Endosulfan degradation by a Rhodococcus strain isolated from earthworm gut

Biodegradation of fipronil: molecular characterization, degradation kinetics, and metabolites

Fipronil (C12H4Cl2F6N4OS) is a commonly used insecticide effective against numerous insects and pests. Its immense application poses harmful effects on various non-target organisms as well. Therefore, searching the effective methods for the degradation of fipronil is imperative and logical. In this study, fipronil-degrading bacterial species are isolated and characterized from diverse environments using a culture-dependent method followed by 16S rRNA gene sequencing. Phylogenetic analysis showed the homology of organisms with Acinetobacter sp., Streptomyces sp., Pseudomonas sp., Agrobacterium sp., Rhodococcus sp., Kocuria sp., Priestia sp., Bacillus sp., Aeromonas sp., and Pantoea sp. The bacterial degradation potential for fipronil was analyzed through high-performance liquid chromatography (HPLC). Incubation-based degradation studies revealed that Pseudomonas sp. and Rhodococcus sp. were found to be the most potent isolates that degraded fipronil at 100 mg L-1 concentration, with removal efficiencies of 85.9 and 83.6%, respectively. Kinetic parameter studies, following the Michaelis-Menten model, also revealed the high degradation efficiency of these isolates. Gas chromatography-mass spectrometry (GC-MS) analysis revealed fipronil sulfide, benzaldehyde, (phenyl methylene) hydrazone, isomenthone, etc., as major metabolites of fipronil degradation. Overall investigation suggests that native bacterial species isolated from the contaminated environments could be efficiently utilized for the biodegradation of fipronil. The outcome derived from this study has immense significance in formulating an approach for bioremediation of fipronil-contaminated surroundings.

Earthworms synergize with indigenous soil functional microorganisms to accelerate the preferential degradation of the highly toxic S-enantiomer of the fungicide imazalil in soil

The roles of soil and earthworm gut microorganisms in the degradation of the chiral fungicide imazalil (IMA) enantiomers were systemically studied in soil-earthworm systems. S-IMA degraded slower than R-IMA in soil without earthworms. After the addition of earthworms, S-IMA degraded faster than R-IMA. Methylibium was the potential degradative bacterium likely related to the preferential degradation of R-IMA in soil. However, the addition of earthworms significantly decreased the relative abundance of Methylibium, especially in R-IMA-treated soil. Meanwhile, a new potential degradative bacterium Aeromonas first appeared in soil-earthworm systems. Compared with enantiomer-treated soil, the relative abundance of indigenous soil bacterium Kaistobacter significantly boomed in enantiomer-treated soil with earthworms. Interestingly, Kaistobacter in the earthworm gut also obviously increased after exposure to enantiomers, particularly in S-IMA-treated soil, which was associated with the significant increase in Kaistobacter in soil. More importantly, the relative abundances of Aeromonas and Kaistobacter in S-IMA-treated soil were obviously higher than those in R-IMA-treated soil after the addition of earthworms. Moreover, these two potential degradative bacteria were also potential bacterial hosts of the biodegradation genes p450 and bph. Collectively, gut microorganisms are important helpers in soil pollution remediation by participating in the preferential degradation of S-IMA mediated by indigenous soil microorganisms.

Biodegradation of neonicotinoid insecticide acetamiprid by earthworm gut bacteria Brucella intermedium PDB13 and its ecotoxicity

Extensive use of neonicotinoid insecticides in recent decade had contaminated water and soil systems and poses serious environmental and health risk. Microbial degradation of toxic contaminants in the environment has been established as a sustainable tool towards its remediation. Under this context, the present study focused on the biodegradation of neonicotinoid insecticide acetamiprid, by bacterial strain Brucella intermedia PDB13 isolated from the gut of the acetamiprid exposed earthworms. To enhance acetamiprid biodegradation, suitable parameters such as pH, temperature, inoculum size and acetamiprid concentration range were optimised using Response Surface Methodology (RSM). The experimental results showed that the Brucella intermedium PDB13 can tolerate and degrade relatively high concentrations of acetamiprid (50 - 350 mg L^-1). The results confirmed that maximum degradation of about 89.72% was achieved under optimized conditions. Further, confirmation of acetamiprid biodegradation was assessed through the occurrence of its degraded metabolites through HPLC, FTIR, and LCMS analysis. Based on this analysis, possible acetamiprid biodegradation pathway by Brucella intermedia PDB13 was proposed. Additionally, cytotoxicity, earthworm acute toxicity, and zebrafish embryo toxicity studies were also performed to assess the toxicity variations between the parent compound and its metabolites. The acetamiprid treated group resulted in cytotoxic effects apparently, with the increase in aberrant cells frequency (22.5 ± 3.3), when compared with its metabolites (2.3 ± 4.3) and control (1.9 ± 5.6) respectively. All these results evidently reported the degradation potential of Brucella intermedia PDB13, thereby establishing the scope for further advanced biodegradation studies towards mitigating the pesticide pollution.

Effect of the coexistence of endosulfan on the lindane biodegradation by Novosphingobium barchaimii and microbial enrichment cultures

Organochlorine pesticides, especially lindane and endosulfan, have been demonstrated to be both biodegradable and frequently coexistent, but their inhibitory effect has never been studied. In this study, we investigated the effect of endosulfan coexistence on lindane degradation to a lindane-degrading isolate, Novosphingobium barchaimii strain LL02, and mixed enrichment cultures from two different inocula. Our results of the lindane degradation batch experiments demonstrated that endosulfan concentration above 20 mg L^-1 causes significant inhibition to the lindane degradation efficiency of the strain LL02. Besides, the acidic conditions at pH 5.0 to 6.0 further decreased its lindane degradation rate constants by 57% compared to the neutral and alkaline conditions. For the mixed microbial cultures, the lindane degradation efficiency in the lindane/endosulfan co-contamination conditions decreased by 35.7%-50.7% compared to the lindane alone conditions. From our 16S rRNA amplicon sequencing results through the PacBio platform, most of the predominant bacteria in the lindane-enriched cultures were depressed in the lindane/endosulfan-enriched cultures. Moreover, bacteria of Burkholderia australis, Chujaibacter soli, Flavitalea flava, and one Rhodanobacteraceae bacterium were relatively highly abundant in the co-contamination enrichment cultures, suggesting their potential for lindane degradation under the endosulfan stress. Our results demonstrated that endosulfan coexistence causes inhibitory impacts on lindane biodegradation toward both lindane-degrading bacteria and mixed microbial cultures. The coexistence of multiple organochlorine pesticides on the biodegradation efficiencies should be carefully considered when applying bioremediation to remove organochlorine pesticide contamination.

Biodegradation of Endosulfan-a Chlorinated Cyclodiene Pesticide by Indigenous Pseudomonas sp. MSCAS BT01

Endosulfan remains as a lipophilic insecticide that causes serious medical problems because of biological stability and toxicity also found in air, water, soil sediments, and foodstuffs. Henceforward, the present study reveals a novel bacterial species isolated from pesticide-contaminated soil for enhanced endosulfan degradation. Next, isolated bacterial species was characterized with biochemical assays and 16S rRNA sequencing technique. Subsequently, the optimal conditions for endosulfan biodegradation such as pH, concentration of endosulfan, and bacterial growth were estimated with non-sulfur medium (NSM). Sequentially, the amount of endosulfan and compound degradation were analyzed through thin-layer chromatography and gas chromatography/mass spectrometry. Overall, the obtained results revealed the endosulfan acting as primary carbon source for bacterial growth. From the GC-MS analysis, the metabolic products released during endosulfan degradation by Pseudomonas sp. MSCAS BT01 were compared with standard GC-MS spectra. The highest (98%) endosulfan degradation was obtained at pH 7.0. The complete endosulfan degradation was achieved at 14th day of incubation and the less toxic endosulfan diol produced was observed via GC-MS. To conclude, the pesticide-contaminated isolate Pseudomonas sp. MSCAS BT01 emerged as a promising bioremediation tool and effectively employed to degrade endosulfan from contaminated soils, sediments, and wastewaters in the days yet to come.

Actinomycetes from Caves: An Overview of Their Diversity, Biotechnological Properties, and Insights for Their Use in Soil Environments

The environmental conditions of caves shape microbiota. Within caves' microbial communities, actinomycetes are among the most abundant bacteria. Cave actinomycetes have gained increasing attention during the last decades due to novel bioactive compounds with antibacterial, antioxidant and anticancer activities. However, their potential role in soil environments is still unknown. This review summarises the literature dealing with actinomycetes from caves, underlining for the first time their potential roles in soil environments. We provide an overview of their diversity and biotechnological properties, underling their potential role in soil environments applications. The contribution of caves' actinomycetes in soil fertility and bioremediation and crops biostimulation and biocontrol are discussed. The survey on the literature show that several actinomycetes genera are present in cave ecosystems, mainly Streptomyces, Micromonospora, and Nocardiopsis. Among caves' actinomycetes, Streptomyces is the most studied genus due to its ubiquity, survival capabilities, and metabolic versatility. Despite actinomycetes' outstanding capabilities and versatility, we still have inadequate information regarding cave actinomycetes distribution, population dynamics, biogeochemical processes, and metabolisms. Research on cave actinomycetes needs to be encouraged, especially concerning environmental soil applications to improve soil fertility and health and to antagonise phytopathogens.

Isolation of lindane- and endosulfan-degrading bacteria and dominance analysis in the microbial communities by culture-dependent and independent methods

　　Bioremediation for lindane and endosulfan removal is a cost-effective approach, but its effectiveness depends on the ability to isolate degrading functionalized microorganisms. Researchers have isolated many lindane and endosulfan degrading bacteria from enrichment cultures based on culture-dependent methods during the past decades. However, it is unknown whether the isolated bacteria can reflect the indigenous predominant degraders in enriching cultures. In this study, we compared the culture-dependent method with selective medium isolation with culture-independent method (PacBio SMRT sequencing of full-length 16S rRNA amplicon) to analyze the bacterial communities from four distinct lindane (LA1 and LC1) and endosulfan (EA1 and EC1) enrichment cultures. From all the isolates we harvested from lindane (63 isolates) and endosulfan (61 isolates) enrichment cultures, their BLAST alignment can only match 5.49 % and 4.32 % of the bacterial operational taxonomic units (OTUs), respectively. Rhodanbacter lindaniclasticus and Pandoraea thiooxydans were the rarely seen potential degrading representatives that were simultaneously enriched and isolated. This study is the first comparative analysis of microbial communities from lindane and endosulfan enrichment culture using culture-dependent and culture-independent methods. Our results suggested that developing a target-specific and efficient microbial isolation method is necessary to harvest and study representative degrading bacteria in the community.

Vermicomposting Process to Endosulfan Lactone Removal in Solid Substrate Using Eisenia fetida

Pesticide by-products found in soil are usually more toxic and persistent than the pesticides themselves. For example, Endosulfan lactone (EL) (a by-product of the organochloride pesticide endosulfan). EL is created by the enzymatic activity (and related oxidative processes) of microorganisms in the soil. A sustainable method of EL removal is the introduction of Eisenia fetida earthworm. In this paper, it will be demonstrated the impact of vermicomposting process related to Eisenia fetida earthworm on EL by measuring initial and final concentrations of the compound and overall enzymatic activity in sterile and non-sterile solid substrate over 56 days. As a baseline, it be observed there were higher EL removals in non-sterile solid substrate (90.86%) at day 5 than in sterile solid substrate (83.86%) at day 14. In samples with Eisenia fetida, the presence of EL in non-sterile solid substrate was 36%, however in sterile solid substrate it was only 18% at day 1 and 7, with a maximum enzyme activity of 0.4659 mmol/mg protein per min at day 7. The evidence found in this study suggests that EL removal in a non-sterile solid substrate is higher when a vermicomposting is present and that the influence of microorganisms from the solid substrate with the earthworm, increases removal.

Gut bacteria of the silkworm Bombyx mori facilitate host resistance against the toxic effects of organophosphate insecticides

Organophosphate insecticides that are heavily used in agriculture for pest control have caused growing environmental problems and public health concerns worldwide. Ironically, insecticide resistance develops quickly in major lepidopteran pests, partially via their microbial symbionts. To investigate the possible mechanisms by which the microbiota confers insecticide resistance to Lepidoptera, the model organism silkworm Bombyx mori (Lepidoptera: Bombycidae) was fed different antibiotics to induce gut dysbiosis (microbiota imbalance). Larvae treated with polymyxin showed a significantly lower survival rate when exposed to chlorpyrifos. Through high-throughput sequencing, we found that the abundances of Stenotrophomonas and Enterococcus spp. changed substantially after treatment. To assess the roles played by these two groups of bacteria in chlorpyrifos resistance, a germ-free (GF) silkworm rearing protocol was established to avoid the influence of natural microbiota and antibiotics. Monoassociation of GF silkworms with Stenotrophomonas enhanced host resistance to chlorpyrifos, but not in Enterococcus-fed larvae, consistent with larval detoxification activity. GC-μECD detection of chlorpyrifos residues in feces indicated that neither Stenotrophomonas nor Enterococcus degraded chlorpyrifos directly in the gut. However, gut metabolomics analysis revealed a highly species-specific pattern, with higher levels of essential amino acid produced in the gut of silkworm larvae monoassociated with Stenotrophomonas. This critical nutrient provisioning significantly increased host fitness and thereby allowed larvae to circumvent the deleterious effects of these toxic chemicals more efficiently. Altogether, our study not only suggests a new mechanism for insecticide resistance in notorious lepidopteran pests but also provides a useful template for investigating the interplay between host and gut bacteria in complex environmental systems.

Bioremediation of diesel and gasoline-contaminated soil by co-vermicomposting amended with activated sludge: Diesel and gasoline degradation and kinetics

Present study aims to examine the efficiency of co-vermicomposting amended with activated sludge and E. fetida earthworm for bioremediation of diesel and gasoline from contaminated soil. The diesel and gasoline removal efficiency and degradation rates coefficients were estimated with gas chromatography (GC) analysis and first-order kinetics. The removal of gasoline and diesel in different co-vermicomposting processes with and without E. fetida ranged between 65-100% and 24.94-63.93%, respectively within 90- day experiment. Removal of gasoline and diesel increased in soil with addition of earthworm (E. fetida); higher degradation rate coefficients (k) were observed for co-vermicomposting with earthworm compared with co-vermicomposting processes. The highest k (0.014) for diesel degradation was estimated for microcosm reactor 4 (R4), where high numbers of E. fetida accelerate the less biodegradable organic contaminant from the soil matrices. The reasonable survival rates of earthworms in exposure to high concentration of petroleum-derivatives contaminated soils indicated increased activity of ligninolytic diesel-degrading earthworms and microorganisms. Therefore, co-vermicomposting amended with activated sludge is suggested as feasible and promising technologies for bioremediation of high content of organic contaminants from the soil matrices.

Bioaccumulation, physiological distribution, and biotransformation of tetrabromobisphenol a (TBBPA) in the geophagous earthworm Metaphire guillelmi - hint for detoxification strategy

The mechanisms underlying the bioaccumulation and detoxification of tetrabromobisphenol A (TBBPA) by terrestrial invertebrates are poorly understood. We used uniformly ring-¹⁴C-labelled TBBPA to investigate the bioaccumulation kinetics, metabolites distribution, and subsequent detoxification strategy of TBBPA in the geophagous earthworm Metaphire guillelmi in soil. The modeling of bioaccumulation kinetics showed a higher biota-soil-accumulation-factor of total ¹⁴C than that of the parent compound TBBPA, indicating that most of the ingested TBBPA was transformed into metabolites or sequestered as bound residues in the earthworms. Bound-residue formation in the digestive tract may hinder the accumulation of TBBPA in other parts of the body. Nonetheless, via the circulatory system, TBBPA was transferred to other tissues, especially the clitellum region, where sensitive organs are located. In the clitellum region, TBBPA was quickly transformed to less toxic dimethyl TBBPA ether and rapidly depurated through feces. We conclude that the detoxification of TBBPA in M. guillelmi occurred via bound-residue formation in the digestive tract as well as the generation and depuration of O-methylation metabolites. Our results provided direct evidence of TBBPA detoxification in earthworms. Further researches are needed to confirm whether O-methylation coupled with depuration is a common detoxification strategy for phenolic xenobiotics in other soil organisms needs to be determined.

Contributions of enzymes and gut microbes to biotransformation of perfluorooctane sulfonamide in earthworms (Eisenia fetida)

Perfluorooctane sulfonamide (FOSA) is known as a key intermediate of perfluorooctane sulfonic acid (PFOS) precursors, which can be frequently detected in the environment and biota. FOSA could be bioaccumulated in earthworms from soil, but the contributions of enzymes and gut microbes involved in the biotransformation of FOSA in earthworms have not been identified. Therefore, the effects of enzyme inhibitors and intestinal microflora on biotransformation of FOSA in earthworms were investigated in the present study. FOSA was biotransformed to form PFOS by earthworms obtained from in vivo and in vitro tests. The addition of FOSA had significantly positive effects on cytolchrome P450 (CYP450) and glutathione-s-transferase (GST) activities, suggesting CYP450 and GST are likely involved in the enzymatic transformation. In addition, both 1-Aminobenzotriazole (ABT) and ezatiostat hydrochloride (TLK199), which were selected to inhibit the CYP and GST enzymes, respectively, demonstrated inhibition effects on biotransformation of FOSA in earthworms with a dose-dependent relationship. However, the concentrations of FOSA weren't changed by the bacteria isolated from worm gut, suggesting that gut bacteria did not contribute to FOSA biotransformation in earthworms. The results of this study confirm that the transformation of FOSA in earthworms is mediated mainly by enzymes rather than by gut microbes.

Impact of pesticide monocrotophos on microbial populations and histology of intestine in the Indian earthworm Lampito mauritii (Kinberg)

Soil contamination has enlarged over the decades due to intensive use of pesticides and chemical fertilizers in agronomy. Earthworms are significant organisms in the soil community. Earthworms are the major role in soil fertility in most ecological system and the production of biogenic structures. Moreover, earthworm gut mucus enhances the beneficial soil microorganism potential biological activities. They are used as model organisms for assessing the ecological risks of chemicals. Enrichment of essential nutrients in soil through earthworm is a cost-effective and eco-friendly approach. In India, the organophosphorus pesticide monocrotophos is commonly used to control agricultural pests. Hence, it is important to study the effect of monocrotophos on the gut microbiota in Lampito mauritii. A 15-day exposure to a low (1/10th of the LC₅₀ after 96 h i.e., 0.093 ppm kg^-1) and high sublethal concentration (1/3rd of the LC₅₀ after 96 h i.e., 0.311 ppm kg^-1) of monocrotophos led to reduced proliferation of the gut microbiota in L. mauritii. However, exposure for 30 days led to a recuperation of the microbial populations to near control values. Among the eight bacterial and five fungal species that inhabit the gut of L. mauritii, only six bacterial and three fungal species were able to survive after exposure to monocrotophos. In addition to the study, histopathological changes were observed in the intestine of L.mauritii after application of lower sublethal concentration of monocrotophos. Severe pathological changes such as vacuolization, degenerated nuclei, damaged villi and congestion of the blood sinuses were noticed in the intestine on 1st and, 5th day of the experiment. But in 30th day the damages were slowly recovered due to degradation of monocrotophos by the presence of some pesticides degrading bacterial and fungal species and regenerative capability of chloragogen cells in the intestine. The results suggested that reduced microbial populations and pathological damages in intestine were observed during the application of monocrotophos. So, the monocrotophos have several harmful impacts on earthworms.

Deltamethrin impact in a cabbage planted soil: Degradation and effect on microbial community structure

Synthetic pyrethroids (SPs) are one of the most common pesticides used worldwide. Their use has greatly increased in the last decades and its' continuous application lead to added pesticides concentration in soil. Consequently, SPs may enter the food chain, affecting the environment and human health. The degradation over time of the pyrethroid pesticide deltamethrin applied to cabbages was monitored. The evolution was followed both on cabbages and the surrounding soils, and the soil microbial community characterized by next-generation sequencing of the 16S rRNA gene. The main shift in the microbial community structure was observed during the first 30 days after pesticides' application. The modification in the microbial community composition, where an increased abundance of Nocardioides sp. and Sphingomonas sp. were observed, was correlated respectively with the conversions of deltamethrin and its metabolite, 3-phenoxybenzoic acid (3-PBA). Although deltamethrin was not found in any of the tested samples (soil and cabbage) after 180 days, it caused an environmental impact much further than the 7 days security interval. These findings suggest that deltamethrin application can disturb soil microbial community and that natural biodegradation can have an important part in pesticides soil decontamination.

Influence of Novel Highly Pathogenic Avian Influenza A (H5N1) Virus Infection on Migrating Whooper Swans Fecal Microbiota

The migration of wild birds plays an important role in the transmission and spread of H5 highly pathogenic avian influenza (HPAI) virus, posing a severe risk to animal and human health. Substantial evidence suggests that altered gut microbial community is implicated in the infection of respiratory influenza virus. However, the influence of H5N1 infection in gut microbiota of migratory birds remains unknown. In January 2015, a novel recombinant H5N1 virus emerged and killed about 100 migratory birds, mainly including whooper swans in Sanmenxia Reservoir Area of China. Here, we describe the first fecal microbiome diversity study of H5N1-infected migratory birds. By investigating the influence of H5N1 infection on fecal bacterial communities in infected and uninfected individuals, we found that H5N1 infection shaped the gut microbiota composition by a difference in the dominance of some genera, such as Aeromonas and Lactobacillus. We also found a decreased α diversity and increased β diversity in infectious individuals. Our results highlight that increases in changes in pathogen-containing gut communities occur when individuals become infected with H5N1. Our study may provide the first evidence that there are statistical association among H5N1 presence and fecal microbiota compositional shifts, and properties of the fecal microbiota may serve as the risk of gut-linked disease in migrates with H5N1 and further aggravate the disease transmission.

Response of the bacterial community in an on-farm biopurification system, to which diverse pesticides are introduced over an agricultural season

A biopurification system (BPS) is used on-farm to clean pesticide-contaminated wastewater. Due to high pesticide loads, a BPS represents a hot spot for the proliferation and selection as well as the genetic adaptation of discrete pesticide degrading microorganisms. However, while considerable knowledge exists on the biodegradation of specific pesticides in BPSs, the bacterial community composition of these systems has hardly been explored. In this work, the Shannon diversity, the richness and the composition of the bacterial community within an operational BPS receiving wastewater contaminated with various pesticides was, for the first time, elucidated over the course of an agricultural season, using DGGE profiling and pyrosequencing of 16S rRNA gene fragments amplified from total community DNA. During the agricultural season, an increase in the concentration of pesticides in the BPS was observed along with the detection of significant community changes including a decrease in microbial diversity. Additionally, a significant increase in the relative abundance of Proteobacteria, mainly the Gammaproteobacteria, was found, and OTUs (operational taxonomic units) affiliated to Pseudomonas responded positively during the course of the season. Furthermore, a banding-pattern analysis of 16S rRNA gene-based DGGE fingerprinting, targeting the Alpha- and Betaproteobacteria as well as the Actinobacteria, indicated that the Betaproteobacteria might play an important role. Interestingly, a decrease of Firmicutes and Bacteroidetes was observed, indicating their selective disadvantage in a BPS, to which pesticides have been introduced.

Impact of the composition of the bacterial population and additional carbon source on the pathway and kinetics of degradation of endosulfan isomers

Abiotic and bacterial degradation is presented for the two isomers α- and β- of the organochlorine pesticide endosulfan, denoted as ES-1 and ES-2, respectively. Biodegradation studies were conducted with two indigenous species Pseudomonas putida (P. putida) and Rhodococcus sp. Both ES isomers rapidly hydrolyzed in water at pH ≥ 7 but the hydrolysis was inhibited in the presence of biomass. The pesticide partitioned onto the biomass making it unavailable for abiotic hydrolytic reaction. Spontaneous temperature dependent abiotic conversion of ES-2 to ES-1 was reported in the presence of dual air-water phases but was not observed in the abiotic aqueous phase. Biodegradation experiments with pure isomers showed a small amount of interconversion (∼5%) in either direction and ruled out any preferential interconversion of the ES-2 isomer to ES-1 or vice versa. Both the species were shown to degrade ES-2 at a higher rate compared to ES-1 which may lead to enrichment of ES-1 in agricultural fields in short-term following application of the pesticide. P. putida degraded both the ES isomers through oxidative and hydrolytic pathways while the Rhodococcus sp. used only the hydrolytic pathway. Since ES-S (product of the oxidative pathway) is orders of magnitude more toxic than the parent isomers, the short term toxicity of a field following the application of the pesticide may increase if the composition of the indigenous bacterial population is such that the oxidative pathway is preferred over the hydrolytic one. The presence of an additional carbon source increased the rates of degradation of both the isomers but the enhancement was greater for the degradation rate of ES-2 than ES-1.

Actinobacteria: Current research and perspectives for bioremediation of pesticides and heavy metals

Actinobacteria exhibit cosmopolitan distribution since their members are widely distributed in aquatic and terrestrial ecosystems. In the environment they play relevant ecological roles including recycling of substances, degradation of complex polymers, and production of bioactive molecules. Biotechnological potential of actinobacteria in the environment was demonstrated by their ability to remove organic and inorganic pollutants. This ability is the reason why actinobacteria have received special attention as candidates for bioremediation, which has gained importance because of the widespread release of contaminants into the environment. Among organic contaminants, pesticides are widely used for pest control, although the negative impact of these chemicals in the environmental balance is increasingly becoming apparent. Similarly, the extensive application of heavy metals in industrial processes lead to highly contaminated areas worldwide. Several studies focused in the use of actinobacteria for cleaning up the environment were performed in the last 15 years. Strategies such as bioaugmentation, biostimulation, cell immobilization, production of biosurfactants, design of defined mixed cultures and the use of plant-microbe systems were developed to enhance the capabilities of actinobacteria in bioremediation. In this review, we compiled and discussed works focused in the study of different bioremediation strategies using actinobacteria and how they contributed to the improvement of the already existing strategies. In addition, we discuss the importance of omic studies to elucidate mechanisms and regulations that bacteria use to cope with pollutant toxicity, since they are still little known in actinobacteria. A brief account of sources and harmful effects of pesticides and heavy metals is also given.

Microbial degradation of endosulfan in contaminated soil with the elution of surfactants

In this work, an endosulfan-degrading strain was isolated from the aged soil contaminated by endosulfan, and identified as Ochrobactrum sp. EB-4 by 16S rDNA sequence analysis. The microbial degradation characteristics of endosulfan in three eluents (Tween 80 + SDS, Tween 80 + Na2SiO3, Tween 80 + SDS + Na2SiO3) were investigated. The results showed that the degradation percents of α-, β-endosulfan in the three eluents were 86.83 %∼92.91 % and 88.90 %∼93.94 % in 15 days, respectively. The degradation process can be well described by the first-order kinetic model, and the half-times of α-endosulfan in eluent 1∼eluent 3 were 3.83, 5.29, and 4.53 days, while those of β-endosulfan were 3.35, 4.50 and 3.79 days, respectively. The endosulfan diol and endosulfan sulfate as main metabolites were detected, and the former can be further degraded by this strain, which revealed that the simultaneously happened hydrolysis and oxidation reactions were the main degradation processes, and dominated by hydrolysis reaction. After 5 days of washing with the eluents, 56.00∼84.33 % of α-endosulfan, and 46.49∼68.56 % of β-endosulfan in soil were eluted, respectively, and can be entirely biodegraded in 12 days, which indicated that the microbial degradation was the rate-determining step.

Rapid degradation of endosulfan by zero-valent zinc in water and soil

Endosulfan has been included in the list of persistent organic pollutants (POPs) in 2011. The degradation of endosulfan by zero-valent zinc in water and soil was first investigated. The results showed that >90% endosulfan could be degraded in 180 min. The degradation was accelerated under acidic conditions with the absence of dissolved oxygen, while the nature of the soil only exhibited a negligible effect. The half-life was decreased from 130.75 min to 41.75 min with the increment of Zn(0) from 0.1 g to 1 g in soil. The use of Zn(0) was more effective than Fe(0) for the degradation of endosulfan with a half-life of 110 min and 330 min. The cationic surfactant was more effective at enhancing the degradation of endosulfan than anionic and nonionic surfactant. The degradation pathway was speculated, and four chlorine of endosulfan were proposed to be reduced. The method exhibited obvious advantages over traditional endosulfan treatments, and the research results will lay a foundation for practical application of the method.

Biodegradation of endosulfan in broth medium and in soil microcosm by Klebsiella sp. M3

Nine endosulfan degrading bacterial strains were isolated by soil enrichment with endosulfan. Bacterial strain M3 was the most efficient degrader. Endosulfan degradation was accompanied by a decrease in pH of the medium and an increase in chloride ion concentration. The bacterium was tested for its ability to degrade endosulfan at different concentrations in broth and soil. Maximum degradation occurred at concentrations of 50 μg/ml of broth and 100 μg/g of soil. Values of Ks and Vmax were different for (α)- and (β)-endosulfan in broth. The kinetic indices (Vmax/Ks) for α-endosulfan and β-endosulfan were 0.051 and 0.048 day(-1) respectively, indicating that (α)-endosulfan was more rapidly degraded. Bacterial strain M3 was identified as Klebsiella sp. M3 on the basis of 16S rDNA sequence similarity (GenBank accession number JX273762).

Endosulfan induced alteration in bacterial protein profile and RNA yield of Klebsiella sp. M3, Achromobacter sp. M6, and Rhodococcus sp. M2

Three bacterial strains identified as Klebsiella sp. M3, Achromobacter sp. M6 and Rhodococcus sp. M2 were isolated by soil enrichment with endosulfan followed by shake flask enrichment technique. They were efficiently degrading endosulfan in the NSM (non sulfur medium) broth. Degradation of endosulfan was faster with the cell free extract of bacterial cells grown in the sulfur deficient medium (NSM) supplemented with endosulfan than that of nutrient rich medium (Luria Bertani). In the cell free extract of NSM supplemented with endosulfan as sole sulfur source, a unique band was visualized on SDS-PAGE but not with magnesium sulfate as the sole sulfur source in NSM and LB with endosulfan. Expression of a unique polypeptide band was speculated to be induced by endosulfan under sulfur starved condition. These unique polypeptide bands were identified as OmpK35 protein, sulfate binding protein and outer membrane porin protein, respectively, in Klebsiella sp. M3, Achromobacter sp. M6 and Rhodococcus sp. M2. Endosulfan showed dose dependent negative effect on total RNA yield of bacterial strains in nutrient rich medium. Absence of plasmid DNA indicated the presence of endosulfan metabolizing gene on genomic DNA.

Captivity results in disparate loss of gut microbial diversity in closely related hosts

The gastrointestinal tracts of animals contain diverse communities of microbes that provide a number of services to their hosts. There is recent concern that these communities may be lost as animals enter captive breeding programmes, due to changes in diet and/or exposure to environmental sources. However, empirical evidence documenting the effects of captivity and captive birth on gut communities is lacking. We conducted three studies to advance our knowledge in this area. First, we compared changes in microbial diversity of the gut communities of two species of woodrats (Neotoma albigula, a dietary generalist, and Neotoma stephensi, which specializes on juniper) before and after 6-9 months in captivity. Second, we investigated whether reintroduction of the natural diet of N. stephensi could restore microbial diversity. Third, we compared the microbial communities between offspring born in captivity and their mothers. We found that the dietary specialist, N. stephensi, lost a greater proportion of its native gut microbiota and overall diversity in response to captivity compared with N. albigula. Addition of the natural diet increased the proportion of the original microbiota but did not restore overall diversity in N. stephensi. Offspring of N. albigula more closely resembled their mothers compared with offspring-mother pairs of N. stephensi. This research suggests that the microbiota of dietary specialists may be more susceptible to captivity. Furthermore, this work highlights the need for further studies investigating the mechanisms underlying how loss of microbial diversity may vary between hosts and what an acceptable level of diversity loss may be to a host. This knowledge will aid conservation biologists in designing captive breeding programmes effective at maintaining microbial diversity. Sequence Accession Numbers: NCBI's Sequence Read Archive (SRA) - SRP033616.

A short-term study on the interaction of bacteria, fungi and endosulfan in soil microcosm

Endosulfan is one of the few organic chlorine insecticides still in use today in many developing countries. It has medium toxicity for fish and aquatic invertebrates. In this study, we added different concentrations of endosulfan to a series of soil samples collected from Baihua Park in Jinan, Shandong Province, China. Interactions of exogenous endosulfan, bacteria and fungi were analyzed by monitoring the changes in microbe-specific phospholipid fatty acids (PLFA), residual endosulfan and its metabolites which include; endosulfan sulfate, endosulfan lactone and endosulfan diol during a 9 days incubation period. Our results showed that endosulfan reduced fungi biomass by 47% on average after 9 days, while bacteria biomass increased 76% on average. In addition, we found that endosulfan degraded 8.62% in natural soil (NE), 5.51% in strepolin soil (SSE) and 2.47% in sterile soil (SE). Further analysis of the endosulfan metabolites in NE and SSE, revealed that the amount of endosulfan sulfate (ES) significantly increased and that of endosulfan lactone (EL) slightly decreased in both samples after 9 days. However, that of endosulfan diol (ED) increased in NE and decreased in SSE. After collective analysis our data demonstrated that fungi and bacteria responded differently to exogeous endosulfan, in a way that could promote the formation of endosulfan diol during endosulfan degradation.

Expression and inducibility of endosulfan metabolizing gene in Rhodococcus strain isolated from earthworm gut microflora for its application in bioremediation

The metabolizing potential of a bacterial strain Rhodococcus MTCC 6716, isolated from the gut of an Indian earthworm (Metaphire posthuma) was studied for endosulfan bioremediation. In the present work, the optimum conditions for the maximum growth, kinetic of endosulfan degradation, regression equation, half life and correlation coefficient were studied. Endosulfan induced alterations in the expression of mRNA and protein of specific endosulfan metabolizing marker gene (Esd) was studied. Maximum growth of bacteria was observed at pH 7.0, 30°C and 0.085 M sodium chloride concentration in a liquid culture medium. Endosulfan was degraded by Rhodococcus strain up to 97.23% within 15 days without producing toxic metabolite and with strong correlation coefficient (-0.728) and half life 5.99 days. Endosulfan degradation was mediated through gene(s) present in genomic DNA. Expression of marker gene was found endosulfan concentration dependent. The results suggest that this novel strain (Rhodococcus) may be utilized for bioremediation of endosulfan.

Toxicity and transformation of insecticide fenamiphos to the earthworm Eisenia fetida

This study was conducted to investigate the toxicity of the organophosphate insecticide fenamiphos to earthworms (Eisenia fetida) under laboratory conditions. Earthworms were exposed to soils differing in their physico-chemical properties spiked with fenamiphos at concentrations ranging from 10 to 200 mg kg(-1) for a period of 4 weeks. Residues of fenamiphos and its metabolites were determined in both soils and earthworms after 4 weeks of pesticide exposure. Fenamiphos was degraded faster in the alkaline soil than in the neutral and acidic soils. Median lethal concentration of fenamiphos in the neutral soil was 228 mg kg(-1) soil. Residues of fenamiphos caused a significant reduction in the biomass of worms, especially the ones exposed to the pesticide in the acidic soil. In vitro experiments suggested that fenamiphos was biotransformed in the earthworms principally to its oxide metabolite. To our knowledge, this is the first study demonstrating the biotransformation of fenamiphos by E. fetida.

Gut wall bacteria of earthworms: a natural selection process

Earthworms and microorganisms are interdependent and their interactions regulate the biogeochemistry of terrestrial soils. Investigating earthworm-microorganism interactions, we tested the hypothesis that differences in burrowing and feeding habits of anecic and endogeic earthworms are reflected by the existence of ecological group-specific gut wall bacterial communities. Bacterial community was detected using automated ribosomal intergenic spacer analysis of 16S and 23S genes and ribotype data was used to assess diversity and community composition. Using soil and earthworm samples collected from adjacent wheat-barley and grass-clover fields, we found that the anecic Lumbricus terrestris and L. friendi, the endogeic Aporrectodea caliginosa and A. longa (classically defined as anecic, but now known to possess endogeic characteristics) contain ecological group-specific gut wall-associated bacterial communities. The abundance of specific gut wall-associated bacteria (identified by sequence analysis of ribotype bands), including Proteobacteria, Firmicutes and an actinobacterium, was ecological group dependent. A microcosm study, conducted using A. caliginosa and L. terrestris and five different feeding regimes, indicated that food resource can cause shifts in gut wall-associated bacterial community, but the magnitude of these shifts did not obscure the delineation between ecological group specificity. Using A. caliginosa and A. longa samples collected in six different arable fields, we deduced that, within an ecological group, habitat was a more important determinant of gut wall-associated bacterial community composition than was host species. Hence, we conclude that the selection of bacteria associated with the gut wall of earthworms is a natural selection process and the strongest determinant of this process is in the order ecological group>habitat>species.

Biodegradation of dimethyl phthalate, diethyl phthalate and di-n-butyl phthalate by Rhodococcus sp. L4 isolated from activated sludge

In this study, an aerobic bacterial strain capable of utilizing dimethyl phthalate (DMP), diethyl phthalate (DEP) and di-n-butyl phthalate (DBP) as sole carbon source and energy was isolated from activated sludge collected from a dyeing plant. According to its morphology, physiochemical characteristics and 16S rDNA sequence, the strain was identified as Rhodococcus ruber. The biodegradation batch tests of DMP, DEP and DBP by the Rhodococcus sp. L4 showed the optimal pH value, temperature and substrate concentration: pH 7.0-8.0, 30-37 degrees C and PAEs concentration <or=450 mg/L. Kinetics of degradation have also been performed at different initial concentrations. The results show that the degradation can be described with exponential model. The half-life of degradation was about 1.30 days when the concentration of PAEs mixture was lower than 300 mg/L. PAEs contaminated water samples (300 mg/L) with non-emulsification and completed emulsification were prepared to investigate the effect on PAEs degradation rate. Little difference between the above two sample preparations was observed in terms of ultimate degradation rate. Rhodococcus sp. L4 can also grow on phenol, sodium benzoate or naphthalene solution as sole carbon source and energy which suggests its ability in resisting environmental toxicants. This work provides some new evidence for the possibility of applying Rhodococcus for contaminated water remediation in the area of industry.

Earthworm assisted bioremediation of organic contaminants

Due to their biological, chemical and physical actions, earthworms can be directly employed within bioremediation strategies to promote biodegradation of organic contaminants. Earthworms have been shown to aerate and bioturbate soils and improve their nutritional status and fertility, which are variables known to limit bioremediation. Earthworms have also been shown to retard the binding of organic contaminants to soils, release previously soil-bound contaminants for subsequent degradation, and promote and disperse organic contaminant degrading microorganisms. This review discusses these earthworm actions upon the soil environment and how they might influence the fate and behaviour of soil associated organic contaminants, subsequently improving bioremediation potential. The latter part of this review considers organic compounds in the following order: agrochemicals, petroleum and crude oil hydrocarbons, PAHs and PCBs.