Bacterial diversity and community structure of a sub-surface aquifer exposed to realistic low herbicide concentrations

Use of groundwater and reclaimed water for agricultural irrigation: Farmers' practices and attitudes and related environmental and health risks

Agricultural reuse of treated wastewater (TWW) for irrigation is widely practiced. Its conjunctive use with freshwater is becoming more common to guarantee food security, while the rationale behind and its sustainability are quite arguable. The objective of this study is to better understand the drivers of the conjunctive use of TWW and groundwater (GW) in Nabeul region, Tunisia, and the potential environmental and health impacts taking into account farmers' practices and attitudes toward reuse. TWW used for irrigation exhibited relatively high salinity and high microbiological load. GW has a very high salinity. TWW and GW showed low concentrations of heavy metals (Al, Cd, Co, Cu, Cr, Mn, Ni, Pb, and Zn). Concentrations of pharmaceutical compounds were between Limits of Quantification and 13 μg/L. In GW, values were relatively high, especially for caffeine, carbamazepine, ofloxacin, and ketoprofen. Farmers have a low perception of the polluting load of TWW and GW and of their potential long-term impacts on agricultural environment, human health, and agricultural productivity. GW availability has facilitated its conjunctive use with TWW, either to augment water quantity and/or to improve its quality. Despite its low quality, GW timeliness for irrigation was the main driver to guarantee a better yield and quality of produces. Soil microbial community, bacterial biomass, denitrifying potential and carbon oxidation profiles were similar under TWW, GW and their conjunctive use. Though an effect of the sampling period was observed with a high abundance of denitrifying bacteria in the wet season and a low carbon oxidation activity at the end of the dry season. The conjunctive use of TWW and GW is very likely unsustainable from health and environmental perspectives. Balancing farmers' economic profit against the preservation of agricultural activity, linked to cultural and natural heritage, remains one of the challenges for decision-makers and regional stakeholders.

Selective pressure on microbial communities in a drinking water aquifer - Geochemical parameters vs. micropollutants

Groundwater quality is crucial for drinking water production, but groundwater resources are increasingly threatened by contamination with pesticides. As pesticides often occur at micropollutant concentrations, they are unattractive carbon sources for microorganisms and typically remain recalcitrant. Exploring microbial communities in aquifers used for drinking water production is an essential first step towards understanding the fate of micropollutants in groundwater. In this study, we investigated the interaction between groundwater geochemistry, pesticide presence, and microbial communities in an aquifer used for drinking water production. Two groundwater monitoring wells in The Netherlands were sampled in 2014, 2015, and 2016. In both wells, water was sampled from five discrete depths ranging from 13 to 54 m and was analyzed for geochemical parameters, pesticide concentrations and microbial community composition using 16S rRNA gene sequencing and qPCR. Groundwater geochemistry was stable throughout the study period and pesticides were heterogeneously distributed at low concentrations (μg L^-1 range). Microbial community composition was also stable throughout the sampling period. Integration of a unique dataset of chemical and microbial data showed that geochemical parameters and to a lesser extent pesticides exerted selective pressure on microbial communities. Microbial communities in both wells showed similar composition in the deeper aquifer, where pumping results in horizontal flow. This study provides insight into groundwater parameters that shape microbial community composition. This information can contribute to the future implementation of remediation technologies to guarantee safe drinking water production.

The Effect of Syringic Acid and Phenoxy Herbicide 4-chloro-2-methylphenoxyacetic acid (MCPA) on Soil, Rhizosphere, and Plant Endosphere Microbiome

The integration of phytoremediation and biostimulation can improve pollutant removal from the environment. Plant secondary metabolites (PSMs), which are structurally related to xenobiotics, can stimulate the presence of microbial community members, exhibiting specialized functions toward detoxifying, and thus mitigating soil toxicity. In this study, we evaluated the effects of enrichment of 4-chloro-2-methylphenoxyacetic acid (MCPA) contaminated soil (unplanted and zucchini-planted) with syringic acid (SA) on the bacterial community structure in soil, the rhizosphere, and zucchini endosphere. Additionally, we measured the concentration of MCPA in soil and fresh biomass of zucchini. The diversity of bacterial communities differed significantly between the studied compartments (i.e., unplanted soil, rhizospheric soil, and plant endosphere: roots or leaves) and between used treatments (MCPA or/and SA application). The highest diversity indices were observed for unplanted soil and rhizosphere. Although the lowest diversity was observed among leaf endophytes, this community was significantly affected by MCPA or SA: the compounds applied separately favored the growth of Actinobacteria (especially Pseudarthrobacter), while their simultaneous addition promoted the growth of Firmicutes (especially Psychrobacillus). The application of MCPA + SA together lead also to enhanced growth of Pseudomonas, Burkholderia, Sphingomonas, and Pandoraea in the rhizosphere, while SA increased the occurrence of Pseudomonas in leaves. In addition, SA appeared to have a positive influence on the degradative potential of the bacterial communities against MCPA: its addition, followed by zucchini planting, significantly increased the removal of the herbicide (50%) from the soil without affecting, neither positively nor negatively, the plant growth.

Side Effects of Pesticides and Metabolites in Groundwater: Impact on Denitrification

The impact of two pesticides (S-metolachlor and propiconazole) and their respective main metabolites (ESA-metolachlor and 1,2,4-triazole) on bacterial denitrification in groundwater was studied. For this, the denitrification activity and the bacterial diversity of a microbial community sampled from a nitrate-contaminated groundwater were monitored during 20 days in lab experiments in the presence or absence of pesticides or metabolites at 2 or 10 μg/L. The kinetics of nitrate reduction along with nitrite and N₂O production all suggested that S-metolachlor had no or only little impact, whereas its metabolite ESA-metolachlor inhibited denitrification by 65% at 10 μg/L. Propiconazole and 1,2,4-triazole also inhibited denitrification at both concentrations, but to a lesser extent (29–38%) than ESA-metolachlor. When inhibition occurred, pesticides affected the reduction of nitrate into nitrite step. However, no significant differences were detected on the abundance of nitrate reductase narG and napA genes, suggesting an impact of pesticides/metabolites at the protein level rather than on denitrifying bacteria abundance. 16S rRNA gene Illumina sequencing indicated no major modification of bacterial diversity in the presence or absence of pesticides/metabolites, except for ESA-metolachlor and propiconazole at 10 μg/L that tended to increase or decrease Shannon and InvSimpson indices, respectively. General growth parameters suggested no impact of pesticides, except for propiconazole at 10 μg/L that partially inhibited acetate uptake and induced a decrease in microbial biomass. In conclusion, pesticides and metabolites can have side effects at environmental concentrations on microbial denitrification in groundwater and may thus affect ecosystem services based on microbial activities.

Augmentation of Granular Anaerobic Sludge with Algalytic Bacteria Enhances Methane Production from Microalgal Biomass

The efficiency of anaerobic digestion relies upon activity of the inoculum converting organic substrate into biogas. Often, metabolic capacity of the inoculum needs to be augmented with new capabilities to accommodate changes in the substrate feed composition. However, bioaugmentation is not a widely used strategy possibly due to the lack of studies demonstrating successful applications. This study describes the bioaugmentation of granular anaerobic sludge digesting mixed algal biomass in batch-scale reactors. The addition of an algalytic bacterial mixture to the granular consortium increased methane yield by 11%. This study also investigated changes in the microbial 16SrRNA composition of the augmented and non-augmented granular inoculum, which demonstrates a significant change in the hydrolytic microbial community. Overall, the studies’ results aim to provide a feasible checklist to assess the success rates of bioaugmentation of anaerobic digestion applications.

Toward Integrative Bacterial Monitoring of Metolachlor Toxicity in Groundwater

Common herbicides such as metolachlor (MET), and their transformation products, are frequently detected in groundwater worldwide. Little is known about the response of groundwater bacterial communities to herbicide exposure, and its potential use for ecotoxicological assessment. The response of bacterial communities exposed to different levels of MET from the Ariège alluvial aquifer (Southwest of France) was investigated in situ and in laboratory experiments. Variations in both chemistry and bacterial communities were observed in groundwater, but T-RFLP analysis did not allow to uncover a pesticide-specific effect on endogenous bacterial communities. To circumvent issues of hydrogeochemical and seasonal variations in situ, groundwater samples from two monitoring wells of the Ariège aquifer with contrasting records of pesticide contamination were exposed to different levels of MET in laboratory experiments. The standard Microtox® acute toxicity assay did not indicate toxic effects of MET, even at 5 mg L-1 (i.e., 1000-fold higher than in contaminated groundwater). Analysis of MET transformation products and compound-specific isotope analysis (CSIA) in laboratory experiments demonstrated MET biodegradation but did not correlate with MET exposure. High-throughput sequencing analysis (Illumina MiSeq) of bacterial communities based on amplicons of the 16S rRNA gene revealed that bacterial community differed mainly by groundwater origin rather than by its response to MET exposure. OTUs correlating with MET addition ranged between 0.4 to 3.6% of the total. Predictive analysis of bacterial functions impacted by pesticides using PICRUSt suggested only minor changes in bacterial functions with increasing MET exposure. Taken together, results highlight MET biodegradation in groundwater, and the potential use of bacterial communities as sensitive indicators of herbicide contamination in aquifers. Although detected effects of MET on groundwater bacterial communities were modest, this study illustrates the potential of integrating DNA- and isotopic analysis-based approaches to improve ecotoxicological assessment of pesticide-contaminated aquifers. GRAPHICAL ABSTRACTAn integrative approach was develop to investigate in situ and in laboratory experiments the response of bacterial communities exposed to different levels of MET from the Ariége alluvial aquifer (Southwest of France).

Qualitative Analysis of Microbial Dynamics during Anaerobic Digestion of Microalgal Biomass in a UASB Reactor

Anaerobic digestion (AD) is a microbiologically coordinated process with dynamic relationships between bacterial players. Current understanding of dynamic changes in the bacterial composition during the AD process is incomplete. The objective of this research was to assess changes in bacterial community composition that coordinates with anaerobic codigestion of microalgal biomass cultivated on municipal wastewater. An upflow anaerobic sludge blanket reactor was used to achieve high rates of microalgae decomposition and biogas production. Samples of the sludge were collected throughout AD and extracted DNA was subjected to next-generation sequencing using methanogen mcrA gene specific and universal bacterial primers. Analysis of the data revealed that samples taken at different stages of AD had varying bacterial composition. A group consisting of Bacteroidales, Pseudomonadales, and Enterobacteriales was identified to be putatively responsible for the hydrolysis of microalgal biomass. The methanogenesis phase was dominated by Methanosarcina mazei. Results of observed changes in the composition of microbial communities during AD can be used as a road map to stimulate key bacterial species identified at each phase of AD to increase yield of biogas and rate of substrate decomposition. This research demonstrates a successful exploitation of methane production from microalgae without any biomass pretreatment.

Effect of pesticides and metabolites on groundwater bacterial community

We assessed the effect of pesticides, especially commonly detected herbicides, on bacterial communities in groundwater. To this end, we used a combined approach with i) triazine-spiked experiments at environmentally relevant concentrations (1 and 10μg/L) in waters with contrasting contamination histories, and ii) in situ monitoring in a rural aquifer, where many additional biotic and abiotic parameters also affect the community. Microbial community was characterized by fingerprinting techniques (CE-SSCP), gene presence (atzA/B/C/D/E/F and amoA genes) and abundance (16S RNA, napA and narG genes). During triazine-spiked experiments, the bacterial community structure in reference water was modified following an exposure to atrazine (ATZ) and/or its metabolite desethylatrazine (DEA) at 1μg/L; in historically-contaminated water, the bacterial community structure was modified following an exposure to 10μg/L ATZ/DEA. Similarly, biodiversity indices and biomass in the reference water appeared affected at lower triazine concentrations than in the historically-contaminated water, though these end-points are less sensitive than the community structure. Our results thus suggest that the history of contamination induced a community tolerance to the tested triazines. ATZ and DEA were not degraded during the experiment and this was consistent with the absence of atz genes involved in their degradation in none of the tested conditions. In field monitoring, triazines that represent a historical and diffuse contamination of groundwater, participate in the microbial community structure, confirming the triazine effect observed under laboratory conditions. Other herbicides, such as chloroacetanilides that are applied today, did not appear to affect the whole community structure; they however induced a slight, but significant, increase in the abundance of nitrate-reducing bacteria. To our best knowledge, this is the first study on the microbial ecotoxicology of pesticides and their metabolites at environmentally relevant concentrations in groundwater.

Resilience of aggregated microbial communities subjected to drought--small-scale studies

The response of microbial communities to disturbance is a major concern for microbial ecologists since potential modifications in their composition and functioning may affect ecosystems to a larger extent. Microbial ecosystems may be resistant (not affected) or may present engineering (return to initial state) or ecological resilience. In the latter case, when the disturbance is released, the ecosystem evolves towards a new equilibrium state. The aim of this study was to determine if variations in the magnitude of a disturbance could induce either engineering or ecological resilience. We used phototrophic biofilms grown in mesocosms as a model of microbial ecosystem and increasing drought duration (1-8 weeks) as a range of disturbances. Biofilm composition (algal and prokaryotic), photosynthetic activity (PhytoPAM), and potential functional diversity (Biolog) were determined at the end of dry phase and after a 2-week rewetting phase in individual aquaria. We only observed an ecological resilience of the biofilm, with a resistance of phototrophic component for the weakest disturbance. After rewetting, the biofilm could fulfill the same functions, but its species composition was highly modified. We observed a shift from cyanobacteria dominance towards diatom dominance. The disturbance caused a transition towards a new steady state of the biofilm. We also observed a positive effect of stress duration on biofilm productivity after resilience.

Microbial diversity and PAH catabolic genes tracking spatial heterogeneity of PAH concentrations

We analyzed the within-site spatial heterogeneity of microbial community diversity, polyaromatic hydrocarbon (PAH) catabolic genotypes, and physiochemical soil properties at a creosote contaminated site. Genetic diversity and community structure were evaluated from an analysis of denaturant gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified sequences of 16S rRNA gene. The potential PAH degradation capability was determined from PCR amplification of a suit of aromatic dioxygenase genes. Microbial diversity, evenness, and PAH genotypes were patchily distributed, and hot and cold spots of their distribution coincided with hot and cold spots of the PAH distribution. The analyses revealed a positive covariation between microbial diversity, biomass, evenness, and PAH concentration, implying that the creosote contamination at this site promotes diversity and abundance. Three patchily distributed PAH-degrading genotypes, NAH, phnA, and pdo1, were identified, and their abundances were positively correlated with the PAH concentration and the fraction of soil organic carbon. The covariation of the PAH concentration with the number and spatial distribution of catabolic genotypes suggests that a field site capacity to degrade PAHs may vary with the extent of contamination.

Microbial Community-Level Physiological Profiles (CLPP) and herbicide mineralization potential in groundwater affected by agricultural land use

Diffuse groundwater pollution from agricultural land use may impact the microbial groundwater community, which was investigated as Community-Level Physiological Profiles (CLPP) using EcoPlate™. Water was sampled from seven piezometers and a spring in a small agricultural catchment with diffuse herbicide and nitrate pollution. Based on the Shannon-Wiener and Simpson's diversity indices the diversity in the microbial communities was high. The response from the EcoPlates™ showed which substrates support groundwater bacteria, and all 31 carbon sources were utilized by organisms from at least one water sample. However, only nine carbon sources were utilized by all water samples: d-Mannitol, N-acetyl-d-glucosamine, putrescine, d-galacturonic acid, itaconic acid, 4-hydroxy benzoic acid, tween 40, tween 80, and l-asparagine. In all water samples the microorganisms preferred d-mannitol, d-galacturonic acid, tween 40, and 4-hydroxy benzoic acid as substrates, whereas none preferred 2-hydroxy benzoic acid, α-d-lactose, d,l-α-glycerol phosphate, α-ketobutyric acid, l-threonine and glycyl-l-glutamic acid. Principal Component Analysis of the CLPP's clustered the most agriculturally affected groundwater samples, indicating that the agricultural land use affects the groundwater microbial communities. Furthermore, the ability to mineralize atrazine and isoproturon, which have been used in the catchment, was also associated with this cluster.

Genetic difference but functional similarity among fish gut bacterial communities through molecular and biochemical fingerprints

Considering the major involvement of gut microflora in the digestive function of various macro-organisms, bacterial communities inhabiting fish guts may be the main actors of organic matter degradation by fish. Nevertheless, the extent and the sources of variability in the degradation potential of gut bacterial communities are largely overlooked. Using Biolog Ecoplate™ and denaturing gradient gel electrophoresis (DGGE), we explored functional (i.e. the ability to degrade organic matter) and genetic (i.e. identification of DGGE banding patterns) diversity of fish gut bacterial communities, respectively. Gut bacterial communities were extracted from fish species characterized by different diets sampled along a salinity gradient in the Patos-Mirim lagoons complex (Brazil). We found that functional diversity was surprisingly unrelated to genetic diversity of gut bacterial communities. Functional diversity was not affected by the sampling site but by fish species and diet, whereas genetic diversity was significantly influenced by all three factors. Overall, the functional diversity was consistently high across fish individuals and species, suggesting a wide functional niche breadth and a high potential of organic matter degradation. We conclude that fish gut bacterial communities may strongly contribute to nutrient cycling regardless of their genetic diversity and environment.

Biological degradation of simazine by mixed-microbial cultures immobilized on sepiolite and tepojal beads

Simazine degradation by mixed microbial cultures was carried out in biological reactors with tepojal and sepiolite beads. The inoculum used is derived from a biotechnological product applied to plant roots, which contains mixed microbial cultures. This inoculum presented a stable adherence to the microorganism support throughout the experiment. In this research, the supports were evaluated in relation to both biofilm formation and simazine removal. For this study, hydraulic and mass starting-up parameters were established for simazine degradation and for the use of these reactors in the two types of supports. Tepojal had never been used before as a microbial support in any previous research paper. Tepojal demonstrated to be more efficient than sepiolite. Statistical analysis was done for the relationship among the parameters of chemical oxygen demand, colony formation units, total suspended solids, and volatile suspended solids.

Removal of benzene and toluene in polyurethane biofilter immobilized with Rhodococcus sp. EH831 under transient loading

The performance of a polyurethane (PU) biofilter inoculated with Rhodococcus sp. EH831 was evaluated under different transient loading conditions, such as shutdown, intermittent and fluctuating loading. A mixture of benzene and toluene vapors was employed as model pollutants. When the biofilter was restarted after a 2 week-shutdown, during which neither clean air nor water was supplied, the benzene and toluene removal capacities were rapidly restored after a re-adaptation period of only 1 day. A comparison of the removal capacity under continuous and intermittent loading revealed that constant and periodic loading (8 h on/16 h off per day) and a 2 day-shutdown did not significantly influence the biofilter performance, although the removals of benzene and toluene were relatively unstable and lower under intermittent loading during the initial week. The result of quantitative real-time PCR showed that Rhodococcus sp. EH831 could be maintained during transient loading periods (10(10)-10(11) CFU/g-dry PU) irrespective of the different operating conditions.

Changes in bacterial diversity and community structure following pesticides addition to soil estimated by cultivation technique

An experiment was conducted under laboratory conditions to investigate the effect of increasing concentrations of fenitrothion (2, 10 and 200 mg a.i./kg soil), diuron (1.5, 7.5 and 150 mg a.i./kg soil) and thiram (3.5, 17.5 and 350 mg a.i./kg soil) on soil respiration, bacterial counts and changes in culturable fraction of soil bacteria. To ascertain these changes, the community structure, bacterial biodiversity and process of colony formation, based on the r/K strategy concept, EP- and CD-indices and the FOR model, respectively, were determined. The results showed that the measured parameters were generally unaffected by the lowest dosages of pesticides, corresponding to the recommended field rates. The highest dosages of fenitrothion and thiram suppressed the peak SIR by 15-70% and 20-80%, respectively, while diuron increased respiration rate by 17-25% during the 28-day experiment. Also, the total numbers of bacteria increased in pesticide-treated soils. However, the reverse effect on day 1 and, in addition, in case of the highest dosages of insecticide on days 14 and 28, was observed. Analysis of the community structure revealed that in all soil treatments bacterial communities were generally dominated by K-strategists. Moreover, differences in the distribution of individual bacteria classes and the gradual domination of bacteria populations belonging to r-strategists during the experiment, as compared to control, was observed. However, on day 1, at the highest pesticide dosages, fast growing bacteria constituted only 1-10% of the total colonies number during 48 h of plate incubation, whereas in remaining samples they reached from 20 to 40% of total cfu. This effect, in case of fenitrothion, lasted till the end of the experiment. At the highest dosages of fenitrothion, diuron and at all dosages of thiram the decrease of biodiversity, as indicated by EP- and CD-indices on day 1, was found. At the next sampling time, no significant retarding or stimulating effect was detected. However, in case of CD values the higher differences were observed. The significant impact of pesticides on the physiological state of soil bacteria was not found. They were generally in dormant state (lambda < 0.5), but immediately after pesticides application, the additional reduction of frequency of bacterial cell proliferation (max. decrease of lambda value to 0.15 for thiram on day 14) and prolonged retardation time of colony appearance (max. increase of t(r) value to 1.39 for fenitrothion on day 1) on agar plates were found.

Nutrient effects on the genetic and functional diversity of aquatic bacterial communities

Studies on the effects of biodiversity on ecosystem functioning have generally revealed a positive asymptotic relationship between biodiversity and single functions, suggesting species redundancy with respect to these functions. However, most research was performed on specific processes and did not consider ecosystem 'multifunctionality'. There is also little information on the relationship between genetic and functional diversity. To analyze this relationship, we performed a microcosm experiment on a complex lake assemblage of decomposers, in the presence of the green alga Scenedesmus obliquus, which acted as carbon source for decomposers. By manipulating nutrient enrichment and the N : P input ratio, we observed that the structures of particle-associated and free bacterial assemblages were highly predictable in response to stoichiometric constraints. For a given treatment, the taxonomic compositions of free and particle-associated bacterial communities appeared close to each other only when phosphorus was not depleted. A coinertia analysis revealed a clear coupling between the genetic diversity of the microbial community, assessed using PCR-denatured gradient gel electrophoresis, and its potential functional diversity, studied with Biolog Ecoplates. This suggests that an ecologically relevant fraction of bacterial communities is characterized by lower level of redundancy than frequently thought, highlighting the necessity of exploring further the role of biodiversity in multifunctionality within ecosystems.

Biodegradation in contaminated aquifers: incorporating microbial/molecular methods

In order to evaluate natural attenuation in contaminated aquifers, there has been a recent recognition that a multidisciplinary approach, incorporating microbial and molecular methods, is required. Observed decreases in contaminant mass and identified footprints of biogeochemical reactions are often used as evidence of intrinsic bioremediation, but characterizing the structure and function of the microbial populations at contaminated sites is needed. In this paper, we review the experimental approaches and microbial methods that are available as tools to evaluate the controls on microbially mediated degradation processes in contaminated aquifers. We discuss the emerging technologies used in biogeochemical studies and present a synthesis of recent studies that serve as models of integrating microbiological approaches with more traditional geochemical and hydrogeologic approaches in order to address important biogeochemical questions about contaminant fate.

A multiphasic characterization of the impact of the herbicide acetochlor on freshwater bacterial communities

Acetochlor is the third most frequently detected herbicide in natural waters; however, it is unknown if exposure to environmentally relevant concentrations of acetochlor will impact bacterial community structure and function. This study examined the impact of acetochlor on freshwater heterotrophic bacteria number, and community structure and function using direct counting, community level physiological profiling (CLPP) and denaturing gradient gel electrophoresis (DGGE) analysis. Acetochlor concentration did not appear to correlate with the number of total (P=0.69) and viable (P=0.80) bacteria, even at concentrations up to 500 microg l(-1). However, CLPP indicated that acetochlor increased functional diversity as shown by (i) an increase in the number of carbon sources utilized by the microbial community, relative to nonexposed controls and (ii) increased functional evenness within the heterotrophic bacterial community. Conversely, DGGE fingerprints suggested that exposure to acetochlor generally decreased the community complexity, as the average number of DGGE bands in most treatments was significantly less than in the control treatment. Cluster analysis of DGGE fingerprints revealed three distinct, dose-dependent clusters (i) communities exposed to 0, 1 and 5 microg l(-1); (ii) 50 and 100 microg l(-1) and (iii) 500 microg l(-1), indicating a relationship between acetochlor concentration bacterial community changes. This study indicated that while exposure to environmentally relevant concentrations of acetochlor resulted in no significant impact to the number of freshwater bacteria, impacts to the function and structure of the community were revealed by adopting a multiphasic approach.

Effects of 2,4-dichlorophenol, pentachlorophenol and vegetation on microbial characteristics in a heavy metal polluted soil

The aim of this study was to evaluate the soil microbial characteristics in historically heavy-metal polluted soil, which was also affected by organic co-contaminants, 2,4-dichlorophenol or pentachlorophenol, which often occur due to the conventional use of pesticides. It was observed that the normalized microbial biomass (microbial biomass per unit soil organic C) of the contaminated soil was very low, less than 1% in both non-planted and ryegrass planted soil, and showed a decreasing trend with the treatment of organic co-contaminants. The microbial biomass and substrate-induced respiration (SIR) in the ryegrass planted soil were much larger, as compared with the non-planted soil with or without organic pollutants. The different resistant bacterial community and its physiological diversity in the rhizosphere further suggested that the effect of vegetation on microbial activity was not just a general increase in the mass or activity of pre-existing microorganisms, but rather acted selectively on microbial growth so that the relative abundance of different microbial groups in soil was changed. In sum, high concentrations of organic co-contaminants, especially pentachlorophenol (PCP), could strengthen the deterioration of microbial ecology. The adverse effect of heavy metal-organic pollutants on the soil microbial biomass and activity might be the reason for the slow degradation of PCP that has high chlorinated and high toxicity. Vegetation might be the efficient way to assist in improving and restoring the utilization of agricultural ecosystems. The beneficial microbial effect of vegetation could cause the rapid dissipation of 2,4-dichlorophenol (2,4-DCP) that has less chlorinated and less toxicity in the planted soils.

Strong impact on the polycyclic aromatic hydrocarbon (PAH)-degrading community of a PAH-polluted soil but marginal effect on PAH degradation when priming with bioremediated soil dominated by mycobacteria

Bioaugmentation of soil polluted with polycyclic aromatic hydrocarbons (PAHs) is often disappointing because of the low survival rate and low activity of the introduced degrader bacteria. We therefore investigated the possibility of priming PAH degradation in soil by adding 2% of bioremediated soil with a high capacity for PAH degradation. The culturable PAH-degrading community of the bioremediated primer soil was dominated by Mycobacterium spp. A microcosm containing pristine soil artificially polluted with PAHs and primed with bioremediated soil showed a fast, 100- to 1,000-fold increase in numbers of culturable phenanthrene-, pyrene-, and fluoranthene degraders and a 160-fold increase in copy numbers of the mycobacterial PAH dioxygenase gene pdo1. A nonpolluted microcosm primed with bioremediated soil showed a high rate of survival of the introduced degrader community during the 112 days of incubation. A nonprimed control microcosm containing pristine soil artificially polluted with PAHs showed only small increases in the numbers of culturable PAH degraders and no pdo1 genes. Initial PAH degradation rates were highest in the primed microcosm, but later, the degradation rates were comparable in primed and nonprimed soil. Thus, the proliferation and persistence of the introduced, soil-adapted degraders had only a marginal effect on PAH degradation. Given the small effect of priming with bioremediated soil and the likely presence of PAH degraders in almost all PAH-contaminated soils, it seems questionable to prime PAH-contaminated soil with bioremediated soil as a means of large-scale soil bioremediation.

Assessment of self-organizing maps to analyze sole-carbon source utilization profiles

The use of community-level physiological profiles obtained with Biolog microplates is widely employed to consider the functional diversity of bacterial communities. Biolog produces a great amount of data which analysis has been the subject of many studies. In most cases, after some transformations, these data were investigated with classical multivariate analyses. Here we provided an alternative to this method, that is the use of an artificial intelligence technique, the Self-Organizing Maps (SOM, unsupervised neural network). We used data from a microcosm study of algae-associated bacterial communities placed in various nutritive conditions. Analyses were carried out on the net absorbances at two incubation times for each substrates and on the chemical guild categorization of the total bacterial activity. Compared to Principal Components Analysis and cluster analysis, SOM appeared as a valuable tool for community classification, and to establish clear relationships between clusters of bacterial communities and sole-carbon sources utilization. Specifically, SOM offered a clear bidimensional projection of a relatively large volume of data and were easier to interpret than plots commonly obtained with multivariate analyses. They would be recommended to pattern the temporal evolution of communities' functional diversity.