effects of soil fumigation with methyl bromide (MeBr; CH(3)Br) and methyl iodide (MeI, iodomethane; CH(3)I) on the microbial community structure and diversity in two soils and determine the effects of microbial diversity on the survival of Escherichia coli O157:H7 from contaminated irrigation water. Polymerase chain reaction (PCR) was used to amplify 16S rRNA from total bacterial community composition and the products were subjected to denaturing gradient gel electrophoresis (DGGE). The Shannon-Weaver index of diversity (H') was used to determine the effects of both fumigants on soil microbial diversity. The effect was more severe in sandy soil than in clay soil at the normal application rate of MeBr and MeI. Our results showed that MeBr and MeI have about the same effects on soil microbial diversity. The two fumigants had greater impact on microbial diversity in sandy soil than in clay soil and this resulted in higher survival of E. coli O157:H7 in sandy soil than in clay soil during the 50 days that the study was conducted. MeBr has been used as soil fumigant for >40 years with no serious detrimental effects on agricultural production and our research also suggests that the use of MeI may also produce no long-term detrimental effects on agricultural production since both fumigants had about the same effects on soil microbial communities. Therefore, soil systems with reduced microbial diversity may offer greater opportunities for the survival of pathogenic bacteria such as E. coli O157:H7.

Influence of soil fumigation by methyl bromide and methyl iodide on rhizosphere and phyllosphere microbial community structure

Rhizosphere and phyllosphere microbial communities were evaluated on roots and leaves of growth chamber-grown lettuce (Lactuca sativa (L.) cv. Green Forest) plants by culture-dependent and -independent methods after soil fumigation. Denaturing gradient gel electrophoresis (DGGE) with 16S rRNA primers followed by cloning and sequencing was used to identify major rRNA bands from the rhizosphere and phyllosphere. Three weeks after fumigation, there were no differences (P = 0.16) in rhizosphere microbial communities between the fumigated treatments and the control. The same effect was observed during week seven after fumigation (P=0.49). Also, no significant differences (P=0.49) were found in the phyllosphere microbial communities between the fumigated treatments and the control during the growth period of the plant. A majority of the bands in the rhizosphere were related to known bacterial sequences with a 96 to 100 % sequence similarity. Some of the derived sequences were related to Pseudomonas syringae pv. tomato DC300 and Bradyrhizobium japonicum USDA 110. A total of 23 isolates were identified from leaf surface by both culture-dependent and independent methods, and only Photorhabdus luminescens was found on leaf surface using both techniques. All the Biolog isolates from phyllosphere were from the Proteobacteria phylum compared to the culture-independent bands from the leaves that were from different bacterial phyla. Based on our data, methyl bromide (MeBr) and methyl iodide (MeI) did not have any significant negative effects on rhizosphere and phyllosphere microbial communities throughout the growing period of lettuce.

Impact of plant density and microbial composition on water quality from a free water surface constructed wetland

AIMS

To correlate microbial community composition and water quality changes within wetland cells containing varying plant densities and composition in a free water surface (FWS) constructed wetland.

METHODS AND RESULTS

Water chemistry was monitored weekly for nitrate, orthophosphate, and suspended solids, at various sites throughout the wetland for 6 months. Treatment ponds with 50% plant cover had about a 96.3% nitrate removal. The average change between the influent and effluent was 50-60% nitrate removal and 40-50% orthophosphate removal. Community profile of total DNA, generated by using denaturing gradient gel electrophoresis (DGGE), was used to determine the major microbial composition associated with the wetland sediment, rhizosphere, and surface water. Bacterial cloned libraries were constructed, and 300 clones were analysed by amplified ribosomal DNA restriction analysis (ARDRA) and grouped into operational taxonomic units (OTUs). A total of 35, 31, and 36 different OTU were obtained from sediment, rhizosphere, and surface water, respectively. The bacterial members within the dominant group of our clone library belonged to unclassified taxa, while the second predominant group consisted of members of the phylum Proteobacteria. The dominant organisms within the class were in the gamma, beta, and delta classes.

CONCLUSION

Microbial diversity as determined by Shannon-Weaver index (H) was higher in the wetland cells with 50% plant density than the 100%. This was in agreement with the most efficient wetland contaminant removal units.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides evidence that wetlands with 50% plant cover may promote the growth of diverse microbial communities that facilitate decomposition of chemical pollutants in surface water, and improve water quality.

Changes in developing plant microbial community structure as affected by contaminated water

The effects of sand and clay soils and water contaminated by Escherichia coli O157:H7 on the development of rhizosphere and phyllosphere microbial communities were analyzed to determine the influence of plant age on microbial community structure and composition. Community bacterial nucleic acids were extracted from lettuce rhizosphere and phyllosphere samples at different stages of plant development after the soils were irrigated with water contaminated with E. coli O157:H7 at planting and 15 days after planting. PCR was used to amplify 16S ribosomal RNA (rRNA) for total bacterial community composition and the products were subjected to denaturing gradient gel electrophoresis (DGGE). Prominent DGGE bands were excised and sequenced to gain insight into the identities of predominant bacterial populations. The majority of DGGE band sequences were related to bacterial genera previously associated with the rhizosphere and phyllosphere, such as Pseudomonas, Acidobacterium, Bacillus and Agrobacterium. The PCR-DGGE patterns observed for rhizosphere samples were more complex than those obtained from the bulk soil and the phyllosphere. The Shannon index of diversity (H) was used to determine the complexity of the DGGE bands from the phyllosphere, rhizosphere and the bulk soils at different growth stages. A higher diversity was observed in the clay soil than sandy soil during the first week. Few changes in diversity were observed after the first week. The results show that microbial community development in lettuce may take about 7-12 days and this may be the most likely period for maximum pathogen contamination in plants.

Detection and quantification of Escherichia coli O157:H7 in environmental samples by real-time PCR

AIMS

To apply the real-time Polymerase chain reaction (PCR) method to detect and quantify Escherichia coli O157:H7 in soil, manure, faeces and dairy waste washwater.

METHODS AND RESULTS

Soil samples were spiked with E. coli O157:H7 and subjected to a single enrichment step prior to multiplex PCR. Other environmental samples suspected of harbouring E.coli O157:H7 were also analysed. The sensitivity of the primers was confirmed with DNA from E.coli O157:H7 strain 3081 spiked into soil by multiplex PCR assay. A linear relationship was measured between the fluorescence threshold cycle (C T ) value and colony counts (CFU ml(-1)) in spiked soil and other environmental samples. The detection limit for E.coli O157:H7 in the real-time PCR assay was 3.5 x 10(3) CFU ml(-1) in pure culture and 2.6 x 10(4) CFU g(-1) in the environmental samples. Use of a 16-h enrichment step for spiked samples enabled detection of <10 CFU g(-1) soil. E. coli colony counts as determined by the real-time PCR assay, were in the range of 2.0 x 10(2) to 6.0 x 10(5) CFU PCR (-1) in manure, faeces and waste washwater.

CONCLUSIONS

The real-time PCR-based assay enabled sensitive and rapid quantification of E. coli O157:H7 in soil and other environmental samples.

SIGNIFICANCE AND IMPACT OF THE STUDY

The ability to quantitatively determine cell counts of E.coli O157:H7 in large numbers of environmental samples, represents considerable advancement in the area of pathogen quantification for risk assessment and transport studies.

Microcosm enrichment of 1,3-dichloropropene-degrading soil microbial communities in a compost-amended soil

AIMS

A microcosm-enrichment approach was used to investigate bacterial populations that may represent 1,3-dichloropropene (1,3-D)-degrading micro-organisms in compost-amended soil.

METHODS AND RESULTS

After 8 weeks of incubation, with repeated application of 1,3-D, volatilization fluxes were much lower for compost-amended soil (CM) than with the unamended soils, indicating accelerated degradation due to addition of compost, or development of new microbial populations with enhanced degradation capacity. Denaturing gradient gel electrophoresis (DGGE) profiles of the PCR-amplified region of 16S rDNA genes were used to identify dominant bacterial populations in the fumigant-degrading soil. The DGGE results indicated that specific bacterial types had been enriched, and a more diverse fingerprint was observed in the community derived from the compost-amended soil compared with the unamended soil. Fragments from 16 different DGGE bands were cloned, sequenced and compared with published 16S rDNA sequences. Two clones, designated E1 and E4, were unique to all soils to which compost was added, and corresponded to strains of Pseudomonas and Actinomadura, respectively.

CONCLUSIONS

The results show that the addition of compost to soil increases specific microbial populations and results in the accelerated degradation of fumigants.

SIGNIFICANCE AND IMPACT OF THE STUDY

Application of compost manure to soil can help degrade soil fumigants at a faster rate.

Impact of fumigants on soil microbial communities

Agricultural soils are typically fumigated to provide effective control of nematodes, soilborne pathogens, and weeds in preparation for planting of high-value cash crops. The ability of soil microbial communities to recover after treatment with fumigants was examined using culture-dependent (Biolog) and culture-independent (phospholipid fatty acid [PLFA] analysis and denaturing gradient gel electrophoresis [DGGE] of 16S ribosomal DNA [rDNA] fragments amplified directly from soil DNA) approaches. Changes in soil microbial community structure were examined in a microcosm experiment following the application of methyl bromide (MeBr), methyl isothiocyanate, 1,3-dichloropropene (1,3-D), and chloropicrin. Variations among Biolog fingerprints showed that the effect of MeBr on heterotrophic microbial activities was most severe in the first week and that thereafter the effects of MeBr and the other fumigants were expressed at much lower levels. The results of PLFA analysis demonstrated a community shift in all treatments to a community dominated by gram-positive bacterial biomass. Different 16S rDNA profiles from fumigated soils were quantified by analyzing the DGGE band patterns. The Shannon-Weaver index of diversity, H, was calculated for each fumigated soil sample. High diversity indices were maintained between the control soil and the fumigant-treated soils, except for MeBr (H decreased from 1.14 to 0.13). After 12 weeks of incubation, H increased to 0.73 in the MeBr-treated samples. Sequence analysis of clones generated from unique bands showed the presence of taxonomically unique clones that had emerged from the MeBr-treated samples and were dominated by clones closely related to Bacillus spp. and Heliothrix oregonensis. Variations in the data were much higher in the Biolog assay than in the PLFA and DGGE assays, suggesting a high sensitivity of PLFA analysis and DGGE in monitoring the effects of fumigants on soil community composition and structure. Our results indicate that MeBr has the greatest impact on soil microbial communities and that 1,3-D has the least impact.