Identifying sources of antibiotic resistance genes in the environment using the microbial Find, Inform, and Test framework

Introduction

Antimicrobial resistance (AMR) is an increasing public health concern for humans, animals, and the environment. However, the contributions of spatially distributed sources of AMR in the environment are not well defined.

Methods

To identify the sources of environmental AMR, the novel microbial Find, Inform, and Test (FIT) model was applied to a panel of five antibiotic resistance-associated genes (ARGs), namely, erm(B), tet(W), qnrA, sul1, and intI1, quantified from riverbed sediment and surface water from a mixed-use region.

Results

A one standard deviation increase in the modeled contributions of elevated AMR from bovine sources or land-applied waste sources [land application of biosolids, sludge, and industrial wastewater (i.e., food processing) and domestic (i.e., municipal and septage)] was associated with 34-80% and 33-77% increases in the relative abundances of the ARGs in riverbed sediment and surface water, respectively. Sources influenced environmental AMR at overland distances of up to 13 km.

Discussion

Our study corroborates previous evidence of offsite migration of microbial pollution from bovine sources and newly suggests offsite migration from land-applied waste. With FIT, we estimated the distance-based influence range overland and downstream around sources to model the impact these sources may have on AMR at unsampled sites. This modeling supports targeted monitoring of AMR from sources for future exposure and risk mitigation efforts.

Recycled concrete aggregates are an economic form of urban riparian erosion management with limited impacts on freshwater chemistry and microbial diversity

Urban streams are at high risk of riparian erosion which impacts adjacent infrastructure stability. Methods to prevent stream erosion have been proposed including using recycled concrete (RC) materials to help stabilize the streambed; however, little is known about the environmental and biological impacts of using RC in urban streams. RC, new concrete (NC), and river rock controls were evaluated for their impact on water chemistry, water quality, and microbial community composition over 6.5 months in controlled laboratory mesocosms. Concentrations of 19 metals, nutrients, and pH of mesocosms containing RC were not significantly different from the river rock mesocosm throughout the experiment; however, NC mesocosms contained significantly higher (p < 0.05) concentrations of Co, As, Al, and V in mesocosm water samples compared to both RC and the river rock control. Microbial community diversity was not significantly impacted by mesocosm treatment. Microbial sequences mapping to taxa including Rhodoferax, Acidovorax, Nitrosomonas, and Novosphingobium were significantly more abundant (p < 0.01) in RC and NC mesocosm samples; however, the overall microbial community structure was similar across treatment types. Results from this study suggest that RC does not significantly alter the stream environment including microbial community diversity and is a viable option for use in stream restoration projects.

Characterizing Differences in Sources of and Contributions to Fecal Contamination of Sediment and Surface Water with the Microbial FIT Framework

Surface water monitoring and microbial source tracking (MST) are used to identify host sources of fecal pollution and protect public health. However, knowledge of the locations of spatial sources and their relative impacts on the environment is needed to effectively mitigate health risks. Additionally, sediment samples may offer time-integrated information compared to transient surface water. Thus, we implemented the newly developed microbial find, inform, and test framework to identify spatial sources and their impacts on human (HuBac) and bovine (BoBac) MST markers, quantified from both riverbed sediment and surface water in a bovine-dense region. Dairy feeding operations and low-intensity developed land-cover were associated with 99% (p-value < 0.05) and 108% (p-value < 0.05) increases, respectively, in the relative abundance of BoBac in sediment, and with 79% (p-value < 0.05) and 39% increases in surface water. Septic systems were associated with a 48% increase in the relative abundance of HuBac in sediment and a 56% increase in surface water. Stronger source signals were observed for sediment responses compared to water. By defining source locations, predicting river impacts, and estimating source influence ranges in a Great Lakes region, this work informs pollution mitigation strategies of local and global significance.

Antibiotic resistance patterns of Escherichia coli isolates from the clinic through the wastewater pathway

Antimicrobial resistance (AMR) remains one of the leading global health threats. This study compared antimicrobial resistance patterns among E. coli isolates from clinical uropathogenic Escherichia coli (UPEC) to hospital wastewater populations and throughout an urban wastewater treatment facility - influent, pre- and post-chlorinated effluents. Antibiotic susceptibility of 201 isolates were analyzed against eleven different antibiotics, and the presence of twelve antibiotic resistant genes and type 1 integrase were identified. AMR exhibited the following pattern: UPEC (46.8%) > hospital wastewater (37.8%) > urban post-chlorinated effluent (27.6%) > pre-chlorinated effluent (21.4%) > urban influent wastewater (13.3%). However, multi-drug resistance against three or more antimicrobial classes was more prevalent among hospital wastewater populations (29.7%) compared to other sources. E. coli from wastewaters disinfected with chlorine were significantly correlated with increased trimethoprim-sulfamethoxazole resistance in E. coli compared to raw and treated wastewater populations. bla_CTX-M-1 group was the most common extended spectrum beta-lactamase in E. coli from hospital wastewater (90%), although UPEC strains also encoded bla_CTX-M-1 group (50%) and bla_TEM (100%) genes. Among tetracycline-resistant populations, tetA and tetB were the only resistance genes identified throughout wastewater populations that were associated with increased phenotypic resistance. Further characterization of the E. coli populations identified phylogroup B2 predominating among clinical UPEC populations and correlated with the highest AMR, whereas the elevated rate of multi-drug resistance among hospital wastewater was mostly phylogroup A. Together, our findings highlight hospital wastewater as a rich source of AMR and multi-drug resistant bacterial populations.

Microbial Find, Inform, and Test Model for Identifying Spatially Distributed Contamination Sources: Framework Foundation and Demonstration of Ruminant Bacteroides Abundance in River Sediments

Microbial pollution in rivers poses known ecological and health risks, yet causal and mechanistic linkages to sources remain difficult to establish. Host-associated microbial source tracking (MST) markers help to assess the microbial risks by linking hosts to contamination but do not identify the source locations. Land-use regression (LUR) models have been used to screen the source locations using spatial predictors but could be improved by characterizing transport (i.e., hauling, decay overland, and downstream). We introduce the microbial Find, Inform, and Test (FIT) framework, which expands previous LUR approaches and develops novel spatial predictor models to characterize the transported contributions. We applied FIT to characterize the sources of BoBac, a ruminant Bacteroides MST marker, quantified in riverbed sediment samples from Kewaunee County, Wisconsin. A 1 standard deviation increase in contributions from land-applied manure hauled from animal feeding operations (AFOs) was associated with a 77% (p-value <0.05) increase in the relative abundance of ruminant Bacteroides (BoBac-copies-per-16S-rRNA-copies) in the sediment. This is the first work finding an association between the upstream land-applied manure and the offsite bovine-associated fecal markers. These findings have implications for the sediment as a reservoir for microbial pollution associated with AFOs (e.g., pathogens and antibiotic-resistant bacteria). This framework and application advance statistical analysis in MST and water quality modeling more broadly.

Manure derived nutrients alter microbial community composition and increase the presence of potential pathogens in freshwater sediment

AIM

To determine the impact of an acute, pulse disturbance of nutrients from manure on freshwater sediment microbiomes in an experimental system.

METHODS AND RESULTS

A controlled freshwater mesocosm experiment was designed to compare the effect of disturbance from nutrients derived from sterile manure (SM), disturbance from equivalent concentrations of laboratory-derived nutrients, and a nondisturbed control on freshwater sediment microbial community composition and function using 16S rRNA amplicon sequencing. Sediment microbiomes impacted by nutrients from SM showed no sign of compositional recovery after 28 days but those impacted by laboratory-derived chemicals lead to a new steady-state (p < 0.05). Carbon and nitrate sources within disturbed mesocosms were the primary drivers of altered microbial community composition. Additionally, multiple potential pathogens (based on exact sequence matching at the species level) were enriched in mesocosms treated with SM.

CONCLUSIONS

Nutrient disturbance from SM, in the absence of the manure microbial community, alters the microbiome of sediments without recovery after 28 days and enriches potential pathogens.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results suggest manure land application practices should be re-evaluated to account for impact of nutrient disturbance on environmental microbiomes in addition to the impact of the manure microbial community.

Survivor microbial populations in post-chlorinated wastewater are strongly associated with untreated hospital sewage and include ceftazidime and meropenem resistant populations

Wastewater treatment plant (WWTP) effluent has been implicated in the spread of antibiotic resistant bacteria (ARB), including pathogens, as the WWTP environment contains multiple selective pressures that may increase mutation rates, pathogen survivability, and induce gene transfer between bacteria. In WWTPs receiving hospital sewage, this selective effect may be more pronounced due to increased concentrations of antibiotics, ARB, and clinical pathogens from hospital sewage. To determine the extent to which hospital sewage contributes to the microbial community of disinfected wastewater which is released into the environment, we used 16S rRNA sequencing of hospital sewage, WWTP influent, primary effluent, Post-Chlorinated Effluent, and receiving sediments in a combined sewage system to track changes in microbial community composition. We also sequenced the culturable survivor community resistant to β-lactam antibiotics within disinfected effluent. Using molecular source tracking, we found that the hospital sewage microbiome contributes an average of 11.49% of the microbial community in Post-Chlorinated Effluents, suggesting microorganisms identified within hospital sewage can survive or are enriched by the chlorination disinfection process. Additionally, we identified 28 potential pathogens to the species level, seven of which remained detectable in Post-Chlorinated Effluent and environmental sediments. When Post-Chlorinated Effluents were cultured on media containing β-lactam antibiotics ceftazidime and meropenem, a diverse antibiotic resistant survivor community was identified including potential human pathogens Bacillus cereus, Bacillus pumilus, and Chryseobacterium indologenes. Together, these results indicate that although wastewater treatment does significantly reduce pathogenic loads and ARBs, their continual presence in disinfected wastewater and receiving sediments suggests additional treatment and microbial tracking systems are needed to reduce human and animal health risks.

Freshwater Sediment Microbial Communities Are Not Resilient to Disturbance From Agricultural Land Runoff

Microorganisms are critically important for the function of surface water ecosystems but are frequently subjected to anthropogenic disturbances at either acute (pulse) or long-term (press) scales. Response and recovery of microbial community composition and function following pulse disturbance is well-studied in controlled, laboratory scale experiments but is less well-understood in natural environments undergoing continual press disturbance. The objectives of this study were to determine the drivers of sediment microbial compositional and functional changes in freshwaters receiving continual press disturbance from agricultural land runoff and to evaluate the ability of the native microbial community to resist disturbance related changes as a proxy for freshwater ecosystem health. Freshwater sediments were collected seasonally over 1 year in Kewaunee County, Wisconsin, a region impacted by concentrated dairy cattle farming, manure fertilization, and associated agricultural runoff which together serve as a press disturbance. Using 16S rRNA gene amplicon sequencing, we found that sediments in locations strongly impacted by intensive agriculture contain significantly higher abundances (p < 0.01) of the genera Thiobacillus, Methylotenera, Crenotrhix, Nitrospira, and Rhodoferax compared to reference sediments, and functions including nitrate reduction, nitrite reduction, and nitrogen respiration are significantly higher (p < 0.05) at locations in close proximity to large farms. Nine species-level potential human pathogens were identified in riverine sediments including Acinetobacer lwoffi and Arcobacter skirrowii, two pathogens associated with the cattle microbiome. Microbial community composition at locations in close proximity to intensive agriculture was not resistant nor resilient to agricultural runoff disturbance within 5 months post-disturbance but did reach a new, stable microbial composition. From this data, we conclude that sediment microbial community composition is sensitive and shifts in response to chemical and microbial pollution from intensive agriculture, has a low capacity to resist infiltration by non-native, harmful bacteria and, overall, the natural buffering capacity of freshwater ecosystems is unable to fully resist the impacts from agricultural press disturbance.

Antimicrobial Resistance Traits of Escherichia coli Isolated from Dairy Manure and Freshwater Ecosystems Are Similar to One Another but Differ from Associated Clinical Isolates

Antimicrobial resistance (AMR) is a prevalent global health problem across human and veterinary medicine. The One Health approach to AMR is necessary to mitigate transmission between sources of resistance and decrease the spread of resistant bacteria among humans, animals, and the environment. Our primary goal was to identify associations in resistance traits between Escherichia coli isolated from clinical (n = 103), dairy manure (n = 65), and freshwater ecosystem (n = 64) environments within the same geographic location and timeframe. Clinical E. coli isolates showed the most phenotypic resistance (47.5%), followed by environmental isolates (15.6%) and manure isolates (7.7%), with the most common resistances to ampicillin, ampicillin-sulbactam, and cefotaxime antibiotics. An isolate subset was screened for extended spectrum beta-lactamase (ESBL) production resulting in the identification of 35 ESBL producers. The most common ESBL gene identified was bla_TEM-1. Additionally, we found nine different plasmid replicon types including IncFIA-FIB, which were frequently associated with ESBL producer isolates. Molecular phylotyping revealed a significant portion of clinical E. coli were associated with phylotype B2, whereas manure and environmental isolates were more diverse. Manure and environmental isolates were significantly different from clinical isolates based on analyzed traits, suggesting more transmission occurs between these two sources in the sampled environment.

Poultry and beef meat as potential seedbeds for antimicrobial resistant enterotoxigenic Bacillus species: a materializing epidemiological and potential severe health hazard

Although Bacillus cereus is of particular concern in food safety and public health, the role of other Bacillus species was overlooked. Therefore, we investigated the presence of eight enterotoxigenic genes, a hemolytic gene and phenotypic antibiotic resistance profiles of Bacillus species in retail meat samples. From 255 samples, 124 Bacillus isolates were recovered, 27 belonged to B. cereus and 97 were non-B. cereus species. Interestingly, the non-B. cereus isolates carried the virulence genes and exhibited phenotypic virulence characteristics as the B. cereus. However, correlation matrix analysis revealed the B. cereus group positively correlates with the presence of the genes hblA, hblC, and plc, and the detection of hemolysis (p < 0.05), while the other Bacillus sp. groups are negatively correlated. Tests for antimicrobial resistance against ten antibiotics revealed extensive drug and multi-drug resistant isolates. Statistical analyses didn't support a correlation of antibiotic resistance to tested virulence factors suggesting independence of these phenotypic markers and virulence genes. Of special interest was the isolation of Paenibacillus alvei and Geobacillus stearothermophilus from the imported meat samples being the first recorded. The isolation of non-B. cereus species carrying enterotoxigenic genes in meat within Egypt, suggests their impact on food safety and public health and should therefore not be minimised, posing an area that requires further research.

Copper Oxide Nanoparticles Impact Several Toxicological Endpoints and Cause Neurodegeneration in Caenorhabditis elegans

Engineered nanoparticles are becoming increasingly incorporated into technology and consumer products. In 2014, over 300 tons of copper oxide nanoparticles were manufactured in the United States. The increased production of nanoparticles raises concerns regarding the potential introduction into the environment or human exposure. Copper oxide nanoparticles commonly release copper ions into solutions, which contribute to their toxicity. We quantified the inhibitory effects of both copper oxide nanoparticles and copper sulfate on C. elegans toxicological endpoints to elucidate their biological effects. Several toxicological endpoints were analyzed in C. elegans, including nematode reproduction, feeding behavior, and average body length. We examined three wild C. elegans isolates together with the Bristol N2 laboratory strain to explore the influence of different genotypic backgrounds on the physiological response to copper challenge. All strains exhibited greater sensitivity to copper oxide nanoparticles compared to copper sulfate, as indicated by reduction of average body length and feeding behavior. Reproduction was significantly reduced only at the highest copper dose, though still more pronounced with copper oxide nanoparticles compared to copper sulfate treatment. Furthermore, we investigated the effects of copper oxide nanoparticles and copper sulfate on neurons, cells with known vulnerability to heavy metal toxicity. Degeneration of dopaminergic neurons was observed in up to 10% of the population after copper oxide nanoparticle exposure. Additionally, mutants in the divalent-metal transporters, smf-1 or smf-2, showed increased tolerance to copper exposure, implicating both transporters in copper-induced neurodegeneration. These results highlight the complex nature of CuO nanoparticle toxicity, in which a nanoparticle-specific effect was observed in some traits (average body length, feeding behavior) and a copper ion specific effect was observed for other traits (neurodegeneration, response to stress).

Chronic exposure to triclosan sustains microbial community shifts and alters antibiotic resistance gene levels in anaerobic digesters

Triclosan, an antimicrobial chemical found in consumer personal care products, has been shown to stimulate antibiotic resistance in pathogenic bacteria. Although many studies focus on antibiotic resistance pertinent to medical scenarios, resistance developed in natural and engineered environments is less studied and has become an emerging concern for human health. In this study, the impacts of chronic triclosan (TCS) exposure on antibiotic resistance genes (ARGs) and microbial community structure were assessed in lab-scale anaerobic digesters. TCS concentrations from below detection to 2500 mg kg(-1) dry solids were amended into anaerobic digesters over 110 days and acclimated for >3 solid retention time values. Four steady state TCS concentrations were chosen (30-2500 mg kg(-1)). Relative abundance of mexB, a gene coding for a component of a multidrug efflux pump, was significantly higher in all TCS-amended digesters (30 mg kg(-1) or higher) relative to the control. TCS selected for bacteria carrying tet(L) and against those carrying erm(F) at concentrations which inhibited digester function; the pH decrease associated with digester failure was suspected to cause this selection. Little to no impact of TCS was observed on intI1 relative abundance. Microbial communities were also surveyed by high-throughput 16S rRNA gene sequencing. Compared to the control digesters, significant shifts in community structure towards clades containing commensal and pathogenic bacteria were observed in digesters containing TCS. Based on these results, TCS should be included in studies and risk assessments that attempt to elucidate relationships between chemical stressors (e.g. antibiotics), antibiotic resistance genes, and public health.

Effect of benzene and ethylbenzene on the transcription of methyl-tert-butyl ether degradation genes of Methylibium petroleiphilum PM1

Methyl-tert-butyl ether (MTBE) and its degradation by-product, tert-butyl alcohol (TBA), are widespread contaminants detected frequently in groundwater in California. Since MTBE was used as a fuel oxygenate for almost two decades, leaking underground fuel storage tanks are an important source of contamination. Gasoline components such as BTEX (benzene, toluene, ethylbenzene and xylenes) are often present in mixtures with MTBE and TBA. Investigations of interactions between BTEX and MTBE degradation have not yielded consistent trends, and the molecular mechanisms of BTEX compounds' impact on MTBE degradation are not well understood. We investigated trends in transcription of biodegradation genes in the MTBE-degrading bacterium, Methylibium petroleiphilum PM1 upon exposure to MTBE, TBA, ethylbenzene and benzene as individual compounds or in mixtures. We designed real-time quantitative PCR assays to target functional genes of strain PM1 and provide evidence for induction of genes mdpA (MTBE monooxygenase), mdpJ (TBA hydroxylase) and bmoA (benzene monooxygenase) in response to MTBE, TBA and benzene, respectively. Delayed induction of mdpA and mdpJ transcription occurred with mixtures of benzene and MTBE or TBA, respectively. bmoA transcription was similar in the presence of MTBE or TBA with benzene as in their absence. Our results also indicate that ethylbenzene, previously proposed as an inhibitor of MTBE degradation in some bacteria, inhibits transcription of mdpA, mdpJ and bmoAgenes in strain PM1.

Triclocarban Influences Antibiotic Resistance and Alters Anaerobic Digester Microbial Community Structure

Triclocarban (TCC) is one of the most abundant organic micropollutants detected in biosolids. Lab-scale anaerobic digesters were amended with TCC at concentrations ranging from the background concentration of seed biosolids (30 mg/kg) to toxic concentrations of 850 mg/kg to determine the effect on methane production, relative abundance of antibiotic resistance genes, and microbial community structure. Additionally, the TCC addition rate was varied to determine the impacts of acclimation time. At environmentally relevant TCC concentrations (max detect = 440 mg/kg), digesters maintained function. Digesters receiving 450 mg/kg of TCC maintained function under gradual TCC addition, but volatile fatty acid concentrations increased, pH decreased, and methane production ceased when immediately fed this concentration. The concentrations of the mexB gene (encoding for a multidrug efflux pump) were higher with all concentrations of TCC compared to a control, but higher TCC concentrations did not correlate with increased mexB abundance. The relative abundance of the gene tet(L) was greater in the digesters that no longer produced methane, and no effect on the relative abundance of the class 1 integron integrase encoding gene (intI1) was observed. Illumina sequencing revealed substantial community shifts in digesters that functionally failed from increased levels of TCC. More subtle, yet significant, community shifts were observed in digesters amended with TCC levels that did not inhibit function. This research demonstrates that TCC can select for a multidrug resistance encoding gene in mixed community anaerobic environments, and this selection occurs at concentrations (30 mg/kg) that can be found in full-scale anaerobic digesters (U.S. median concentration = 22 mg/kg, mean = 39 mg/kg).

Copper oxide nanoparticles inhibit the metabolic activity of Saccharomyces cerevisiae

Copper oxide nanoparticles (CuO NPs) are used increasingly in industrial applications and consumer products and thus may pose risk to human and environmental health. The interaction of CuO NPs with complex media and the impact on cell metabolism when exposed to sublethal concentrations are largely unknown. In the present study, the short-term effects of 2 different sized manufactured CuO NPs on metabolic activity of Saccharomyces cerevisiae were studied. The role of released Cu(2+) during dissolution of NPs in the growth media and the CuO nanostructure were considered. Characterization showed that the 28 nm and 64 nm CuO NPs used in the present study have different primary diameter, similar hydrodynamic diameter, and significantly different concentrations of dissolved Cu(2+) ions in the growth media released from the same initial NP mass. Exposures to CuO NPs or the released Cu(2+) fraction, at doses that do not have impact on cell viability, showed significant inhibition on S. cerevisiae cellular metabolic activity. A greater CuO NP effect on the metabolic activity of S. cerevisiae growth under respiring conditions was observed. Under the tested conditions the observed metabolic inhibition from the NPs was not explained fully by the released Cu ions from the dissolving NPs.

Detection of multi-drug resistant Escherichia coli in the urban waterways of Milwaukee, WI

Urban waterways represent a natural reservoir of antibiotic resistance which may provide a source of transferable genetic elements to human commensal bacteria and pathogens. The objective of this study was to evaluate antibiotic resistance of Escherichia coli isolated from the urban waterways of Milwaukee, WI compared to those from Milwaukee sewage and a clinical setting in Milwaukee. Antibiotics covering 10 different families were utilized to determine the phenotypic antibiotic resistance for all 259 E. coli isolates. All obtained isolates were determined to be multi-drug resistant. The E. coli isolates were also screened for the presence of the genetic determinants of resistance including ermB (macrolide resistance), tet(M) (tetracycline resistance), and β-lactamases (bla OXA, bla SHV, and bla PSE). E. coli from urban waterways showed a greater incidence of antibiotic resistance to 8 of 17 antibiotics tested compared to human derived sources. These E. coli isolates also demonstrated a greater incidence of resistance to higher numbers of antibiotics compared to the human derived isolates. The urban waterways demonstrated a greater abundance of isolates with co-occurrence of antibiotic resistance than human derived sources. When screened for five different antibiotic resistance genes conferring macrolide, tetracycline, and β-lactam resistance, clinical E. coli isolates were more likely to harbor ermB and bla OXA than isolates from urban waterway. These results indicate that Milwaukee's urban waterways may select or allow for a greater incidence of multiple antibiotic resistance organisms and likely harbor a different antibiotic resistance gene pool than clinical sources. The implications of this study are significant to understanding the presence of resistance in urban freshwater environments by supporting the idea that sediment from urban waterways serves as a reservoir of antibiotic resistance.

Gene mdpC plays a regulatory role in the methyl-tert-butyl ether degradation pathway of Methylibium petroleiphilum strain PM1

Among the few bacteria known to utilize methyl tert-butyl ether (MTBE) as a sole carbon source, Methylibium petroleiphilum PM1 is a well-characterized organism with a sequenced genome; however, knowledge of the genetic regulation of its MTBE degradation pathway is limited. We investigated the role of a putative transcriptional activator gene, mdpC, in the induction of MTBE-degradation genes mdpA (encoding MTBE monooxygenase) and mdpJ (encoding tert-butyl alcohol hydroxylase) of strain PM1 in a gene-knockout mutant mdpC(-). We also utilized quantitative reverse transcriptase PCR assays targeting genes mdpA, mdpJ and mdpC to determine the effects of the mutation on transcription of these genes. Our results indicate that gene mdpC is involved in the induction of both mdpA and mdpJ in response to MTBE and tert-butyl alcohol (TBA) exposure in PM1. An additional independent mechanism may be involved in the induction of mdpJ in the presence of TBA.

The polycyclic aromatic hydrocarbon degradation potential of Gulf of Mexico native coastal microbial communities after the Deepwater Horizon oil spill

The Deepwater Horizon (DWH) blowout resulted in oil transport, including polycyclic aromatic hydrocarbons (PAHs) to the Gulf of Mexico shoreline. The microbial communities of these shorelines are thought to be responsible for the intrinsic degradation of PAHs. To investigate the Gulf Coast beach microbial community response to hydrocarbon exposure, we examined the functional gene diversity, bacterial community composition, and PAH degradation capacity of a heavily oiled and non-oiled beach following the oil exposure. With a non-expression functional gene microarray targeting 539 gene families, we detected 28,748 coding sequences. Of these sequences, 10% were uniquely associated with the severely oil-contaminated beach and 6.0% with the non-oiled beach. There was little variation in the functional genes detected between the two beaches; however the relative abundance of functional genes involved in oil degradation pathways, including polycyclic aromatic hydrocarbons (PAHs), were greater in the oiled beach. The microbial PAH degradation potentials of both beaches, were tested in mesocosms. Mesocosms were constructed in glass columns using sands with native microbial communities, circulated with artificial sea water and challenged with a mixture of PAHs. The low-molecular weight PAHs, fluorene and naphthalene, showed rapid depletion in all mesocosms while the high-molecular weight benzo[α]pyrene was not degraded by either microbial community. Both the heavily oiled and the non-impacted coastal communities showed little variation in their biodegradation ability for low molecular weight PAHs. Massively-parallel sequencing of 16S rRNA genes from mesocosm DNA showed that known PAH degraders and genera frequently associated with oil hydrocarbon degradation represented a major portion of the bacterial community. The observed similar response by microbial communities from beaches with a different recent history of oil exposure suggests that Gulf Coast beach communities are primed for PAH degradation.

Selenium biotransformations in an engineered aquatic ecosystem for bioremediation of agricultural wastewater via brine shrimp production

An engineered aquatic ecosystem was specifically designed to bioremediate selenium (Se), occurring as oxidized inorganic selenate from hypersalinized agricultural drainage water while producing brine shrimp enriched in organic Se and omega-3 and omega-6 fatty acids for use in value added nutraceutical food supplements. Selenate was successfully bioremediated by microalgal metabolism into organic Se (seleno-amino acids) and partially removed via gaseous volatile Se formation. Furthermore, filter-feeding brine shrimp that accumulated this organic Se were removed by net harvest. Thriving in this engineered pond system, brine shrimp ( Artemia franciscana Kellogg) and brine fly (Ephydridae sp.) have major ecological relevance as important food sources for large populations of waterfowl, breeding, and migratory shore birds. This aquatic ecosystem was an ideal model for study because it mimics trophic interactions in a Se polluted wetland. Inorganic selenate in drainage water was metabolized differently in microalgae, bacteria, and diatoms where it was accumulated and reduced into various inorganic forms (selenite, selenide, or elemental Se) or partially incorporated into organic Se mainly as selenomethionine. Brine shrimp and brine fly larva then bioaccumulated Se from ingesting aquatic microorganisms and further metabolized Se predominately into organic Se forms. Importantly, adult brine flies, which hatched from aquatic larva, bioaccumulated the highest Se concentrations of all organisms tested.

Successful treatment of an MTBE-impacted aquifer using a bioreactor self-colonized by native aquifer bacteria

A field-scale fixed bed bioreactor was used to successfully treat an MTBE-contaminated aquifer in North Hollywood, CA without requiring inoculation with introduced bacteria. Native bacteria from the MTBE-impacted aquifer rapidly colonized the bioreactor, entering the bioreactor in the contaminated groundwater pumped from the site, and biodegraded MTBE with greater than 99 % removal efficiency. DNA sequencing of the 16S rRNA gene identified MTBE-degrading bacteria Methylibium petroleiphilum in the bioreactor. Quantitative PCR showed M. petroleiphilum enriched by three orders of magnitude in the bioreactor above densities pre-existing in the groundwater. Because treatment was carried out by indigenous rather than introduced organisms, regulatory approval was obtained for implementation of a full-scale bioreactor to continue treatment of the aquifer. In addition, after confirmation of MTBE removal in the bioreactor to below maximum contaminant limit levels (MCL; MTBE = 5 μg L(-1)), treated water was approved for reinjection back into the aquifer rather than requiring discharge to a water treatment system. This is the first treatment system in California to be approved for reinjection of biologically treated effluent into a drinking water aquifer. This study demonstrated the potential for using native microbial communities already present in the aquifer as an inoculum for ex-situ bioreactors, circumventing the need to establish non-native, non-acclimated and potentially costly inoculants. Understanding and harnessing the metabolic potential of native organisms circumvents some of the issues associated with introducing non-native organisms into drinking water aquifers, and can provide a low-cost and efficient remediation technology that can streamline future bioremediation approval processes.

To duckweeds (Landoltia punctata), nanoparticulate copper oxide is more inhibitory than the soluble copper in the bulk solution

CuO nanoparticles (CuO-NP) were synthesized in a hydrogen diffusion flame. Particle size and morphology were characterized using scanning mobility particle sizing, Brunauer-Emmett-Teller analysis, dynamic light scattering, and transmission electron microscopy. The solubility of CuO-NP varied with both pH and presence of other ions. CuO-NP and comparable doses of soluble Cu were applied to duckweeds, Landoltia punctata. Growth was inhibited 50% by either 0.6 mg L(-1) soluble copper or by 1.0 mg L(-1) CuO-NP that released only 0.16 mg L(-1) soluble Cu into growth medium. A significant decrease of chlorophyll was observed in plants stressed by 1.0 mg L(-1) CuO-NP, but not in the comparable 0.2 mg L(-1) soluble Cu treatment. The Cu content of fronds exposed to CuO-NP is four times higher than in fronds exposed to an equivalent dose of soluble copper, and this is enough to explain the inhibitory effects on growth and chlorophyll content.

Mathematical model of Chlorella minutissima UTEX2341 growth and lipid production under photoheterotrophic fermentation conditions

To reduce the cost of algal biomass production, mathematical model was developed for the first time to describe microalgae growth, lipid production and glycerin consumption under photoheterotrophic conditions based on logistic, Luedeking-Piret and Luedeking-Piret-like equations. All experiments were conducted in a 2 L batch reactor without considering CO(2) effect on algae's growth and lipid production. Biomass and lipid production increased with glycerin as carbon source and were well described by the logistic and Luedeking-Piret equations respectively. Model predictions were in satisfactory agreement with measured data and the mode of lipid production was growth-associated. Sensitivity analysis was applied to examine the effects of certain important parameters on model performance. Results showed that S(0), the initial concentration of glycerin, was the most significant factor for algae growth and lipid production. This model is applicable for prediction of other single cell algal species but model testing is recommended before scaling up the fermentation of process.

Effect of nitrate, acetate, and hydrogen on native perchlorate-reducing microbial communities and their activity in vadose soil

The effect of nitrate, acetate, and hydrogen on native perchlorate-reducing bacteria (PRB) was examined by conducting microcosm tests using vadose soil collected from a perchlorate-contaminated site. The rate of perchlorate reduction was enhanced by hydrogen amendment and inhibited by acetate amendment, compared with unamendment. Nitrate was reduced before perchlorate in all amendments. In hydrogen-amended and unamended soils, nitrate delayed perchlorate reduction, suggesting that the PRB preferentially use nitrate as an electron acceptor. In contrast, nitrate eliminated the inhibitory effect of acetate amendment on perchlorate reduction and increased the rate and the extent, possibly because the preceding nitrate reduction/denitrification decreased the acetate concentration that was inhibitory to the native PRB. In hydrogen-amended and unamended soils, perchlorate reductase gene (pcrA) copies, representing PRB densities, increased with either perchlorate or nitrate reduction, suggesting that either perchlorate or nitrate stimulates the growth of the PRB. In contrast, in acetate-amended soil pcrA increased only when perchlorate was depleted: a large portion of the PRB may have not utilized nitrate in this amendment. Nitrate addition did not alter the distribution of the dominant pcrA clones in hydrogen-amended soil, likely because of the functional redundancy of PRB as nitrate-reducers/denitrifiers, whereas acetate selected different pcrA clones from those with hydrogen amendment.

Magnetic scanometric DNA microarray detection of methyl tertiary butyl ether degrading bacteria for environmental monitoring

A magnetoresistive biosensing platform based on a single magnetic tunnel junction (MTJ) scanning probe and DNA microarrays labeled with magnetic particles has been developed to provide an inexpensive, sensitive and reliable detection of DNA. The biosensing platform was demonstrated on a DNA microarray assay for quantifying bacteria capable of degrading methyl tertiary butyl ether (MTBE), where concentrations as low as 10 pM were detectable. Synthetic probe bacterial DNA was immobilized on a microarray glass slide surface, hybridized with the 48 base pair long biotinylated target DNA and subsequently incubated with streptavidin-coated 2.8 μm diameter magnetic particles. The biosensing platform then makes use of a micron-sized MTJ sensor that was raster scanned across a 3 mm by 5 mm glass slide area to capture the stray magnetic field from the tagged DNA and extract two dimensional magnetic field images of the microarray. The magnetic field output is then averaged over each 100 μm diameter DNA array spot to extract the magnetic spot intensity, analogous to the fluorescence spot intensity used in conventional optical scanners. The magnetic scanning result is compared with results from a commercial laser scanner and particle coverage optical counting to demonstrate the dynamic range and linear sensitivity of the biosensing platform as a potentially inexpensive, sensitive and portable alternative for DNA microarray detection for field applications.

Quantitative gene monitoring of microbial tetracycline resistance using magnetic luminescent nanoparticles

A magnetic/luminescent nanoparticles (MLNPs) based DNA hybridization method was developed for quantitative monitoring of antibiotic resistance genes and gene-expression in environmental samples. Manipulation of magnetic field enabled the separation of the MLNPs-DNA hybrids from the solution and the fluorescence of MLNPs normalized the quantity of target DNA. In our newly developed MLNPs-DNA assay, linear standard curves (R(2) = 0.99) of target gene was determined with the detection limit of 620 gene copies. The potential risk of increased bacterial antibiotic resistance was assessed by quantitative monitoring of tetracycline resistance (i.e., tetQ gene) in wastewater microcosms. The gene abundance and its expression showed a significant increase of tetQ gene copies with the addition of tetracycline, triclosan (TCS), or triclocarban (TCC). A real-time PCR assay was employed to verify the quantification capability of the MLNPs-DNA assay and accordingly both assays have shown strong correlation (R(2) = 0.93). This non-PCR based MLNPs-DNA assay has demonstrated its potential for gene quantification via a rapid, simple, and high throughput platform and its novel use of internal calibration standards.

Luminescent lanthanide nanoparticles as labels in DNA microarrays for quantification of methyl tertiary butyl ether degrading bacteria

We report application of lanthanide nanoparticles for DNA quantification in a microarray platform as a substitute for conventional organic fluorophores. A non-PCR based DNA microarray assay for quantifying bacteria capable of biodegrading methyl tertiary-butyl ether (MTBE) was demonstrated. Probe DNA was immobilized on a glass surface, hybridized with biotinylated target DNA and subsequently incubated with Neutravidin-biofunctionalized nanoparticles. The fluorescence spot intensities, measured by a commercial laser scanner, show a linear relationship (R2 = 0.98) with bacterial 16S rDNA over a range of target DNA concentrations, while the background fluorescence remained low. In addition, nanoparticles fluorescence shows a stronger intensity than Quasar570 (Cy3). Present sensitivity of the assay is 10 pM of target DNA. The selectivity of the DNA-nanoparticle-probes to discriminate a non-target DNA with two base pairs mismatch in the 16S rDNA gene sequence was shown. The use of Eu:Gd2O3 nanoparticles as biolabels provides a relatively non-toxic, inexpensive, rapid and sensitive alternative to the materials currently used in DNA microarrays.

Effects of arbuscular mycorrhizas on ammonia oxidizing bacteria in an organic farm soil

Arbuscular mycorrhizal fungi (AMF) are potentially important in nutrient cycling in agricultural soils and particularly in soils managed for organic production; little is known, however, about the interrelationships between AMF and other members of soil microbial communities. Ammonia oxidizing bacteria (AOB) are a trophic group of bacteria having an enormous impact on nitrogen availability in soils and are expected to be influenced by the presence of AMF. In a field study, we utilized a unique genetic system comprised of a mycorrhiza defective tomato mutant (named rmc) and its mycorrhiza wild-type progenitor (named 76RMYC+). We examined the effect of AMF by comparing AOB community composition and populations in soil containing roots of the two tomato genotypes in an organically managed soil. Responses of AOB to soil N and P amendments were also studied in the same experiment. Phylogenetic analysis of cloned AOB sequences, derived from excised denaturing gradient gel electrophoresis (DGGE) bands, revealed that the organic farm soil supported a diverse yet stable AOB community, which was neither influenced by mycorrhizal colonization of roots nor by N and P addition to the soil. Real-time TaqMan polymerase chain reaction (PCR) was used to quantify AOB population sizes and showed no difference between any of the treatments. An alternative real-time PCR protocol for quantification of AOB utilizing SYBR green yielded similar results as the TaqMan real-time PCR method, although with slightly lower resolution. This alternative method is advantageous in not requiring the detailed background information about AOB community composition required for adaptation of the TaqMan system for a new soil.

Quantitative DNA hybridization in solution using magnetic/luminescent core–shell nanoparticles

Nanoscale magnetic/luminescent core-shell particles were used for DNA quantification in a hybridization-in-solution approach. We demonstrated a rapid, simple, and non-polymerase chain reaction-based DNA hybridization-in-solution assay for quantifying bacteria capable of biodegrading methyl tertiary-butyl ether. Fe3O4/Eu:Gd2O3 core-shell nanoparticles synthesized by spray pyrolysis were biofunctionalized with NeutrAvidin. Following immobilization of a biotinylated probe DNA on the particles' surfaces via passive adsorption, target DNA labeled with fluorescein isothiocyanate was hybridized with probe DNA. The hybridized DNA complex was separated from solution with a magnet, while nonhybridized DNA remained in solution. The normalized fluorescence (fluorescein isothiocyanate/nanoparticles) measured with a spectrofluorometer indicated a linear quantification (R(2)=0.98) of the target bacterial 16 S rDNA. The rate of hybridization increased concurrently with the target DNA concentration. In addition, this approach differentiated between the signal outputs from perfectly complementary target and two-base mismatched target DNA in a range of concentrations, showing the specificity of the assay and the possibility for environmental applications.

Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel oxygenates methyl tert-butyl ether and ethanol

High-density whole-genome cDNA microarrays were used to investigate substrate-dependent gene expression of Methylibium petroleiphilum PM1, one of the best-characterized aerobic methyl tert-butyl ether (MTBE)-degrading bacteria. Differential gene expression profiling was conducted with PM1 grown on MTBE and ethanol as sole carbon sources. Based on microarray high scores and protein similarity analysis, an MTBE regulon located on the megaplasmid was identified for further investigation. Putative functions for enzymes encoded in this regulon are described with relevance to the predicted MTBE degradation pathway. A new unique dioxygenase enzyme system that carries out the hydroxylation of tert-butyl alcohol to 2-methyl-2-hydroxy-1-propanol in M. petroleiphilum PM1 was discovered. Hypotheses regarding the acquisition and evolution of MTBE genes as well as the involvement of IS elements in these complex processes were formulated. The pathways for toluene, phenol, and alkane oxidation via toluene monooxygenase, phenol hydroxylase, and propane monooxygenase, respectively, were upregulated in MTBE-grown cells compared to ethanol-grown cells. Four out of nine putative cyclohexanone monooxygenases were also upregulated in MTBE-grown cells. The expression data allowed prediction of several hitherto-unknown enzymes of the upper MTBE degradation pathway in M. petroleiphilum PM1 and aided our understanding of the regulation of metabolic processes that may occur in response to pollutant mixtures and perturbations in the environment.

Whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1

Methylibium petroleiphilum PM1 is a methylotroph distinguished by its ability to completely metabolize the fuel oxygenate methyl tert-butyl ether (MTBE). Strain PM1 also degrades aromatic (benzene, toluene, and xylene) and straight-chain (C(5) to C(12)) hydrocarbons present in petroleum products. Whole-genome analysis of PM1 revealed an approximately 4-Mb circular chromosome and an approximately 600-kb megaplasmid, containing 3,831 and 646 genes, respectively. Aromatic hydrocarbon and alkane degradation, metal resistance, and methylotrophy are encoded on the chromosome. The megaplasmid contains an unusual t-RNA island, numerous insertion sequences, and large repeated elements, including a 40-kb region also present on the chromosome and a 29-kb tandem repeat encoding phosphonate transport and cobalamin biosynthesis. The megaplasmid also codes for alkane degradation and was shown to play an essential role in MTBE degradation through plasmid-curing experiments. Discrepancies between the insertion sequence element distribution patterns, the distributions of best BLASTP hits among major phylogenetic groups, and the G+C contents of the chromosome (69.2%) and plasmid (66%), together with comparative genome hybridization experiments, suggest that the plasmid was recently acquired and apparently carries the genetic information responsible for PM1's ability to degrade MTBE. Comparative genomic hybridization analysis with two PM1-like MTBE-degrading environmental isolates (approximately 99% identical 16S rRNA gene sequences) showed that the plasmid was highly conserved (ca. 99% identical), whereas the chromosomes were too diverse to conduct resequencing analysis. PM1's genome sequence provides a foundation for investigating MTBE biodegradation and exploring the genetic regulation of multiple biodegradation pathways in M. petroleiphilum and other MTBE-degrading beta-proteobacteria.

Application of real-time PCR to study effects of ammonium on population size of ammonia-oxidizing bacteria in soil

Ammonium oxidation by autotrophic ammonia-oxidizing bacteria (AOB) is a key process in agricultural and natural ecosystems and has a large global impact. In the past, the ecology and physiology of AOB were not well understood because these organisms are notoriously difficult to culture. Recent applications of molecular techniques have advanced our knowledge of AOB, but the necessity of using PCR-based techniques has made quantitative measurements difficult. A quantitative real-time PCR assay targeting part of the ammonia-monooxygenase gene (amoA) was developed to estimate AOB population size in soil. This assay has a detection limit of 1.3 x 10(5) cells/g of dry soil. The effect of the ammonium concentration on AOB population density was measured in soil microcosms by applying 0, 1.5, or 7.5 mM ammonium sulfate. AOB population size and ammonium and nitrate concentrations were monitored for 28 days after (NH4)2SO4 application. AOB populations in amended treatments increased from an initial density of approximately 4 x 10(6) cells/g of dry soil to peak values (day 7) of 35 x 10(6) and 66 x 10(6) cells/g of dry soil in the 1.5 and 7.5 mM treatments, respectively. The population size of total bacteria (quantified by real-time PCR with a universal bacterial probe) remained between 0.7 x 10(9) and 2.2 x 10(9) cells/g of soil, regardless of the ammonia concentration. A fertilization experiment was conducted in a tomato field plot to test whether the changes in AOB density observed in microcosms could also be detected in the field. AOB population size increased from 8.9 x 10(6) to 38.0 x 10(6) cells/g of soil by day 39. Generation times were 28 and 52 h in the 1.5 and 7.5 mM treatments, respectively, in the microcosm experiment and 373 h in the ammonium treatment in the field study. Estimated oxidation rates per cell ranged initially from 0.5 to 25.0 fmol of NH4+ h(-1) cell(-1) and decreased with time in both microcosms and the field. Growth yields were 5.6 x 10(6), 17.5 x 10(6), and 1.7 x 10(6) cells/mol of NH4+ in the 1.5 and 7.5 mM microcosm treatments and the field study, respectively. In a second field experiment, AOB population size was significantly greater in annually fertilized versus unfertilized soil, even though the last ammonium application occurred 8 months prior to measurement, suggesting a long-term effect of ammonium fertilization on AOB population size.

Detection and quantification of methyl tert-butyl ether-degrading strain PM1 by real-time TaqMan PCR

The fuel oxygenate methyl tert-butyl ether (MTBE), a widely distributed groundwater contaminant, shows potential for treatment by in situ bioremediation. The bacterial strain PM1 rapidly mineralizes and grows on MTBE in laboratory cultures and can degrade the contaminant when inoculated into groundwater or soil microcosms. We applied the TaqMan quantitative PCR method to detect and quantify strain PM1 in laboratory and field samples. Specific primers and probes were designed for the 16S ribosomal DNA region, and specificity of the primers was confirmed with DNA from 15 related bacterial strains. A linear relationship was measured between the threshold fluorescence (C(T)) value and the quantity of PM1 DNA or PM1 cell density. The detection limit for PM1 TaqMan assay was 2 PM1 cells/ml in pure culture or 180 PM1 cells/ml in a mixture of PM1 with Escherichia coli cells. We could measure PM1 densities in solution culture, groundwater, and sediment samples spiked with PM1 as well as in groundwater collected from an MTBE bioaugmentation field study. In a microcosm biodegradation study, increases in the population density of PM1 corresponded to the rate of removal of MTBE.

Molecular ecological analysis of the succession and diversity of sulfate-reducing bacteria in the mouse gastrointestinal tract

Intestinal sulfate-reducing bacteria (SRB) growth and resultant hydrogen sulfide production may damage the gastrointestinal epithelium and thereby contribute to chronic intestinal disorders. However, the ecology and phylogenetic diversity of intestinal dissimilatory SRB populations are poorly understood, and endogenous or exogenous sources of available sulfate are not well defined. The succession of intestinal SRB was therefore compared in inbred C57BL/6J mice using a PCR-based metabolic molecular ecology (MME) approach that targets a conserved region of subunit A of the adenosine-5'-phosphosulfate (APS) reductase gene. The APS reductase-based MME strategy revealed intestinal SRB in the stomach and small intestine of 1-, 4-, and 7-day-old mice and throughout the gastrointestinal tract of 14-, 21-, 30-, 60-, and 90-day-old mice. Phylogenetic analysis of APS reductase amplicons obtained from the stomach, middle small intestine, and cecum of neonatal mice revealed that Desulfotomaculum spp. may be a predominant SRB group in the neonatal mouse intestine. Dot blot hybridizations with SRB-specific 16S ribosomal DNA (rDNA) probes demonstrated SRB colonization of the cecum and colon pre- and postweaning and colonization of the stomach and small intestine of mature mice only. The 16S rDNA hybridization data further demonstrated that SRB populations were most numerous in intestinal regions harboring sulfomucin-containing goblet cells, regardless of age. Reverse transcriptase PCR analysis demonstrated APS reductase mRNA expression in all intestinal segments of 30-day-old mice, including the stomach. These results demonstrate for the first time widespread colonization of the mouse intestine by dissimilatory SRB and evidence of spatial-specific SRB populations and sulfomucin patterns along the gastrointestinal tract.

Desulfotomaculum genus- and subgenus-specific 16S rRNA hybridization probes for environmental studies

Based on comparative analysis of 16S rRNA sequences and the recently established phylogeny of the genus Desulfotomaculum, a set of phylogenetically nested hybridization probes was developed and characterized. A genus-specific probe targets all known Desulfotomaculum species (with the exception of Desulfotomaculum acetoxidans), and five specific probes target subclusters within the Desulfotomaculum genus. The dissociation temperature of each probe was determined experimentally. Probe specificities were verified through hybridizations with pure culture rRNA isolated from a wide variety of target and non-target organisms and through an evaluation of probe 'nesting' using samples obtained from four different environments. Fixation and hybridization conditions for fluorescence in situ hybridizations were also optimized. The probes were used in quantitative membrane hybridizations to determine the abundance of Desulfotomaculum species in thermophilic anaerobic digesters, in soil, in human faeces and in pig colon samples. Desulfotomaculum rRNA accounted for 0.3-2.1% of the total rRNA in the digesters, 2.6-6.6% in soil, 1.5-3.3% in human faeces and 2.5-6.2% in pig colon samples.