Role of indigenous bacteria in dark fermentation of organic substrates

International audienceHydrogen production by dark fermentation of complex organic substrates, such as biowaste, can naturally take place with indigenous bacteria or by adding an external microbial inoculum issued from various natural environments. This study aims to determine whether indigenous bacteria associated with thermal pretreatment could impact dark fermentation performances. Biochemical hydrogen potential tests were carried out on seven organic substrates. Results showed a strong influence of the indigenous bacteria which are as effective as thermally pretreated exogenous bacteria to produce H2 and metabolites. High abundance in Clostridiales and/or Enterobacteriales was associated with high H2 yield. This study shows that no inoculum nor pretreatment are required to achieve satisfactory dark fermentation performances from organic waste

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

Morphology and community development with experimental time for the three reactors in the first experiment.

<p>The data for the second experiment can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080692#pone.0080692.s006" target="_blank">Figure S6</a>. Treatment periods were shaded where appropriate (panels C-F). Each monochloramine pulse injection is indicated by an arrow. Vertical gray lines mark Mondays. By performing Principal Component and Principal Coordinate Analyses, most of the variability in the data sets could be summarized in the first Principal Component (PC1) for morphology data and the first Principal Co-ordinate Axis (PCoA1) for the community data. More negative values on PC1 (note inverted axis labels) were related to more complex biofilm morphology. Similarly, the higher the value on PCoA1, the more complex was the community structure. Note the inverted axis in panels <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080692#pone-0080692-g003" target="_blank">Figure <b>3</b></a> and S6A, C and E.</p

Experimental and analytical set-up of the reactor system.

<p>(A) The bubble column reactors: Aeration of the reactors served the purpose of providing oxygen, homogenizing the water column and applying a constant shear stress on the biofilm surface. (B) Monochloramine was added daily or weekly to two of the three reactors. (C) Biofilms were sampled by removing individual polyethylene coupons that were glued onto stainless steel rings. The rings were reinserted into the bubble column. On each coupon, biofilm morphology was analyzed by automated quantitative image analysis. From the same coupon, DNA was extracted and bacterial community dynamics were assessed using molecular community fingerprinting.</p

Linear regressions between morphology data (PC1 in Figure 3A, C and E) and community data (PCoA1 in Figure 3B, D and F).

<p>The regressions for the second experiment can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080692#pone.0080692.s007" target="_blank">Figure S7</a>. Only filled circles were considered for the regressions as these data were sampled during the treatment periods (or the entire experiment for the control reactor). Unfilled circles represent data taken before and after the treatment phases.</p

A description of the varying degrees of complexity for biofilm morphology and community structure.

<p>This description is used in the interpretation of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080692#pone-0080692-g003" target="_blank">Figure 3</a>. (A) Slanted view on three stylized biofilms. A biofilms with a simple morphology is seen at the bottom; more complex morphologies are shown towards the top of the image. (B) Three exemplary community fingerprints as CE-SSCP profiles. Simple bacterial communities are dominated by one member, represented by one peak in the fingerprints. With increasing complexity, dominance of peaks in the profiles is less pronounced and peaks are more evenly distributed. The overall number of peaks increases.</p

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

International audienceThe 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