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.

Study of microbial communities and environmental parameters of seawater collected from three Tunisian fishing harbors in Kerkennah Islands: Statistical analysis of the temporal and spatial dynamics.

Surface seawater, collected from three fishing harbors during different seasons of the years 2015, 2016 and 2017, were assessed for physico-chemical analyses. Results showed that seawater was mainly polluted by hydrocarbons and some heavy metals. Microbial communities' composition and abundance in the studied harbors were performed using molecular approaches. SSCP analysis indicated the presence of Bacteria, Archaea and Eucarya, with dominance of the bacterial domain. Illumina Miseq analysis revealed that the majority of the sequences were affiliated with Bacteria whereas Archaea were detected at low relative abundance. The bacterial community, dominated by Proteobacteria, Bacteroidetes, Planctomycetes, Cyanobacteria, Firmicutes, Actinobacteria and Chloroflexi phyla, are known to be involved in a variety of biodegradation/biotransformation processes including hydrocarbons degradation and heavy metals resistance. The main objectives of this study are to assess, for the first time, the organic/inorganic pollution in surface seawater of Kerkennah Islands harbors, and to explore the potential of next generation marine microbiome monitoring to achieve the planning coastal managing strategies worldwide.

Screening and Application of Ligninolytic Microbial Consortia to Enhance Aerobic Degradation of Solid Digestate.

Recirculation of solid digestate through digesters has been demonstrated to be a potential simple strategy to increase continuous stirred-tank reactor biogas plant efficiency. This study extended this earlier work and investigated solid digestate post-treatment using liquid isolated ligninolytic aerobic consortia in order to increase methane recovery during the recirculation. Based on sampling in several natural environments, an enrichment and selection method was implemented using a Lab-scale Automated and Multiplexed (an)Aerobic Chemostat system to generate ligninolytic aerobic consortia. Then, obtained consortia were further cultivated under liquid form in bottles. Chitinophagia bacteria and Sordariomycetes fungi were the two dominant classes of microorganisms enriched through these steps. Finally, these consortia where mixed with the solid digestate before a short-term aerobic post-treatment. However, consortia addition did not increase the efficiency of aerobic post-treatment of solid digestate and lower methane yields were obtained in comparison to the untreated control. The main reason identified is the respiration of easily degradable fractions (e.g., sugars, proteins, amorphous cellulose) by the selected consortia. Thus, this paper highlights the difficulties of constraining microbial consortia to sole ligninolytic activities on complex feedstock, such as solid digestate, that does not only contain lignocellulosic structures.

Effects of the chlorination and pressure flushing of drippers fed by reclaimed wastewater on biofouling.

Milli-channel baffle labyrinths are widely used in drip irrigation systems. They induce a pressure drop enabling drip irrigation. However, with a section thickness that is measured in mm2, they are sensitive to clogging, which reduces the performance and service life of a drip irrigation system. The impact of chlorination (1.5 ppm of free chlorine during 1 h application) and pressure flushing (0.18 MPa) on the biofouling of non-pressure-compensating drippers, fed by real reclaimed wastewater, was studied at lab scale using optical coherence tomography. The effect of these treatments on microbial composition (bacteria and eukaryotes) was also investigated by High-throughput DNA sequencing. Biofouling was mainly observed in the inlet, outlet and return areas of the milli-labyrinth channel from drippers. Chlorination reduced biofilm development, particularly in the mainstream of the milli-labyrinth channel, and it was more efficient when combined with pressure flushing. Moreover, chlorination was more efficient in maintaining water distribution uniformity (CU < 95% compared to less than 85% for unchlorinated lines). It reduced more efficiently the bacterial concentration (≈1 log) and the diversity of the bacterial community in the dripper biofilms compared to the pressure flushing method. Chlorination significantly modified the microbial communities, promoting chlorine-resistant bacteria such as Comamonadaceae or Azospira. Inversely, several bacterial groups were identified as sensitive to chlorination such as Chloroflexi and Planctomycetes. Nevertheless, one month after stopping the treatments bacterial diversity recovered and the chlorine-sensitive bacteria such as Chloroflexi phylum and the Saprospiraceae, Spirochaetaceae, Christensenellaceae and Hydrogenophilaceae families re-emerged in conjunction with the growth of biofouling, highlighting the resilience of the bacteria originating from drippers. Based on PCoA analyses, the structure of the bacterial communities still clustered separately from non-chlorinated drippers, showing that the effect of chlorination was still detectable one month after stopping the treatment.

Characterization of the microbial diversity in production waters of mesothermic and geothermic Tunisian oilfields.

The microbial diversity of production waters of five Tunisian oilfields was investigated using Single Strand Conformation Polymorphism (SSCP) technique followed by cloning-sequencing. Dynamics of bacterial populations in production waters collected from four wellheads were also evaluated. For all production water samples collected, DNA from Archaea and Eucarya was not sufficiently abundant to permit detection rRNA genes from these groups by PCR-SSCP. In contrast, the bacterial rRNA genes were detected in all samples, except for samples from DOULEB12 and RAMOURA wells. SSCP profiles attested that two of the studied geothermic wells (ASHTART47 and ASHTART48) had shown a clear change over time, whereas a stable diversity was found with the mesophilic DOULEB well (DL3). PCR amplification of rRNA genes was unsuccessful with samples from DOULEB (DL12) at all three sampling time. The bacterial diversity present in production waters collected from pipelines of SERCINA and LITAYEM oilfields was high, while production waters collected from wellheads (ASHTART and DOULEB) exhibited lower diversity. The partial study of the biodiversity showed a dominance of uncultured bacteria and Pseudomonas genus (class of the Gammaproteobacteria) in three of the studied oilfields (ASHTART47, ASHTART48 and DOULEB3). However, for LITAYEM oilfield, a significant dominance of 5 phyla (Proteobacteria, Thermotogae, Firmicutes, Synergistetes, Bacteroidetes) was shown. Our study gives a real picture of the microbiology of some Tunisian oilfield production waters and shows that some of the sequenced bacterial clones have a great similarity to previous sequenced clones described from other oilfields all over the world, indicating that these ecosystems harbour specific microbial communities. These findings can be considered as an indirect indication of the indigenous origin of these clones.

Selective microbial aerosolization in biogas demonstrated by quantitative PCR.

Aerosolization of Bacteria, Archaea, Synergistes, Staphylococcus spp. and Propionibacterium acnes was investigated in situ with quantitative real-time PCR of DNA isolated from sludge and biogases of anaerobic digesters. The data revealed that in biogas, Staphylococcus spp. and P. acnes were, respectively, aerosolized 30 and 220 times more and Archaea and Synergistes, respectively, 8 and 20 times less aerosolized than Bacteria. This is the first demonstration of selective microbial aerosolization for anaerobic digestors microorganisms. This study illustrates the fact that some microbial groups, such as opportunistic pathogens, are more susceptible to be aerosolized, since they use air as a dissemination vector, and that this has to be taken in account when up-grading biogas into natural gas networks.

Diversity of bacteria and fungi in aerosols during screening in a green waste composting plant.

This article outlines a comprehensive analysis of the microbial diversity of aerosols produced during screening in a green waste composting plant using both culture and molecular techniques. Bacteria, thermophilic actinomycetes and fungi were quantified in the aerosols. The structure of the microbial community was examined using a fingerprint technique and DNA libraries. The results show: (i) the very high diversity of bacteria and fungi in aerosols produced during the composting screening stage, (ii) the low percentage of cultivability for bacteria in aerosols, (iii) the abundance of Thermoactinomyces spp. and Aspergillus spp. in compost aerosols.

Dynamics of Legionella spp. and bacterial populations during the proliferation of L. pneumophila in a cooling tower facility.

The dynamics of Legionella spp. and of dominant bacteria were investigated in water from a cooling tower plant over a 9-month period which included several weeks when Legionella pneumophila proliferated. The structural diversity of both the bacteria and the Legionella spp. was monitored by a fingerprint technique, single-strand conformation polymorphism, and Legionella spp. and L. pneumophila were quantified by real-time quantitative PCR. The structure of the bacterial community did not change over time, but it was perturbed periodically by chemical treatment or biofilm detachment. In contrast, the structure of the Legionella sp. population changed in different periods, its dynamics at times showing stability but also a rapid major shift during the proliferation of L. pneumophila in July. The dynamics of the Legionella spp. and of dominant bacteria were not correlated. In particular, no change in the bacterial community structure was observed during the proliferation of L. pneumophila. Legionella spp. present in the cooling tower system were identified by cloning and sequencing of 16S rRNA genes. A high diversity of Legionella spp. was observed before proliferation, including L. lytica, L. fallonii, and other Legionella-like amoebal pathogen types, along with as-yet-undescribed species. During the proliferation of L. pneumophila, Legionella sp. diversity decreased significantly, L. fallonii and L. pneumophila being the main species recovered.