Role of endogenous soil microorganisms in controlling antimicrobial resistance after the exposure to treated wastewater.

The reuse of treated wastewater (TWW) for irrigation appears to be a relevant solution to the challenges of growing water demand and scarcity. However, TWW contains not only micro-pollutants including pharmaceutical residues but also antibiotic resistant bacteria. The reuse of TWW could contribute to the dissemination of antimicrobial resistance in the environment. The purpose of this study was to assess if exogenous bacteria from irrigation waters (TWW or tap water-TP) affect endogenous soil microbial communities (from 2 soils with distinct irrigation history) and key antibiotic resistance gene sul1 and mobile genetic elements intl1 and IS613. Experiments were conducted in microcosms, irrigated in one-shot, and monitored for three months. Results showed that TP or TWW exposure induced a dynamic response of soil microbial communities but with no significant increase of resistance and mobile gene abundances. However, no significant differences were observed between the two water types in the current experimental design. Despite this, the 16S rDNA analysis of the two soils irrigated for two years either with tap water or TWW resulted in soil microbial community differentiation and the identification of biomarkers from Xanthomonadaceae and Planctomycetes families for soils irrigated with TWW. Low-diversity soils were more sensitive to the addition of TWW. Indeed, TWW exposure stimulated the growth of bacterial genera known to be pathogenic, correlating with a sharp increase in the copy number of selected resistance genes (up to 3 logs). These low-diversity soils could thus enable the establishment of exogenous bacteria from TWW which was not observed with native soils. In particular, the emergence of Planctomyces, previously suggested as a biomarker of soil irrigated by TWW, was here demonstrated. Finally, this study showed that water input frequency, initial soil microbial diversity and soil history drive changes within soil endogenous communities and the antibiotic resistance gene pool.

Mechanisms underlying Clostridium pasteurianum's metabolic shift when grown with Geobacter sulfurreducens.

Recently, a study showed that glycerol fermentation by Clostridium pasteurianum could be metabolically redirected when the electroactive bacterium Geobacter sulfurreducens was added in the culture. It was assumed that this metabolic shift of the fermentative species resulted from an interspecies electron transfer. The aim of this study was to find out the mechanisms used for this interaction and how they affect the metabolism of C. pasteurianum. To get insights into the mechanisms involved, several coculture setups and RNA sequencing with differential expression analysis were performed. As a result, a putative interaction model was proposed: G. sulfurreducens produces cobamide molecules that possibly modify C. pasteurianum metabolic pathway at the key enzyme glycerol dehydratase, and affect its vanadium nitrogenase expression. In addition, the results suggested that G. sulfurreducens' electrons could enter C. pasteurianum through its transmembrane flavin-bound polyferredoxin and cellular cytochrome b5-rubredoxin interplay, putatively reinforcing the metabolic shift. Unravelling the mechanisms behind the interaction between fermentative and electroactive bacteria helps to better understand the role of bacterial interactions in fermentation setups. KEY POINTS: • C. pasteurianum-G. sulfurreducens interaction inducing a metabolic shift is mediated • C. pasteurianum's metabolic shift in coculture might be induced by cobamides • Electrons possibly enter C. pasteurianum through a multiflavin polyferredoxin.

Biomethanation processes: new insights on the effect of a high H2 partial pressure on microbial communities.

BACKGROUND: Biomethanation is a promising solution to upgrade the CH4 content in biogas. This process consists in the injection of H2 into an anaerobic digester, using the capacity of indigenous hydrogenotrophic methanogens for converting the injected H2 and the CO2 generated from the anaerobic digestion process into CH4. However, the injection of H2 could cause process disturbances by impacting the microbial communities of the anaerobic digester. Better understanding on how the indigenous microbial community can adapt to high H2 partial pressures is therefore required. RESULTS: Seven microbial inocula issued from industrial bioprocesses treating different types of waste were exposed to a high H2 partial pressure in semi-continuous reactors. After 12 days of operation, even though both CH4 and volatile fatty acids (VFA) were produced as end products, one of them was the main product. Acetate was the most abundant VFA, representing up to 94% of the total VFA production. VFA accumulation strongly anti-correlated with CH4 production according to the source of inoculum. Three clusters of inocula were distinguished: (1) inocula leading to CH4 production, (2) inocula leading to the production of methane and VFA in a low proportion, and (3) inocula leading to the accumulation of mostly VFA, mainly acetate. Interestingly, VFA accumulation was highly correlated to a low proportion of archaea in the inocula, a higher amount of homoacetogens than hydrogenotrophic methanogens and, the absence or the very low abundance in members from the Methanosarcinales order. The best methanogenic performances were obtained when hydrogenotrophic methanogens and Methanosarcina sp. co-dominated all along the operation. CONCLUSIONS: New insights on the microbial community response to high H2 partial pressure are provided in this work. H2 injection in semi-continuous reactors showed a significant impact on microbial communities and their associated metabolic patterns. Hydrogenotrophic methanogens, Methanobacterium sp. or Methanoculleus sp. were highly selected in the reactors, but the presence of co-dominant Methanosarcinales related species were required to produce higher amounts of CH4 than VFA.

Effect of ammonium, electron donor and sulphate transient feeding conditions on sulphidogenesis in sequencing batch bioreactors.

This work aimed to study the effect of transient feeding conditions on sulphidogenesis in 8 sequencing batch bioreactors (SBR). SBR L1 and H1, operated under steady-state conditions were used as the control reactors, while four SBR were tested under transient feeding conditions using moderate (L2 and L3, feast and famine: 2.5 and 0 g SO42-·L-1) and high (H2 and H3, feast and famine: 15 and 0 g SO42-·L-1) loads. The sulphate removal efficiency (RE) was ≥90% in SBR L2, L3 and H1. The NH4+ famine conditions resulted in a higher sulphate RE (≥40% H3) compared to feast conditions (≤20% H2). Besides, the sulphidogenic first-order kinetic constant was 4% larger and the use of electron donor was 16.6% more efficient under NH4+ famine conditions. Sulphidogenesis is robust to transient feeding conditions, but not when applying high loading rates (SBR H2 and H3).

Addition of granular activated carbon and trace elements to favor volatile fatty acid consumption during anaerobic digestion of food waste.

The effect of supplementing granular activated carbon and trace elements on the anaerobic digestion performance of consecutive batch reactors treating food waste was investigated. The results from the first batch suggest that addition of activated carbon favored biomass acclimation, improving acetic acid consumption and enhancing methane production. Adding trace elements allowed a faster consumption of propionic acid. A second batch proved that a synergy existed when activated carbon and trace elements were supplemented simultaneously. The degradation kinetics of propionate oxidation were particularly improved, reducing significantly the batch duration and improving the average methane productivities. Addition of activated carbon favored the growth of archaea and syntrophic bacteria, suggesting that interactions between these microorganisms were enhanced. Interestingly, microbial analyses showed that hydrogenotrophic methanogens were predominant. This study shows for the first time that addition of granular activated carbon and trace elements may be a feasible solution to stabilize food waste anaerobic digestion.

Cooperative growth of Geobacter sulfurreducens and Clostridium pasteurianum with subsequent metabolic shift in glycerol fermentation.

Interspecies electron transfer is a common way to couple metabolic energy balances between different species in mixed culture consortia. Direct interspecies electron transfer (DIET) mechanism has been recently characterised with Geobacter species which couple the electron balance with other species through physical contacts. Using this mechanism could be an efficient and cost-effective way to directly control redox balances in co-culture fermentation. The present study deals with a co-culture of Geobacter sulfurreducens and Clostridium pasteurianum during glycerol fermentation. As a result, it was shown that Geobacter sulfurreducens was able to grow using Clostridium pasteurianum as sole electron acceptor. C. pasteurianum metabolic pattern was significantly altered towards improved 1,3-propanediol and butyrate production (+37% and +38% resp.) at the expense of butanol and ethanol production (-16% and -20% resp.). This metabolic shift was clearly induced by a small electron uptake that represented less than 0.6% of the electrons consumed by C. pasteurianum. A non-linear relationship was found between G. sulfurreducens growth (i.e the electrons transferred between the two species) and the changes in C. pasteurianum metabolite distribution. This study opens up new possibilities for controlling and increasing specificity in mixed culture fermentation.

Influence of process dynamics on the microbial diversity in a nitrifying biofilm reactor: Correlation analysis and simulation study.

For engineers, it is interesting to gain insight in the effect of control strategies on microbial communities, on their turn influencing the process behavior and its stability. This contribution assesses the influence of process dynamics on the microbial community in a biofilm reactor for nitrogen removal, which was controlled according to several strategies aiming at nitrite accumulation. The process dataset, combining conventional chemical and physical data with molecular information, was analyzed through a correlation analysis and in a simulation study. During nitrate formation, an increased nitrogen loading rate (NLR) resulted in a drop of the bulk liquid oxygen concentration without resulting in nitrite accumulation. A biofilm model was able to reproduce the bulk liquid nitrogen concentrations in two periods before and after this increased NLR. As the microbial parameters calibrated for the ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in both periods were different, it was concluded that the increased NLR governed an AOB and NOB population shift. Based on the molecular data, it was assumed that each period was typified by one dominant AOB and probably several subdominant NOB populations. The control strategies for nitrite accumulation influenced the bulk liquid composition by controlling the competition between AOB and NOB. Biotechnol. Bioeng. 2016;113: 1962-1974. © 2016 Wiley Periodicals, Inc.

Biofilm development during the start-up period of anaerobic biofilm reactors: the biofilm Archaea community is highly dependent on the support material.

To evaluate the impact of the nature of the support material on its colonization by a methanogenic consortium, four substrata made of different materials: polyvinyl chloride, 2 polyethylene and polypropylene were tested during the start-up of lab-scale fixed-film reactors. The reactor performances were evaluated and compared together with the analysis of the biofilms. Biofilm growth was quantified and the structure of bacterial and archaeal communities were characterized by molecular fingerprinting profiles (capillary electrophoresis-single strand conformation polymorphism). The composition of the inoculum was shown to have a major impact on the bacterial composition of the biofilm, whatever the nature of the support material or the organic loading rate applied to the reactors during the start-up period. In contrast, the biofilm archaeal populations were independent of the inoculum used but highly dependent on the support material. Supports favouring Archaea colonization, the limiting factor in the overall process, should be preferred.

Disturbance frequency determines morphology and community development in multi-species biofilm at the landscape scale.

Many natural and engineered biofilm systems periodically face disturbances. Here we present how the recovery time of a biofilm between disturbances (expressed as disturbance frequency) shapes the development of morphology and community structure in a multi-species biofilm at the landscape scale. It was hypothesized that a high disturbance frequency favors the development of a stable adapted biofilm system while a low disturbance frequency promotes a dynamic biofilm response. Biofilms were grown in laboratory-scale reactors over a period of 55-70 days and exposed to the biocide monochloramine at two frequencies: daily or weekly pulse injections. One untreated reactor served as control. Biofilm morphology and community structure were followed on comparably large biofilm areas at the landscape scale using automated image analysis (spatial gray level dependence matrices) and community fingerprinting (single-strand conformation polymorphisms). We demonstrated that a weekly disturbed biofilm developed a resilient morphology and community structure. Immediately after the disturbance, the biofilm simplified but recovered its initial complex morphology and community structure between two biocide pulses. In the daily treated reactor, one organism largely dominated a morphologically simple and stable biofilm. Disturbances primarily affected the abundance distribution of already present bacterial taxa but did not promote growth of previously undetected organisms. Our work indicates that disturbances can be used as lever to engineer biofilms by maintaining a biofilm between two developmental states.