Alphaproteobacteria dominate active 2-methyl-4-chlorophenoxyacetic acid herbicide degraders in agricultural soil and drilosphere

Towards enhancing phytoremediation: The effect of syringic acid, a plant secondary metabolite, on the presence of phenoxy herbicide-tolerant endophytic bacteria

Among emerging pollutants, residuals of phenoxy herbicides, including 2-chloro-4-methylphenoxy acid (MCPA), are frequently detected in non-targeted areas. MCPA can be removed from environmental matrices using biological remediation methods including endophyte-assisted phytoremediation. The interactions between selected plants excreting to the rhizosphere plant secondary metabolites (PSMs) and plant-associated bacteria (incl. endophytes) can speed up the removal of organics and increase the plants resistance to pollutants such as MCPA. The role of plant-associated bacteria in endophyte-assisted phytoremediation has been partially described, however neither MCPA-tolerant endophytic bacteria has been isolated nor characterized. So far, promising results were obtained by simultaneous cultivation of Cucurbita pepo (zucchini) and amendment of soil with structurally related PSM syringic acid (SA), which can substantially enhance removal of MCPA from soil. Hence, the main aim of this research was to study the effect of PSM (SA) on the presence of functional MCPA-tolerant endophytic bacteria using a culture-dependent and -independent approach. Comparison between the molecular and microbiological analysis revealed differences between applied methods. However, irrespectively of the genera identification methods, presence of phenolic compounds (MCPA or SA) favorized presence of potential MCPA-degraders. On the basis of MCPA tolerance tests of isolated bacteria, two Pseudomonas endophytic isolates from zucchini roots and three isolates from zucchini leaves i.e. Pseudomonas sp., Paenarthrobacter sp. and Acinetobacter sp. were selected for further screening of plant growth promoting properties (PGPP). MCPA-tolerant endophytic bacteria showed multiple PGPP. Therefore, these isolates can potentially contribute to an improved fitness of plants used for the purpose of enhancing phytoremediation of environments polluted with phenoxy herbicides.

Comparison of the Gut Microbial Communities of Domestic and Wild Mallards (Anas platyrhynchos) Based on High-Throughput Sequencing Technology

Mallards (Anas platyrhynchos) are currently one of the most popular species in rare bird breeding in several southern provinces of China, but there have been no studies comparing the gut microbial communities of domestic and wild mallards. In this study, 16S rRNA gene high-throughput sequencing technology was used to compare the composition and diversity of gut microbial communities in domestic and wild mallards. Alpha diversity analysis showed significant differences in gut microbial communities between the two groups of mallards, and the diversity and richness of gut microbial communities were significantly higher in wild mallards than in domestic mallards. Beta diversity analysis showed that the two groups of stool samples were mostly separated on the principal coordinate analysis (PCoA) plot. In domestic mallards, Firmicutes (68.0% ± 26.5%) was the most abundant bacterial phylum, followed by Proteobacteria (24.5% ± 22.9%), Bacteroidetes (3.1% ± 3.2%), Fusobacteria (2.2% ± 5.9%), and Actinobacteria (1.1% ± 1.8%). The dominant bacterial phyla in wild mallards were Firmicutes (79.0% ± 10.2%), Proteobacteria (12.9% ± 9.5%), Fusobacteria (3.4% ± 2.5%), and Bacteroidetes (2.8% ± 2.4%). At the genus level, a total of 10 dominant genera (Streptococcus, Enterococcus, Clostridium, Lactobacillus, Soilbacillus, Bacillus, Acinetobacter, Comamonas, Shigella, and Cetobacterium) with an average relative abundance greater than 1% were detected in the fecal samples of both groups. The average relative abundance of five potential pathogenic genera (Streptococcus, Enterococcus, Acinetobacter, Comamonas, and Shigella) was higher in domestic mallards than in wild mallards. The enrichment of pathogenic bacteria in the intestinal tract of domestic mallards should be of sufficient concern.

Rhizosphere enzyme activities and microorganisms drive the transformation of organic and inorganic carbon in saline-alkali soil region

Western Jilin Province is one of the world's three major saline-alkali land distribution areas, and is also an important area of global climate change and carbon cycle research. Rhizosphere soil microorganisms and enzymes are the most active components in soil, which are closely related to soil carbon cycle and can reflect soil organic carbon (SOC) dynamics sensitively. Soil inorganic carbon (SIC) is the main existing form of soil carbon pool in arid saline-alkali land, and its quantity distribution affects the pattern of soil carbon accumulation and storage. Previous studies mostly focus on SOC, and pay little attention to SIC. Illumina Miseq high-throughput sequencing technology was used to reveal the changes of community structure in three maize fields (M1, M2 and M3) and three rice fields (R1, R2 and R3), which were affected by different levels of salinization during soil development. It is a new research topic of soil carbon cycle in saline-alkali soil region to investigate the effects of soil microorganisms and soil enzymes on the transformation of SOC and SIC in the rhizosphere. The results showed that the root-soil-microorganism interaction was changed by saline-alkali stress. The activities of catalase, invertase, amylase and β-glucosidase decreased with increasing salinity. At the phylum level, most bacterial abundance decreases with increasing salinity. However, the relative abundance of Proteobacteria and Firmicutes in maize field and Firmicutes, Proteobacteria and Nitrospirae in rice field increased sharply under saline-alkali stress. The results of redundancy analysis showed that the differences of rhizosphere soil between the three maize and three rice fields were mainly affected by ESP, pH and soil salt content. In saline-alkali soil region, β-glucosidase activity and amylase were significantly positively correlated with SOC content in maize fields, while catalase and β-glucosidase were significantly positively correlated with SOC content in rice fields. Actinobacteria, Bacteroidetes and Verrucomicrobia had significant positive effects on SOC content of maize and rice fields. Proteobacteria, Gemmatimonadetes and Nitrospirae were positively correlated with SIC content. These enzymes and microorganisms are beneficial to soil carbon sequestration in saline-alkali soils.

Exposure to fomesafen alters the gut microbiota and the physiology of the earthworm Pheretima guillelmi

The application of herbicide fomesafen plays a crucial role in ensuring global soybean productivity in modern agriculture, but it results in both adverse effects on soil ecosystems and phytotoxicity to succeeding crops. Soil pollution due to herbicides has raised much concern worldwide. However, there has been little investigations concerning their effects on soil fauna, especially on the gut microbial communities of earthworms. In this study, the soil endogeic earthworm Pheretima guillelmi was incubated for 20 days in natural and fomesafen-polluted soils to investigate the effects of the herbicide on gut bacterial microbiota and the earthworm's physiological indices, including energy resource (protein) and antioxidant enzyme (superoxide dismutase, SOD) of earthworms in the soil ecosystem. A significantly different and smaller microbial community was presented in the earthworm's gut compared with the cast and the surrounding soil, with exposure to fomesafen further reducing the bacterial diversity and altering the gut community composition. This was observed as significant changes in the relative abundance of the phyla Actinobacteria, Firmicutes, and Proteobacteria as well as the genera Bacillus, Microvirga, Blastococcus, Nocardioides, and Gaiella. Moreover, exposure to fomesafen reduced earthworms' energy resources and activated the antioxidant system, with both effects being significantly correlated with the gut microbial diversity. These findings unravel the fact that exposure to the herbicide fomesafen may affect non-target soil fauna via changes in their microbiota and physiological indices, thereby contributing new knowledge regarding the adverse impacts of fomesafen on the terrestrial ecosystem.

Modified zeolite-supported biofilm in service of pesticide biodegradation

The development of biofilms on modified natural zeolites was investigated with purpose to obtain biocomposites with biodegradation activity towards pesticides MCPA (2-methyl-4-chlorophenoxyacetic acid) and glyphosate (N-(phosphonomethyl)glycine) for potential application in bioaugmentation of polluted agricultural soils. Microbial communities were selected from agricultural pesticide-contaminated soil/water samples and enriched on the basis of their ability to biodegrade the pesticides. In order to enhance affinity of microbial communities to the support material, the natural mineral zeolite was modified by nontoxic environmentally friendly cations (Li⁺, Na⁺, K⁺, NH₄⁺, H⁺, Mg²⁺, Ca²⁺, Fe³⁺) by methods preserving its structure and characterised using powder XRD, surface area measurement and chemical composition analysis. Kinetics of pesticide degradation by the biocomposites was studied in liquid media. Results showed that according to zeolite modifications, the microbial activity and biodiversity changed. The best biodegradation rate of MCPA and glyphosate reached 0.12-0.13 mg/h with half-life of 16-18 h, which is considerably quicker than observed in natural environment. However, in some cases, biodegradation activity towards pesticides was lost which was connected to unfavourable zeolite modification and accumulation of toxic metabolites. High-throughput sequencing on the 16S rRNA genes of the biofilm communities highlighted the selection of bacteria genera known to metabolise MCPA (Aminobacter, Cupriavidus, Novosphingobium, Pseudomonas, Rhodococcus, Sphingobium and Sphingopyxis) and glyphosate (Pseudomonas). Altogether, results suggested that zeolites do not only have a passive role of biofilm support but also have protective and nutrient-supportive functions that consequently increase biodiversity of the pesticide degraders growing in the biofilm and influence the pesticide biodegradation rate.

Plant metabolomics integrated with transcriptomics and rhizospheric bacterial community indicates the mitigation effects of Klebsiella oxytoca P620 on p-hydroxybenzoic acid stress in cucumber

Accumulation of p-hydroxybenzoic acid (PHBA) in soil causes autotoxicity stress in cucumber. When the stress is mitigated by PHBA-degrading bacteria, plant metabolites have not been detected. To explore mechanisms underlining the mitigation, plant metabolites have not been combined with rhizospheric microbes, antioxidant and soil enzymes. In this study, a strain P620 of Klebsiella decomposed PHBA to acetyl CoA. Cucumber was sown into soil supplemented with P620 and/or PHBA. After addition with P620, P620 colonization and the enriched bacterial genera were observed in rhizosphere. Compared to PHBA stress alone, the combination of P620 application and PHBA stress improved plant growth, decreased PHBA concentration in soil, and increased the activities of five soil enzymes and eight antioxidant enzymes in leaves. Metabolomic and transcriptomic analysis highlighted that P620 application decreased the intensities of MAG(18:3) isomer 4, MAG(18:3) isomer 2, lysoPC 18:3 (2n isomer), 2'-deoxyadenosine-5'-monophosphate, pyridoxine, and glucarate O-phosphoric acid in PHBA-stressed leaves and down-regulated the expression of genes related to these metabolites. We propose a mechanism that P620 application alters microbial communities in PHBA-contaminated soil. Thus, the application reduces PHBA concentration in soil, activates antioxidant and soil enzymes, and also influences metabolites in leaves by affecting plant transcriptome, mitigating PHBA stress in cucumber.

Biodegradation of metoprolol in oxic and anoxic hyporheic zone sediments: unexpected effects on microbial communities

Abstract

Metoprolol is widely used as a beta-blocker and considered an emerging contaminant of environmental concern due to pseudo persistence in wastewater effluents that poses a potential ecotoxicological threat to aquatic ecosystems. Microbial removal of metoprolol in the redox-delineated hyporheic zone (HZ) was investigated using streambed sediments supplemented with 15 or 150 μM metoprolol in a laboratory microcosm incubation under oxic and anoxic conditions. Metoprolol disappeared from the aqueous phase under oxic and anoxic conditions within 65 and 72 days, respectively. Metoprolol was refed twice after initial depletion resulting in accelerated disappearance under both conditions. Metoprolol disappearance was marginal in sterile control microcosms with autoclaved sediment. Metoprolol was transformed mainly to metoprolol acid in oxic microcosms, while metoprolol acid and α-hydroxymetoprolol were formed in anoxic microcosms. Transformation products were transient and disappeared within 30 days under both conditions. Effects of metoprolol on the HZ bacterial community were evaluated using DNA- and RNA-based time-resolved amplicon Illumina MiSeq sequencing targeting the 16S rRNA gene and 16S rRNA, respectively, and were prominent on 16S rRNA rather than 16S rRNA gene level suggesting moderate metoprolol-induced activity-level changes. A positive impact of metoprolol on Sphingomonadaceae and Enterobacteriaceae under oxic and anoxic conditions, respectively, was observed. Nitrifiers were impaired by metoprolol under oxic and anoxic conditions. Collectively, our findings revealed high metoprolol biodegradation potentials in the hyporheic zone under contrasting redox conditions associated with changes in the active microbial communities, thus contributing to the attenuation of micropollutants.

Key points

• High biotic oxic and anoxic metoprolol degradation potentials in the hyporheic zone.

• Key metoprolol-associated taxa included Sphingomonadaceae, Enterobacteraceae, and Promicromonosporaceae.

• Negative impact of metoprolol on nitrifiers.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11466-w.

Ibuprofen Degradation and Associated Bacterial Communities in Hyporheic Zone Sediments

Ibuprofen, a non-steroidal anti-inflammatory pain reliever, is among pharmaceutical residues of environmental concern ubiquitously detected in wastewater effluents and receiving rivers. Thus, ibuprofen removal potentials and associated bacteria in the hyporheic zone sediments of an impacted river were investigated. Microbially mediated ibuprofen degradation was determined in oxic sediment microcosms amended with ibuprofen (5, 40, 200, and 400 µM), or ibuprofen and acetate, relative to an un-amended control. Ibuprofen was removed by the original sediment microbial community as well as in ibuprofen-enrichments obtained by re-feeding of ibuprofen. Here, 1-, 2-, 3-hydroxy- and carboxy-ibuprofen were the primary transformation products. Quantitative real-time PCR analysis revealed a significantly higher 16S rRNA abundance in ibuprofen-amended relative to un-amended incubations. Time-resolved microbial community dynamics evaluated by 16S rRNA gene and 16S rRNA analyses revealed many new ibuprofen responsive taxa of the Acidobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Latescibacteria, and Proteobacteria. Two ibuprofen-degrading strains belonging to the genera Novosphingobium and Pseudomonas were isolated from the ibuprofen-enriched sediments, consuming 400 and 300 µM ibuprofen within three and eight days, respectively. The collective results indicated that the hyporheic zone sediments sustain an efficient biotic (micro-)pollutant degradation potential, and hitherto unknown microbial diversity associated with such (micro)pollutant removal.

Response of soil bacterial and fungal community structure succession to earthworm addition for bioremediation of metolachlor

Synergistic biodegradation of earthworms and soil microorganisms plays a key role in the removal of organic pollutants in soil, yet microbially mediated processes remain unclear, especially regarding the succession of soil microbial interactions. Herein, soil biochemical evaluation, microbial community characterization, and interaction network construction were combined to understand the mechanisms dominating microbial community succession during synergistic bioremediation of metolachlor-polluted soils. The results of the network analysis indicated that metolachlor could render more complex relations but weaker connection strength among soil microorganisms. The addition of earthworms significantly alleviated the stress of metolachlor on soil microbial interactions and resulted in the restoration of interactions to a great extent. Additionally, the soil physicochemical properties, enzyme activities, and microbial community changed greatly with the addition of metolachlor and earthworms. Some soil microorganisms became significantly correlated with soil properties, metolachlor concentrations, and enzyme activities. These results, dominated by the succession of soil microbial communities, provide a new perspective for assessing the remediation effect of contaminated soil by organic pollutants.

Chemical mixtures and fluorescence in situ hybridization analysis of natural microbial community in the Tiber river

The Water Framework Directive (WFD) regulates freshwater and coastal water quality assessment in Europe. Chemical and ecological water quality status is based on measurements of chemical pollutants in water and biota together with other indicators such as temperature, nutrients, species compositions (phytoplankton, microalgae, benthos and fish) and hydromorphological conditions. However, in the current strategy a link between the chemical and the ecological status is missing. In the present WFD, no microbiological indicators are foreseen for integrating the different anthropogenic pressures, including mixtures of chemicals, nutrients and temperature changes, to provide a holistic view of the freshwater ecosystem water quality. The main aim of this work was to evaluate if natural microbial populations can be valuable indicators of multiple stressors (e.g. chemical pollutants, temperature, nutrients etc.) to guide preventive and remediation actions by water authorities. A preliminary survey was conducted to identify four sites reflecting a contamination gradient from the source to the mouth of a river suitable to the objectives of the European Marie Curie project, MicroCoKit. The River Tiber (Italy) was selected as a pilot case study to investigate the correlation between bacteria taxa and the chemical status of the river. The main physicochemical parameters, inorganic elements, organic pollutants and natural microbial community composition were assessed at four selected sites corresponding to pristine, agricultural, industrial and urban areas for three consecutive years. The overall chemical results indicated a correspondence between different groups of contaminants and the main contamination sources at the selected sampling points. Phylogenetic analysis of the microbial community analyzed by Fluorescence In Situ Hybridization method (FISH) revealed differences among the four sampling sites which could reflect an adaptive bacterial response to the different anthropogenic pressures.

Copper in Wood Preservatives Delayed Wood Decomposition and Shifted Soil Fungal but Not Bacterial Community Composition

Copper-based fungicides are routinely used for wood and plant protection, which can lead to an enrichment of copper-tolerant microbial communities in soil. To investigate the effect of such wood preservatives on the soil fungal and bacterial community compositions, five different vineyard and fruit-growing soil environments were evaluated using incubation studies over time. Pine sapwood specimens were impregnated with either water or different biocide treatment solutions containing a mixture of copper, triazoles, and quaternary ammonium compounds (CuTriQAC), a mixture of triazoles and quaternary ammonium compounds (TriQAC), or copper alone (Cu). Specimens were incubated in soil from each sample site for 8, 16, 24, and 32 weeks. The effects of preservative treatment on the modulus of elasticity (MOE) of the wood specimens and on the soil fungal as well as bacterial community composition at the soil-wood interface were assessed by quantitative PCR and amplicon sequencing of the fungal internal transcribed spacer (ITS) region and bacterial 16S rRNA gene. Specimens impregnated with CuTriQAC and Cu showed decreased MOE and reduced fungal and bacterial copy numbers over time compared to those impregnated with water and TriQAC. Fungal but not bacterial community composition was significantly affected by wood preservative treatment. The relative abundance of members of the family Trichocomaceae compared to other genera increased in the presence of the Cu and CuTriQAC treatments at three sites, suggesting these to be Cu-tolerant fungi. In conclusion, the copper-containing treatments resulted in marginally increased MOE, lowered microbial gene copy numbers compared to those in the TriQAC and water treatments, and thus enhanced wood protection against soil microbial wood degradation.IMPORTANCE Copper-containing rather than TRIQAC formulations are efficient wood preservatives irrespective of the origin and composition of the soil microbial communities. However, some fungi appear to be naturally insensitive to copper and should be the focus of future wood preservative formulations to facilitate the life span of wooden construction in contact with soil while also minimizing the overall environmental impact.

Blame It on the Metabolite: 3,5-Dichloroaniline Rather than the Parent Compound Is Responsible for the Decreasing Diversity and Function of Soil Microorganisms

Pesticides are key stressors of soil microorganisms with reciprocal effects on ecosystem functioning. These effects have been mainly attributed to the parent compounds, while the impact of their transformation products (TPs) has been largely overlooked. We assessed in a meadow soil (soil A) the transformation of iprodione and its toxicity in relation to (i) the abundance of functional microbial groups, (ii) the activity of key microbial enzymes, and (iii) the diversity of bacteria, fungi, and ammonia-oxidizing microorganisms (AOM) using amplicon sequencing. 3,5-Dichloroaniline (3,5-DCA), the main iprodione TP, was identified as a key explanatory factor for the persistent reduction in enzymatic activities and potential nitrification (PN) and for the observed structural changes in the bacterial and fungal communities. The abundances of certain bacterial (Actinobacteria, Hyphomicrobiaceae, Ilumatobacter, and Solirubrobacter) and fungal (Pichiaceae) groups were negatively correlated with 3,5-DCA. A subsequent study in a fallow agricultural soil (soil B) showed limited formation of 3,5-DCA, which concurred with the lack of effects on nitrification. Direct 3,5-DCA application in soil B induced a dose-dependent reduction of PN and NO3--N, which recovered with time. In vitro assays with terrestrial AOM verified the greater toxicity of 3,5-DCA over iprodione. "Candidatus Nitrosotalea sinensis" Nd2 was the most sensitive AOM to both compounds. Our findings build on previous evidence on the sensitivity of AOM to pesticides, reinforcing their potential utilization as indicators of the soil microbial toxicity of pesticides in pesticide environmental risk analysis and stressing the need to consider the contribution of TPs in the toxicity of pesticides on the soil microbial community.IMPORTANCE Pesticide toxicity on soil microorganisms is an emerging issue in pesticide risk assessment, dictated by the pivotal role of soil microorganisms in ecosystem services. However, the focus has traditionally been on parent compounds, while transformation products (TPs) are largely overlooked. We tested the hypothesis that TPs can be major contributors to the soil microbial toxicity of pesticides using iprodione and its main TP, 3,5-dichloroaniline, as model compounds. We demonstrated, by measuring functional and structural endpoints, that 3,5-dichloroaniline and not iprodione was associated with adverse effects on soil microorganisms, with nitrification being mostly affected. Pioneering in vitro assays with relevant ammonia-oxidizing bacteria and archaea verified the greater toxicity of 3,5-dichloroaniline. Our findings are expected to advance environmental risk assessment, highlighting the potential of ammonia-oxidizing microorganisms as indicators of the soil microbial toxicity of pesticides and stressing the need to consider the contribution of TPs to pesticide soil microbial toxicity.

Comparative analyses of the gut microbiota among three different wild geese species in the genus Anser

In this study, we characterized for the first time the gut microbiota of Greylag geese (Anser anser) using high-throughput 16S rRNA gene sequencing technology. The results showed that the phyla Firmicutes (78.55%), Fusobacteria (9.38%), Proteobacteria (7.55%), Bacteroidetes (1.82%), Cyanobacteria (1.44%), and Actinobacteria (0.61%) dominated the gut microbial communities in the Greylag geese. Then, the variations of gut microbial community structures and functions among the three geese species, Greylag geese, Bar-headed geese (Anser indicus), and Swan geese (Anser cygnoides), were explored. The greatest gut microbial diversity was found in Bar-headed geese group, while other two groups had the least. The dominant bacterial phyla across all samples were Firmicutes and Proteobacteria, but several characteristic bacterial phyla and genera associated with each group were also detected. At all taxonomic levels, the microbial community structure of Swan geese was different from those of Greylag geese and Bar-headed geese, whereas the latter two groups were less different. Functional KEGG categories and pathways associated with carbohydrate metabolism, energy metabolism, and amino acid metabolism were differentially expressed among different geese species. Taken together, this study could provide valuable information to the vast, and yet little explored, research field of wild birds gut microbiome.

Comparative genome analysis of the vineyard weed endophyte Pseudomonas viridiflava CDRTc14 showing selective herbicidal activity

Microbes produce a variety of secondary metabolites to be explored for herbicidal activities. We investigated an endophyte Pseudomonas viridiflava CDRTc14, which impacted growth of its host Lepidium draba L., to better understand the possible genetic determinants for herbicidal and host-interaction traits. Inoculation tests with a variety of target plants revealed that CDRTc14 shows plant-specific effects ranging from beneficial to negative. Its herbicidal effect appeared to be dose-dependent and resembled phenotypically the germination arrest factor of Pseudomonas fluorescens WH6. CDRTc14 shares 183 genes with the herbicidal strain WH6 but the formylaminooxyvinylglycine (FVG) biosynthetic genes responsible for germination arrest of WH6 was not detected. CDRTc14 showed phosphate solubilizing ability, indole acetic acid and siderophores production in vitro and harbors genes for these functions. Moreover, genes for quorum sensing, hydrogen cyanide and ACC deaminase production were also found in this strain. Although, CDRTc14 is related to plant pathogens, we neither found a complete pathogenicity island in the genome, nor pathogenicity symptoms on susceptible plant species upon CDRTc14 inoculation. Comparison with other related genomes showed several unique genes involved in abiotic stress tolerance in CDRTc14 like genes responsible for heavy metal and herbicide resistance indicating recent adaptation to plant protection measures applied in vineyards.

Enhanced anaerobic degradability of highly polluted pesticides-bearing wastewater under thermophilic conditions

This work presents a sustainable and cost-competitive solution for hardly biodegradable pesticides-bearing wastewater treatment in an anaerobic expanded granular sludge bed (EGSB) reactor at mesophilic (35°C) and thermophilic (55°C). The reactor was operated in continuous mode during 160days, achieving an average COD removal of 33 and 44% under mesophilic and thermophilic conditions, respectively. The increase of temperature improved the biomass activity and the production of methane by 35%. Around 96% of pesticides identified in raw wastewater were not detected in both mesophilic and thermophilic effluents. A dramatic selection of the microbial population in anaerobic granules was caused by the presence of pesticides, which also changed significantly when the temperature was increased. Pesticides caused a significant inhibition on methanogenesis, especially over acetoclastic methanogens. Aerobic biodegradability tests of the resulting anaerobic effluents revealed that aerobic post-treatment is also a feasible and effective option, yielding more than 60% COD reduction.

Influence of oligomeric herbicidal ionic liquids with MCPA and Dicamba anions on the community structure of autochthonic bacteria present in agricultural soil

The aim of this study was to evaluate the impact of selected herbicidal ionic liquids (HILs), which exhibit high efficacy in terms of weed control and low toxicity, but may be persistent due to limited biodegradability, on the community structure of autochthonic bacteria present in agricultural soil. Four different oligomeric HILs (with two types of cations and different ratio of herbicidal anions) were synthesized and characterized by employing (1)H and (13)C NMR. The results of biodegradation assay indicated that none of the tested HILs could be classified as readily biodegradable (biodegradation rate ranged from 0 to 7%). The conducted field studies confirmed that the herbicidal efficacy of the HILs was higher compared to the reference herbicide mixture by 10 to 30%, depending on the dose and weed species. After termination of field studies, the soil treated with the tested HILs was subjected to next generation sequencing in order to investigate the potential changes in the bacterial community structure. Proteobacteria was the dominant phylum in all studied samples. Treatment with the studied HILs resulted in an increase of Actinobacteria compared to the reference herbicidal mixture. Differenced among the studied HILs were generally associated with a significantly higher abundance of Bacteroidetes in case of 1-HIL-Dicamba 1/3 and Firmicutes in case of 2-HIL-Dicamba 1/3.

Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil

Information on microorganisms possessing the ability to metabolize different polycyclic aromatic hydrocarbons (PAHs) in complex environments helps in understanding PAHs behavior in natural environment and developing bioremediation strategies. In the present study, stable-isotope probing (SIP) was applied to investigate degraders of PAHs in a forest soil with the addition of individually (13)C-labeled phenanthrene, anthracene, and fluoranthene. Three distinct phylotypes were identified as the active phenanthrene-, anthracene- and fluoranthene-degrading bacteria. The putative phenanthrene degraders were classified as belonging to the genus Sphingomona. For anthracene, bacteria of the genus Rhodanobacter were the putative degraders, and in the microcosm amended with fluoranthene, the putative degraders were identified as belonging to the phylum Acidobacteria. Our results from DNA-SIP are the first to directly link Rhodanobacter- and Acidobacteria-related bacteria with anthracene and fluoranthene degradation, respectively. The results also illustrate the specificity and diversity of three- and four-ring PAHs degraders in forest soil, contributes to our understanding on natural PAHs biodegradation processes, and also proves the feasibility and practicality of DNA-based SIP for linking functions with identity especially uncultured microorganisms in complex microbial biota.

Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines

Improving the rate and extent of faecal decomposition in basic forms of sanitation such as pit latrines would benefit around 1.7 billion users worldwide, but to do so requires a major advance in our understanding of the biology of these systems. As a critical first step, bacterial diversity and composition was studied in 30 latrines in Tanzania and Vietnam using pyrosequencing of 16S rRNA genes, and correlated with a number of intrinsic environmental factors such as pH, temperature, organic matter content/composition and geographical factors. Clear differences were observed at the operational taxonomic unit, family and phylum level in terms of richness and community composition between latrines in Tanzania and Vietnam. The results also clearly show that environmental variables, particularly substrate type and availability, can exert a strong structuring influence on bacterial communities in latrines from both countries. The origins and significance of these environmental differences are discussed. This work describes the bacterial ecology of pit latrines in combination with inherent latrine characteristics at an unprecedented level of detail. As such, it provides useful baseline information for future studies that aim to understand the factors that affect decomposition rates in pit latrines.

Potential roles for microbial endophytes in herbicide tolerance in plants

Herbicide tolerance in crops and weeds is considered to be monotrophic, i.e. determined by the relative susceptibility of the physiological process targeted and the plant's ability to metabolise and detoxify the agrochemical. A growing body of evidence now suggests that endophytes, microbes that inhabit plant tissues and provide a range of growth, health and defence enhancements, can contribute to other types of abiotic and biotic stress tolerance. The current evidence for herbicide tolerance being bitrophic, with both free-living and plant-associated endophytes contributing to tolerance in the host plant, has been reviewed. We propose that endophytes can directly contribute to herbicide detoxification through their ability to metabolise xenobiotics. In addition, we explore the paradigm that microbes can 'prime' resistance mechanisms in plants such that they enhance herbicide tolerance by inducing the host's stress responses to withstand the downstream toxicity caused by herbicides. This latter mechanism has the potential to contribute to the growth of non-target-site-based herbicide resistance in weeds. Microbial endophytes already contribute to herbicide detoxification in planta, and there is now significant scope to extend these interactions using synthetic biology approaches to engineer new chemical tolerance traits into crops via microbial engineering.

Novel Phenanthrene-Degrading Bacteria Identified by DNA-Stable Isotope Probing

Microorganisms responsible for the degradation of phenanthrene in a clean forest soil sample were identified by DNA-based stable isotope probing (SIP). The soil was artificially amended with either 12C- or 13C-labeled phenanthrene, and soil DNA was extracted on days 3, 6 and 9. Terminal restriction fragment length polymorphism (TRFLP) results revealed that the fragments of 219- and 241-bp in HaeIII digests were distributed throughout the gradient profile at three different sampling time points, and both fragments were more dominant in the heavy fractions of the samples exposed to the 13C-labeled contaminant. 16S rRNA sequencing of the 13C-enriched fraction suggested that Acidobacterium spp. within the class Acidobacteria, and Collimonas spp. within the class Betaproteobacteria, were directly involved in the uptake and degradation of phenanthrene at different times. To our knowledge, this is the first report that the genus Collimonas has the ability to degrade PAHs. Two PAH-RHDα genes were identified in 13C-labeled DNA. However, isolation of pure cultures indicated that strains of Staphylococcus sp. PHE-3, Pseudomonas sp. PHE-1, and Pseudomonas sp. PHE-2 in the soil had high phenanthrene-degrading ability. This emphasizes the role of a culture-independent method in the functional understanding of microbial communities in situ.

Microbial and genetic ecology of tropical Vertisols under intensive chemical farming

There are continued concerns on unscientific usage of chemical fertilizers and pesticides, particularly in many developing countries leading to adverse consequences for soil biological quality and agricultural sustainability. In farmers' fields in tropical Vertisols of peninsular India, "high" fertilizer and pesticide usage at about 2.3 times the recommended rates in black gram (Vigna mungo) did not have a deleterious effect on the abundance of culturable microorganisms, associative nitrogen fixers, nitrifiers, and 16S rRNA gene diversity compared to normal rates. However, "very high" application at about five times the fertilizers and 1.5 times pesticides in chilies (Capsicum annuum) adversely affected the populations of fungi, actinomycetes, and ammonifiers, along with a drastic change in the eubacterial community profile and diversity over normal rates. Actinobacteria were dominant in black gram normal (BG1) (47%), black gram high (BG2) (36%), and chili normal (CH1) (30%) and were least in chili very high (CH2) (14%). Geodermatophilus formed 20% of Actinobacteria in BG1 but disappeared in BG2, CH1, and CH2. Asticcacaulis dominated at "very high" input site (CH2). Diversity of nitrogen fixers was completely altered; Dechloromonas and Anaeromyxobacter were absent in BG1 but proliferated well in BG2. There was reduction in rhizobial nifH sequences in BG2 by 46%. Phylogenetic differences characterized by UniFrac and principal coordinate analysis showed that BG2 and CH2 clustered together depicting a common pattern of genetic shift, while BG1 and CH1 fell at different axis. Overall, there were adverse consequences of "very high" fertilizer and pesticide usage on soil microbial diversity and function in tropical Vertisols.