Decontamination of 16S rRNA gene amplicon sequence datasets based on bacterial load assessment by qPCR

BACKGROUND

Identification of unexpected taxa in 16S rRNA surveys of low-density microbiota, diluted mock communities and cultures demonstrated that a variable fraction of sequence reads originated from exogenous DNA. The sources of these contaminants are reagents used in DNA extraction, PCR, and next-generation sequencing library preparation, and human (skin, oral and respiratory) microbiota from the investigators.

RESULTS

For in silico removal of reagent contaminants, a pipeline was used which combines the relative abundance of operational taxonomic units (OTUs) in V3-4 16S rRNA gene amplicon datasets with bacterial DNA quantification based on qPCR targeting of the V3 segment of the 16S rRNA gene. Serially diluted cultures of Escherichia coli and Staphylococcus aureus were used for 16S rDNA profiling, and DNA from each of these species was used as a qPCR standard. OTUs assigned to Escherichia or Staphylococcus were virtually unaffected by the decontamination procedure, whereas OTUs from Pseudomonas, which is a major reagent contaminant, were completely or nearly completely removed. The decontamination procedure also attenuated the trend of increase in OTU richness in serially diluted cultures.

CONCLUSIONS

Removal of contaminant sequences derived from reagents based on use of qPCR data may improve taxonomic representation in samples with low DNA concentration. Using the described pipeline, OTUs derived from cross-contamination of negative extraction controls were not recognized as contaminants and not removed from the sample dataset.

Into the deep: Evaluation of SourceTracker for assessment of faecal contamination of coastal waters

Faecal contamination of recreational waters is an increasing global health concern. Tracing the source of the contaminant is a vital step towards mitigation and disease prevention. Total 16S rRNA amplicon data for a specific environment (faeces, water, soil) and computational tools such as the Markov-Chain Monte Carlo based SourceTracker can be applied to microbial source tracking (MST) and attribution studies. The current study applied artificial and in-laboratory derived bacterial communities to define the potential and limitations associated with the use of SourceTracker, prior to its application for faecal source tracking at three recreational beaches near Port Phillip Bay (Victoria, Australia). The results demonstrated that at minimum multiple model runs of the SourceTracker modelling tool (i.e. technical replicates) were required to identify potential false positive predictions. The calculation of relative standard deviations (RSDs) for each attributed source improved overall predictive confidence in the results. In general, default parameter settings provided high sensitivity, specificity, accuracy and precision. Application of SourceTracker to recreational beach samples identified treated effluent as major source of human-derived faecal contamination, present in 69% of samples. Site-specific sources, such as raw sewage, stormwater and bacterial populations associated with the Yarra River estuary were also identified. Rainfall and associated sand resuspension at each location correlated with observed human faecal indicators. The results of the optimised SourceTracker analysis suggests that local sources of contamination have the greatest effect on recreational coastal water quality.

Proteolytic bacterial dominance in a full-scale municipal solid waste anaerobic reactor assessed by 454 pyrosequencing technology

Biomethanization entails a good means to reduce the organic fraction (OF) derived from municipal solid wastes (MSW). The bacterial diversity of a full scale MSW anaerobic reactor located in Madrid (Spain) was investigated using high-throughput 454 pyrosequencing. Even though the proteolytic bacteria prevailed throughout all of the process, community shifts were observed from the start-up to the steady-state conditions, with an increasing biodiversity displayed over time. The Bacteroidetes and the Firmicutes were the majority phyla: 55.1 and 40.2% (start-up) and 18.7 and 78.7 (steady-state) of the total reads. The system's lack of evenness remains noteworthy as the sequences affiliated to the proteolytic non-saccharolytic Proteiniphylum, Gallicola and Fastidiosipila genera, together with the saccharolytic Saccharofermentans, were predominant on the system and this predominance appears to correlate with the presence of a high ammonium concentration. The 454 pyrosequencing revealed a great diversity of rare organisms which seemingly do not sustain any metabolic roles in the course of the OF-MSW degradation. However, this scarce and unique microbiota can confer great resilience to the system as a buffer against nutritional and environmental changing conditions, thus opening the door to increase the current knowledge about the bacterial community dynamics taking place during MSW treatment processes.

Bacterial communities and their association with the bio-drying of sewage sludge

Bio-drying is a technology that aims to remove water from a material using the microbial heat originating from organic matter degradation. However, the evolution of bacterial communities that are associated with the drying process has not been researched systematically. This study was performed to investigate the variations of bacterial communities and the relationships among bacterial communities, water evaporation, water generation, and organic matter degradation during the bio-drying of sewage sludge. High-throughput pyrosequencing was used to analyze the bacterial communities, while water evaporation and water generation were determined based on an in situ water vapor monitoring device. The values of water evaporation, water generation, and volatile solids degradation were 412.9 g kg(-1) sewage sludge bio-drying material (SSBM), 65.0 g kg(-1) SSBM, and 70.2 g kg(-1) SSBM, respectively. Rarefaction curves and diversity indices showed that bacterial diversity plummeted after the temperature of the bio-drying pile dramatically increased on d 2, which coincided with a remarkable increase of water evaporation on d 2. Bacterial diversity increased when the pile cooled. During the thermophilic phase, in which Acinetobacter and Bacillus were the dominant genera, the rates of water evaporation, water generation, and VS degradation peaked. These results implied that the elevated temperature reshaped the bacterial communities, which played a key role in water evaporation, and the high temperature also contributed to the effective elimination of pathogens.

Soil Parameters Drive the Structure, Diversity and Metabolic Potentials of the Bacterial Communities Across Temperate Beech Forest Soil Sequences

Soil and climatic conditions as well as land cover and land management have been shown to strongly impact the structure and diversity of the soil bacterial communities. Here, we addressed under a same land cover the potential effect of the edaphic parameters on the soil bacterial communities, excluding potential confounding factors as climate. To do this, we characterized two natural soil sequences occurring in the Montiers experimental site. Spatially distant soil samples were collected below Fagus sylvatica tree stands to assess the effect of soil sequences on the edaphic parameters, as well as the structure and diversity of the bacterial communities. Soil analyses revealed that the two soil sequences were characterized by higher pH and calcium and magnesium contents in the lower plots. Metabolic assays based on Biolog Ecoplates highlighted higher intensity and richness in usable carbon substrates in the lower plots than in the middle and upper plots, although no significant differences occurred in the abundance of bacterial and fungal communities along the soil sequences as assessed using quantitative PCR. Pyrosequencing analysis of 16S ribosomal RNA (rRNA) gene amplicons revealed that Proteobacteria, Acidobacteria and Bacteroidetes were the most abundantly represented phyla. Acidobacteria, Proteobacteria and Chlamydiae were significantly enriched in the most acidic and nutrient-poor soils compared to the Bacteroidetes, which were significantly enriched in the soils presenting the higher pH and nutrient contents. Interestingly, aluminium, nitrogen, calcium, nutrient availability and pH appeared to be the best predictors of the bacterial community structures along the soil sequences.

Aquifer community structure in dependence of lithostratigraphy in groundwater reservoirs

Groundwater microbiology with respect to different host rocks offers new possibilities to describe and map the habitat harboring approximately half of Earths' biomass. The Thuringian Basin (Germany) contains formations of the Permian (Zechstein) and Triassic (Muschelkalk and Buntsandstein) with outcrops and deeper regions at the border and central part. Hydro(geo)chemistry and bacterial community structure of 11 natural springs and 20 groundwater wells were analyzed to define typical patterns for each formation. Widespread were Gammaproteobacteria, while Bacilli were present in all wells. Halotolerant and halophilic taxa were present in Zechstein. The occurrence of specific taxa allowed a clear separation of communities from all three lithostratigraphic groups. These specific taxa could be used to follow fluid movement, e.g., from the underlying Zechstein or from nearby saline reservoirs into Buntsandstein aquifers. Thus, we developed a new tool to identify the lithostratigraphic origin of sources in mixed waters. This was verified with entry of surface water, as species not present in the underground Zechstein environments were isolated from the water samples. Thus, our tool shows a higher resolution as compared to hydrochemistry, which is prone to undergo fast dilution if water mixes with other aquifers. Furthermore, the bacteria well adapted to their respective environment showed geographic clustering allowing to differentiate regional aquifers.

Application of urea-agarose gel electrophoresis to select non-redundant 16S rRNAs for taxonomic studies: palladium(II) removal bacteria

The 16S ribosomal RNA (rRNA) gene has been the most commonly used sequence to characterize bacterial communities. The classical approach to obtain gene sequences to study bacterial diversity implies cloning amplicons, selecting clones, and Sanger sequencing cloned fragments. A more recent approach is direct sequencing of millions of genes using massive parallel technologies, allowing a large-scale biodiversity analysis of many samples simultaneously. However, currently, this technique is still expensive when applied to few samples; therefore, the classical approach is still used. Recently, we found a community able to remove 50 mg/L Pd(II). In this work, aiming to identify the bacteria potentially involved in Pd(II) removal, the separation of urea/heat-denatured DNA fragments by urea-agarose gel electrophoresis was applied for the first time to select 16S rRNA-cloned amplicons for taxonomic studies. The major raise in the percentage of bacteria belonging to genus Clostridium sensu stricto from undetected to 21 and 41 %, respectively, for cultures without, with 5 and 50 mg/L Pd(II) accompanying Pd(II) removal point to this taxa as a potential key agent for the bio-recovery of this metal. Despite sulfate-reducing bacteria were not detected, the hypothesis of Pd(II) removal by activity of these bacteria cannot be ruled out because a slight decrease of sulfate concentration of the medium was verified and the formation of PbS precipitates seems to occur. This work also contributes with knowledge about suitable partial 16S rRNA gene regions for taxonomic studies and shows that unidirectional sequencing is enough when Sanger sequencing cloned 16S rRNA genes for taxonomic studies to genus level.

A Greenhouse Assay on the Effect of Applied Urea Amount on the Rhizospheric Soil Bacterial Communities

The rhizospheric bacteria play key role in plant nutrition and growth promotion. The effects of increased nitrogen inputs on plant rhizospheric soils also have impacted on whole soil microbial communities. In this study, we analyzed the effects of applied nitrogen (urea) on rhizospheric bacterial composition and diversity in a greenhouse assay using the high-throughput sequencing technique. To explore the environmental factors driving the abundance, diversity and composition of soil bacterial communities, the relationship between soil variables and the bacterial communities were also analyzed using the mantel test as well as the redundancy analysis. The results revealed significant bacterial diversity changes at different amounts of applied urea, especially between the control treatment and the N fertilized treatments. Mantel tests showed that the bacterial communities were significantly correlated with the soil nitrate nitrogen, available nitrogen, soil pH, ammonium nitrogen and total organic carbon. The present study deepened the understanding about the rhizospheric soil microbial communities under different amounts of applied urea in greenhouse conditions, and our work revealed the environmental factors affecting the abundance, diversity and composition of rhizospheric bacterial communities.

Dynamics of bacterial assemblages and removal of polycyclic aromatic hydrocarbons in oil-contaminated coastal marine sediments subjected to contrasted oxygen regimes

To study the impact of oxygen regimes on the removal of polycylic aromatic hydrocarbons (PAHs) in oil-spill-affected coastal marine sediments, we used a thin-layer incubation method to ensure that the incubated sediment was fully oxic, anoxic, or was influenced by oxic-anoxic switches without sediment stirring. Hydrocarbon content and microbial assemblages were followed during 60 days to determine PAH degradation kinetics and microbial community dynamics according to the oxygenation regimes. The highest PAH removal, with 69 % reduction, was obtained at the end of the experiment under oxic conditions, whereas weaker removals were obtained under oscillating and anoxic conditions (18 and 12 %, respectively). Bacterial community structure during the experiment was determined using a dual 16S rRNA genes/16S rRNA transcripts approach, allowing the characterization of metabolically active bacteria responsible for the functioning of the bacterial community in the contaminated sediment. The shift of the metabolically active bacterial communities showed that the selection of first responders belonged to Pseudomonas spp. and Labrenzia sp. and included an unidentified Deltaproteobacteria-irrespective of the oxygen regime-followed by the selection of late responders adapted to the oxygen regime. A novel unaffiliated phylotype (B38) was highly active during the last stage of the experiment, at which time, the low-molecular-weight (LMW) PAH biodegradation rates were significant for permanent oxic- and oxygen-oscillating conditions, suggesting that this novel phylotype plays an active role during the restoration phase of the studied ecosystem.

Integron diversity in marine environments

Integrons are bacterial genetic elements known to be active vectors of antibiotic resistance among clinical bacteria. They are also found in bacterial communities from natural environments. Although integrons have become especially efficient for bacterial adaptation in the particular context of antibiotic usage, their role in natural environments in other contexts is still unknown. Indeed, most studies have focused on integrons and the spread of antibiotic resistance in freshwater or soil impacted by anthropogenic activities, with only few on marine environments. Notably, integrons show a wider diversity of both gene cassettes and integrase gene in natural environments than in clinical environments, suggesting a general role of integrons in bacterial adaptation. This article reviews the current knowledge on integrons in marine environments. We also present conclusions of our studies on polluted and nonpolluted backgrounds.

Responses of bacterial communities in seagrass sediments to polycyclic aromatic hydrocarbon-induced stress

The seagrass meadows represent one of the highest productive marine ecosystems, and have the great ecological and economic values. Bacteria play important roles in energy flow, nutrient biogeochemical cycle and organic matter turnover in marine ecosystems. The seagrass meadows are experiencing a world-wide decline, and the pollution is one of the main reasons. Polycyclic aromatic hydrocarbons (PAHs) are thought be the most common. Bacterial communities in the seagrass Enhalus acoroides sediments were analyzed for their responses to PAHs induced stress. Dynamics of the composition and abundance of bacterial communities during the incubation period were explored by polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative PCR assay, respectively. Both the incubation time and the PAHs concentration played significant roles in determining the microbial diversity, as reflected by the detected DGGE bands. Analysis of sequencing results showed that the Gammaproteobacteria were dominant in the seagrass sediments, accounting for 61.29 % of all sequenced bands. As PAHs could be used as carbon source for microbes, the species and diversity of the PAH-added groups (group 1 and 2) presented higher Shannon Wiener index than the group CK, with the group 1 showing the highest values almost through the same incubation stage. Patterns of changes in abundance of the three groups over the experiment time were quite different. The bacterial abundance of the group CK and group 2 decreased sharply from 4.15 × 10(11) and 6.37 × 10(11) to 1.17 × 10(10) and 1.07 × 10(10) copies/g from day 2 to 35, respectively while bacterial abundance of group 1 increased significantly from 1.59 × 10(11) copies/g at day 2 to 8.80 × 10(11) copies/g at day 7, and then dropped from day 14 till the end of the incubation. Statistical analysis (UMPGA and PCA) results suggested that the bacterial community were more likely to be affected by the incubation time than the concentration of the PAHs. This study provided the important information about dynamics of bacterial community under the PAHs stress and revealed the high bacterial diversity in sediments of E. acoroides. Investigation results also indicated that microbial community structure in the seagrass sediment were sensible to the PAHs induced stress, and may be used as potential indicators for the PAHs contamination.

Influence of temperature on volatile fatty acid production and microbial community structure during anaerobic fermentation of microalgae

The objectives of this study were to investigate the effect of operating temperature on volatile fatty acids (VFAs) production from microalgal biomass, and to clarify the relationships between VFAs accumulation at different temperatures and the corresponding bacterial communities. The VFA yields were 0.10±0.017, 0.12±0.008, and 0.34±0.009 g/g VS at 35, 45, and 55 °C, respectively. The proportion of acetic acid decreased from 85.6% to 65.8% as operating temperature increased, whereas that of propionic acid increased from near 0% to 15.5% and that of iso-valeric acid remained relatively stable (10.2-11.2%). Bacterial communities at different operating temperatures consisted mostly of the phyla Proteobacteria, Bacteroidetes, and Firmicutes, which can degrade organic compounds effectively. Bacillus sp. was more predominant at 55 °C than at mesophilic temperatures, suggesting that this microorganism contributed significantly to the higher hydrolysis rate and VFA yield at this operating temperature.

Evidence-based recommendations on storing and handling specimens for analyses of insect microbiota

Research on insect microbiota has greatly expanded over the past decade, along with a growing appreciation of the microbial contributions to insect ecology and evolution. Many of these studies use DNA sequencing to characterize the diversity and composition of insect-associated microbial communities. The choice of strategies used for specimen collection, storage, and handling could introduce biases in molecular assessments of insect microbiota, but such potential influences have not been systematically evaluated. Likewise, although it is common practice to surface sterilize insects prior to DNA extraction, it is not known if this time-consuming step has any effect on microbial community analyses. To resolve these methodological unknowns, we conducted an experiment wherein replicate individual insects of four species were stored intact for two months using five different methods—freezing, ethanol, dimethyl sulfoxide (DMSO), cetrimonium bromide (CTAB), and room-temperature storage without preservative—and then subjected to whole-specimen 16S rRNA gene sequencing to assess whether the structure of the insect-associated bacterial communities was impacted by these different storage strategies. Overall, different insect species harbored markedly distinct bacterial communities, a pattern that was highly robust to the method used to store samples. Storage method had little to no effect on assessments of microbiota composition, and the magnitude of the effect differed among the insect species examined. No single method emerged as “best,” i.e., one consistently having the highest similarity in community structure to control specimens, which were not stored prior to homogenization and DNA sequencing. We also found that surface sterilization did not change bacterial community structure as compared to unsterilized insects, presumably due to the vastly greater microbial biomass inside the insect body relative to its surface. We therefore recommend that researchers can use any of the methods tested here, and base their choice according to practical considerations such as prior use, cost, and availability in the field, although we still advise that all samples within a study be handled in an identical manner when possible. We also suggest that, in large-scale molecular studies of hundreds of insect specimens, surface sterilization may not be worth the time and effort involved. This information should help researchers design sampling strategies and will facilitate cross-comparisons and meta-analyses of microbial community data obtained from insect specimens preserved in different ways.

Shifts in the metabolic function of a benthic estuarine microbial community following a single pulse exposure to silver nanoparticles

The increasing use of silver nanoparticles (AgNPs) as a biocidal agent and their potential accumulation in sediments may threaten non-target natural environmental bacterial communities. In this study a microcosm approach was established to investigate the effects of well characterized OECD AgNPs (NM-300) on the function of the bacterial community inhabiting marine estuarine sediments (salinity 31‰). The results showed that a single pulse of NM-300 AgNPs (1 mg L(-1)) that led to sediment concentrations below 6 mg Ag kg(-1) dry weight inhibited the bacterial utilization of environmentally relevant carbon substrates. As a result, the functional diversity changed, but recovered after 120 h under the experimental conditions. This microcosm study suggests that AgNPs under environmentally relevant experimental conditions can negatively affect bacterial function and provides an insight into the understanding of the bacterial community response and resilience to AgNPs exposure, important for informing relevant regulatory measures.

Effect of historical residual hexachlorocyclohexanes and dichlorodiphenyltrichloroethane on bacterial communities in sediment core collected from an estuary in northeastern China by next-generation sequencing

In this study, we evaluate the influence of hexachlorocyclohexanes (HCHs) and dichlorodiphenyltrichloroethane (DDT) on bacterial communities of sediment core from an estuary formed during the period of 1960-2011. Canonical correspondence analysis showed that o,p'-DDT, o,p'-DDD (mitotane), and depth had important influences on bacterial community distributions (p<0.05). Furthermore, our results found variance explained by all variables was 82.9%, while that by o,p'-DDD was 24.4%, and that of o,p'-DDT was 9.8%, indicating that o,p'-DDD had a greater influence on sediment-dwelling bacteria than o,p'-DDT. Also, bacterial diversity was affected and the Shannon index was significantly negatively correlated with total HCHs (r=-0.579, p<0.05) and total DDTs (r=-0.607, p<0.01), respectively. Furthermore, our results showed that Flavobacteria and Clostridia content can be considered an indicator of pollution of HCHs and DDTs in sediment core samples.

Comparison of bacterial succession in green waste composts amended with inorganic fertiliser and wastewater treatment plant sludge

Replacing CAN with DWS resulted in a stable product capable of supporting similar levels of plant growth to conventional compost. Proteobacteria was the dominant phylum detected in both CAN- and DWS-amended composts with Actinobacteria, Bacteroidetes, Firmicutes and Chloroflexi present also. Proteobacteria in both composts negatively correlated with pH, NO3 concentration and temperature, but were positively influenced by NH4 levels. Sphaerobacter was the most abundant genus in the mature phase of both CAN- and DWS-amended composts but bacterial community structure in mature DWS-amended compost appeared more diverse than that present in mature compost made using CAN.

Mapping axillary microbiota responsible for body odours using a culture-independent approach

BACKGROUND

Human axillary odour is commonly attributed to the bacterial degradation of precursors in sweat secretions. To assess the role of bacterial communities in the formation of body odours, we used a culture-independent approach to study axillary skin microbiota and correlated these data with olfactory analysis.

RESULTS

Twenty-four Caucasian male and female volunteers and four assessors showed that the underarms of non-antiperspirant (non-AP) users have significantly higher global sweat odour intensities and harboured on average about 50 times more bacteria than those of AP users. Global sweat odour and odour descriptors sulfury-cat urine and acid-spicy generally increased from the morning to the afternoon sessions. Among non-AP users, male underarm odours were judged higher in intensity with higher fatty and acid-spicy odours and higher bacterial loads. Although the content of odour precursors in underarm secretions varied widely among individuals, males had a higher acid: sulfur precursor ratio than females did. No direct correlations were found between measured precursor concentration and sweat odours. High-throughput sequencing targeting the 16S rRNA genes of underarm bacteria collected from 11 non-AP users (six females and five males) confirmed the strong dominance of the phyla Firmicutes and Actinobacteria, with 96% of sequences assigned to the genera Staphylococcus, Corynebacterium and Propionibacterium. The proportion of several bacterial taxa showed significant variation between males and females. The genera Anaerococcus and Peptoniphilus and the operational taxonomic units (OTUs) from Staphylococcus haemolyticus and the genus Corynebacterium were more represented in males than in females. The genera Corynebacterium and Propionibacterium were correlated and anti-correlated, respectively, with body odours. Within the genus Staphylococcus, different OTUs were either positively or negatively correlated with axillary odour. The relative abundance of five OTUs (three assigned to S. hominis and one each to Corynebacterium tuberculostearicum and Anaerococcus) were positively correlated with at least one underarm olfactory descriptor.

CONCLUSIONS

Positive and negative correlations between bacterial taxa found at the phylum, genus and OTU levels suggest the existence of mutualism and competition among skin bacteria. Such interactions, and the types and quantities of underarm bacteria, affect the formation of body odours. These findings open the possibility of developing new solutions for odour control.

Interactive effects of hypoxia and polybrominated diphenyl ethers (PBDEs) on microbial community assembly in surface marine sediments

Hypoxia alters the oxidation-reduction balance and the biogeochemical processes in sediments, but little is known about its impacts on the microbial community that is responsible for such processes. In this study, we investigated the effects of hypoxia and the ubiquitously dispersed flame-retardant BDE47 on the bacterial communities in marine surface sediments during a 28-days microcosm experiment. Both hypoxia and BDE47 alone significantly altered the bacterial community and reduced the species and genetic diversity. UniFrac analysis revealed that BDE47 selected certain bacterial species and resulted in major community shifts, whereas hypoxia changed the relative abundances of taxa, suggesting slower but nonetheless significant community shifts. These two stressors targeted mostly different taxa, but they both favored Bacteroidetes and suppressed Gammaproteobacteria. Importantly, the impacts of BDE47 on bacterial communities were different under hypoxic and normoxic conditions, highlighting the need to consider risk assessments for BDE47 in a broader context of interaction with hypoxia.

Comparative molecular analysis of bacterial communities inhabiting pristine and polluted with polycyclic aromatic hydrocarbons Black Sea coastal sediments

Molecular analysis was applied to characterize bacterial community structure in sediment samples collected from pristine site and oil-polluted Black Sea harbor. Amplified Ribosomal DNA Restriction Analysis (ARDRA) revealed a high similarity in the restriction patterns of both samples thus not demonstrating the effect of the pollutant on the structure of the bacterial communities. Constructed 16S rRNA gene libraries gave more detailed assessment of members. Results showed that α- and γ-Proteobacteria were dominant in the oil polluted site, whereas the pristine site was characterized by prevalence of Actinobacteria. The biodegradative potential of the adapted bacterial community in the oil-polluted sediments was demonstrated by the presence of the aromatic ring hydroxylating dioxygenase genes.

Insights into the relationship between antimicrobial residues and bacterial populations in a hospital-urban wastewater treatment plant system

The relationship between antimicrobial residues, antibiotic resistance prevalence and bacterial community composition in hospital effluent and in the receiving wastewater treatment plant was studied. Samples from hospital effluent, raw inflow and final effluent of the receiving wastewater treatment plant were characterized for amoxicillin and ciprofloxacin resistance prevalence, content of heavy metals and antimicrobial residues and bacterial community structure, based on 16S rRNA gene PCR-DGGE analysis. The concentration of fluoroquinolones, arsenic and mercury was in general higher in hospital effluent than in raw inflow, while the opposite was observed for tetracyclines, sulfonamides and penicillin G. The prevalence of ciprofloxacin resistance was significantly higher in hospital effluent than in raw inflow. The concentration of antimicrobial residues was observed to be significantly correlated with the prevalence of antibiotic resistant bacteria and with variations in the bacterial community. Hospital effluent was confirmed as a relevant, although not unique, source of antimicrobial residues and antibiotic resistant bacteria to the wastewater treatment plant. Moreover, given the high loads of antibiotic residues and antibiotic resistant bacteria that may occur in hospital effluents, these wastewater habitats may represent useful models to study and predict the impact of antibiotic residues on bacterial communities.

Dynamics of microbial diversity profiles in waters of different qualities. Approximation to an ecological quality indicator

Over the past two decades, the amount of reclaimed water has increased throughout the world to face the current water shortage, and as a consequence there is an increasing interest to develop good indicators of water quality, beyond the traditional fecal indicators. In order to meet this need, in this work the microbial profiles of different wastewater treatment plant effluents, both secondary and tertiary, were studied and compared with water samples from an uncontaminated natural aquifer. Taking into account the most abundant phylogenetic groups found in these water samples, we calculated the Bacteroidetes, Gammaproteobacteria and Nitrospira/Betaproteobacteria (BGN:β) ratio and found significant differences between the mean ratios of the four water qualities. The secondary effluent ratios were never below 1.3 and the tertiary effluent and groundwater ratios were never over 0.85. Furthermore, calculation of this index with previous published data supports our results and indicates that the BGN:β ratio is a possible alternative indicator of water quality.

Changes in tolerance to herbicide toxicity throughout development stages of phototrophic biofilms

Ecotoxicological experiments have been performed in laboratory-scale microcosms to investigate the sensitivity of phototrophic biofilm communities to the alachlor herbicide, in relation to the stages of phototrophic biofilm maturation (age of the phototrophic biofilms) and physical structure (intact biofilm versus recolonization). The phototrophic biofilms were initially cultivated on artificial supports in a prototype rotating annular bioreactor (RAB) with Taylor-Couette type flow under constant operating conditions. Biofilms were collected after 1.6 and 4.4 weeks of culture providing biofilms with different maturation levels, and then exposed to nominal initial alachlor concentration of 10 μg L(-1) in either intact or recolonized biofilms for 15 days in microcosms (mean time-weighted average concentration - TWAC of 5.52 ± 0.74 μg L(-1)). At the end of the exposure period, alachlor effects were monitored by a combination of biomass descriptors (ash-free dry mass - AFDM, chlorophyll a), structural molecular fingerprinting (T-RFLP), carbon utilization spectra (Biolog) and diatom species composition. We found significant effects that in terms of AFDM, alachlor inhibited growth of the intact phototrophic biofilms. No effect of alachlor was observed on diatom composition or functional and structural properties of the bacterial community regardless of whether they were intact or recolonized. The intact three-dimensional structure of the biofilm did not appear to confer protection from the effects of alachlor. Bacterial community structure and biomass level of 4.4 weeks - intact phototrophic biofilms were significantly influenced by the biofilm maturation processes rather than alachlor exposure. The diatom communities which were largely composed of mobile and colonizer life-form populations were not affected by alachlor. This study showed that the effect of alachlor (at initial concentration of 10 μg L(-1) or mean TWAC of 5.52 ± 0.74 μg L(-1)) is mainly limited to biomass reduction without apparent changes in the ecological succession trajectories of bacterial and diatom communities and suggested that carbon utilization spectra of the biofilm are not damaged resulting. These results confirmed the importance of considering the influence of maturation processes or community age when investigating herbicide effects. This is particularly important with regard to the use of phototrophic biofilms as bio-indicators.

A short-term mineral amendment impacts the mineral weathering bacterial communities in an acidic forest soil

Mineral amendment (i.e. calcium, phosphorous, potassium and/or magnesium) is a management practice used in forestry to improve nutrient availability and recover soil fertility, especially in nutrient-poor forest ecosystems. However, whether this amendment can lead to modifications of the soil characteristics and an improvement in tree growth, and its impact on the soil bacterial communities, especially the mineral weathering bacterial communities, remains poorly documented. In this study, we investigated the short-term impact of a mineral amendment on the taxonomic and functional structure of the mineral weathering bacterial communities. To do this, a plantation of four-year old oak (Quercus petraea) trees amended with or without dolomite [CaMg(CO3)2] was established in the experimental forest site of Breuil-Chenue, which is characterized by an acidic soil and a low availability of calcium and magnesium. Three years after amendment, soil samples were used to isolate bacteria as well as to determine the soil characteristics and the metabolic potentials of these soil microbial communities. Based on a bioassay for quantifying the solubilisation of inorganic phosphorous, we demonstrate that the bacterial isolates coming from the non-amended bulk soil were significantly more efficient than those from the amended bulk soil. No difference was observed between the bacterial isolates coming from the amended and non-amended rhizospheres. Notably, the taxonomic analyses revealed a dominance of bacterial isolates belonging to the Burkholderia genus in both samples. Overall, our results suggest that the bioavailability of nutritive cations into soil impacts the distribution and the efficacy of mineral weathering bacterial communities coming from the soil but not those coming from the rhizosphere.