Biodegradation of DDT by Stenotrophomonas sp. DDT-1: Characterization and genome functional analysis

Microbiology and Biochemistry of Pesticides Biodegradation

Pesticides are chemicals used in agriculture, forestry, and, to some extent, public health. As effective as they can be, due to the limited biodegradability and toxicity of some of them, they can also have negative environmental and health impacts. Pesticide biodegradation is important because it can help mitigate the negative effects of pesticides. Many types of microorganisms, including bacteria, fungi, and algae, can degrade pesticides; microorganisms are able to bioremediate pesticides using diverse metabolic pathways where enzymatic degradation plays a crucial role in achieving chemical transformation of the pesticides. The growing concern about the environmental and health impacts of pesticides is pushing the industry of these products to develop more sustainable alternatives, such as high biodegradable chemicals. The degradative properties of microorganisms could be fully exploited using the advances in genetic engineering and biotechnology, paving the way for more effective bioremediation strategies, new technologies, and novel applications. The purpose of the current review is to discuss the microorganisms that have demonstrated their capacity to degrade pesticides and those categorized by the World Health Organization as important for the impact they may have on human health. A comprehensive list of microorganisms is presented, and some metabolic pathways and enzymes for pesticide degradation and the genetics behind this process are discussed. Due to the high number of microorganisms known to be capable of degrading pesticides and the low number of metabolic pathways that are fully described for this purpose, more research must be conducted in this field, and more enzymes and genes are yet to be discovered with the possibility of finding more efficient metabolic pathways for pesticide biodegradation.

Stenotrophomonas in diversified cropping systems: friend or foe?

In the current scenario, the use of synthetic fertilizers is at its peak, which is an expensive affair, possesses harmful effects to the environment, negatively affecting soil fertility and beneficial soil microfauna as well as human health. Because of this, the demand for natural, chemical-free, and organic foods is increasing day by day. Therefore, in the present circumstances use of biofertilizers for plant growth-promotion and microbe-based biopesticides against biotic stresses are alternative options to reduce the risk of both synthetic fertilizers and pesticides. The plant growth promoting rhizobacteria (PGPR) and microbial biocontrol agents are ecologically safe and effective. Owning their beneficial properties on plant systems without harming the ecosystem, they are catching the widespread interest of researchers, agriculturists, and industrialists. In this context, the genus Stenotrophomonas is an emerging potential source of both biofertilizer and biopesticide. This genus is particularly known for producing osmoprotective substances which play a key role in cellular functions, i.e., DNA replication, DNA-protein interactions, and cellular metabolism to regulate the osmotic balance, and also acts as effective stabilizers of enzymes. Moreover, few species of this genus are disease causing agents in humans that is why; it has become an emerging field of research in the present scenario. In the past, many studies were conducted on exploring the different applications of Stenotrophomonas in various fields, however, further researches are required to explore the various functions of Stenotrophomonas in plant growth promotion and management of pests and diseases under diverse growth conditions and to demonstrate its interaction with plant and soil systems. The present review discusses various plant growth and biocontrol attributes of the genus Stenotrophomonas in various food crops along with knowledge gaps. Additionally, the potential risks and challenges associated with the use of Stenotrophomonas in agriculture systems have also been discussed along with a call for further research in this area.

Assessment of risks, implications, and opportunities of waterborne neurotoxic pesticides

Pesticides are a well-known family of chemicals that have contaminated water systems globally. Four common subfamilies of pesticides include organochlorines, organophosphates, pyrethroids, and carbamate insecticides which have been shown to adversely affect the human nervous system. Studies have shown a link between pesticide exposure and decreased viability, proliferation, migration, and differentiation of murine neural stem cells. Besides human exposure directly through water systems, additional factors such as pesticide bioaccumulation, biomagnification and potential synergism due to co-exposure to other environmental contaminants must be considered. A possible avenue to investigate the molecular mechanisms and biomolecules impacted by the various classes of pesticides includes the field of -omics. Discovery of the precise molecular mechanisms behind pesticide-mediated neurodegenerative disorders may facilitate development of targeted therapeutics. Likewise, discovery of pesticide biodegradation pathways may enable novel approaches for water system bioremediation using genetically engineered microorganisms. In this mini-review, we discuss recently established harmful impacts of various categories of pesticides on the nervous system and the application of -omics field for discovery, validation, and mitigation of pesticide neurotoxicity.

Managing the efficiencies of three different bacterial isolates for removing atrazine from wastewater

Three individual bacterial isolates previously isolated from two types of soil with a different history of atrazine applications were chosen, purified, and subjected to subsequent work. Identification of the individual bacterial isolates was conducted using molecular methods 16S rRNA and then tested for their atrazine degradation potentials. Effects of different parameters like mixing, starvation, UV exposure, and sodium citrate for enhancing the atrazine bioremediation process by identified bacteria were also studied. The molecular method identified individual bacterial isolates as Stenotrophomonas sp. strain SD2 (strain SD2), Bacillus cereus strain BC3 (strain BC3), and Paenarthrobacter ureafaciens strain AD3 (strain AD3). The bacterial isolate strain AD3 was able to degrade 47.95% of atrazine after 28 days. Mixing strain AD3 with strain BC3 showed almost doubled of atrazine degradation percentage (61.39%) of using strain BC3 as an individual isolate (36.59%). The atrazine degradation efficacy for Stenotrophomonas sp. strain SD2, Bacillus cereus strain BC3, and Paenarthrobacter ureafaciens strain AD3 was increased between 1.28 and 4.32 folds after the starvation process. The UV exposure enhanced the efficiencies of the tested isolates either individual or mixtures (from 1.08 to 4.63-fold). Adding sodium citrate as a stimulator to the media of growing the tested isolates enhanced their potential for atrazine degradation.

Biotechnological tools to elucidate the mechanism of pesticide degradation in the environment

Pesticides are widely used in agriculture, households, and industries; however, they have caused severe negative effects on the environment and human health. To clean up pesticide contaminated sites, various technological strategies, i.e. physicochemical and biological, are currently being used throughout the world. Biological approaches have proven to be a viable method for decontaminating pesticide-contaminated soils and water environments. The biological process eliminates contaminants by utilizing microorganisms' catabolic ability. Pesticide degradation rates are influenced by a variety of factors, including the pesticide's structure, concentration, solubility in water, soil type, land use pattern, and microbial activity in the soil. There is currently a knowledge gap in this field of study because researchers are unable to gather collective information on the factors affecting microbial growth, metabolic pathways, optimal conditions for degradation, and genomic, transcriptomic, and proteomic changes caused by pesticide stress on the microbial communities. The use of advanced tools and omics technology in research can bridge the existing gap in our knowledge regarding the bioremediation of pesticides. This review provides new insights on the research gaps and offers potential solutions for pesticide removal from the environment through the use of various microbe-mediated technologies.

Genome Characterisation of an Isoprene-Degrading Alcaligenes sp. Isolated from a Tropical Restored Forest

Isoprene is a climate-active biogenic volatile organic compound (BVOC), emitted into the atmosphere in abundance, mainly from terrestrial plants. Soil is an important sink for isoprene due to its consumption by microbes. In this study, we report the ability of a soil bacterium to degrade isoprene. Strain 13f was isolated from soil beneath wild Himalayan cherry trees in a tropical restored forest. Based on phylogenomic analysis and an Average Nucleotide Identity score of >95%, it most probably belongs to the species Alcaligenes faecalis. Isoprene degradation by Alcaligenes sp. strain 13f was measured by using gas chromatography. When isoprene was supplied as the sole carbon and energy source at the concentration of 7.2 × 105 ppbv and 7.2 × 106 ppbv, 32.6% and 19.6% of isoprene was consumed after 18 days, respectively. Genome analysis of Alcaligenes sp. strain 13f revealed that the genes that are typically found as part of the isoprene monooxygenase gene cluster in other isoprene-degrading bacteria were absent. This discovery suggests that there may be alternative pathways for isoprene metabolism.

Pesticide residues in drinking water, their potential risk to human health and removal options

The application of pesticides in agricultural and public health sectors has resulted in substantially contaminated water resources with residues in many countries. Almost no reviews have addressed pesticide residues in drinking water globally; calculated hazard indices for adults, children, and infants; or discussed the potential health risk of pesticides to the human population. The objectives of this article were to summarize advances in research related to pesticide residues in drinking water; conduct health risk assessments by estimating the daily intake of pesticide residues consumed only from drinking water by adults, children, and infants; and summarize options for pesticide removal from water systems. Approximately 113 pesticide residues were found in drinking water samples from 31 countries worldwide. There were 61, 31, and 21 insecticide, herbicide, and fungicide residues, respectively. Four residues were in toxicity class IA, 14 residues were in toxicity class IB, 55 residues were in toxicity class II, 17 residues were in toxicity class III, and 23 residues were in toxicity class IV. The calculated hazard indices (HIs) exceeded the value of one in many cases. The lowest HI value (0.0001) for children was found in Canada, and the highest HI value (30.97) was found in Egypt, suggesting a high potential health risk to adults, children, and infants. The application of advanced oxidation processes (AOPs) showed efficient removal of many pesticide classes. The combination of adsorption followed by biodegradation was shown to be an effective and efficient purification option. In conclusion, the consumption of water contaminated with pesticide residues may pose risks to human health in exposed populations.

Plasmid-mediated catabolism for the removal of xenobiotics from the environment

The large-scale application of xenobiotics adversely affects the environment. The genes that are present in the chromosome of the bacteria are considered nonmobile, whereas the genes present on the plasmids are considered mobile genetic elements. Plasmids are considered indispensable for xenobiotic degradation into the contaminated environment. In the contaminated sites, bacteria with plasmids can transfer the mobile genetic element into another strain. This mechanism helps in spreading the catabolic genes into the bacterial population at the contaminated sites. The indigenous microbial strains with such degradative plasmids are important for the bioremediation of xenobiotics. Environmental factors play a critical role in the conjugation efficiency, which is involved in the bioremediation of the xenobiotics at the contaminated sites. However, there is still a need for more research to fill in the gaps regarding plasmids and their impact on bioremediation. This review explores the role of bacterial plasmids in the bioremediation of xenobiotics from contaminated environments.

1,1,1-trichloro-2,2-bis (p-chlorophenyl)-ethane (DDT) and 1,1-Dichloro-2,2-bis (p, p'-chlorophenyl) ethylene (DDE) as endocrine disruptors in human and wildlife: A possible implication of mitochondria

1,1,1-trichloro-2,2-bis (p-chlorophenyl)-ethane (DDT) and its main metabolite 1,1-Dichloro-2,2-bis (p, p'-chlorophenyl) ethylene (DDE) act as endocrine disruptors in humans and wildlife. Immunomodulatory functions have also been attributed to both xenobiotics. DDT was banned in the 1970s due to its toxicity, but it is still produced and used for indoor residual spraying with disease vector control purposes. Due to their persistence and lipophilic properties, DDT and DDE can bioaccumulate through the food chain, being stored in organisms' adipose depots. Their endocrine disruptor function is mediated by agonist or antagonist interaction with nuclear receptors. Present review aimed to provide an overview of how DDT and DDE exposure impacts reproductive and immune systems with estrogen-disrupting action in humans and wildlife. Studies showing DDT and DDE impact on mitochondrial function and apoptosis pathway will also be reviewed, suggesting the hypothesis of direct action on mitochondrial steroid receptors.

Do dissipation and transformation of γ-HCH and p,p'-DDT in soil respond to a proxy for climate change? Insights from a field study on the eastern Tibetan Plateau

While the influence of climate change on the fate of persistent organic pollutants (POPs) is becoming a topic of global concern, it has yet to be demonstrated how POPs and their transformation products in soil respond to a changing climate at the local scale. We conducted a year-long field experiment with spiked soils to investigate the impact of climate on the dissipation of γ-hexachlorocyclohexane (γ-HCH) and p,p'-dichlorodiphenyltrichloroethane (p,p'-DDT) as well as the formation of their products. Four sites along an elevational gradient on the eastern Tibetan Plateau were selected to represent four scenarios ranging from a dry and cold to a warm and humid climate. Based on the measured concentrations of the two pesticides and their transformation products, we calculated the dissipation rates of γ-HCH and p,p'-DDT in soil using two biphasic kinetic models, and the formation rates of transformation products using a mid-point rectangular approximation method. The spiked γ-HCH generally showed the expected decrease in dissipation from soils with increasing altitudes, and therefore decreasing temperature and precipitation, whereas dissipation of p,p'-DDT was influenced more by photolysis and sequestration in soil. The formation rates of the primary products of γ-HCH (i.e. γ-HCH→PeCCH and γ-HCH→TeCCH) and p,p'-DDT (i.e. p,p'-DDT→p,p'-DDE and p,p'-DDT→p,p'-DDD) indicate that a warmer and wetter climate favors dechloroelimination (anaerobic biodegradation) over dehydrochlorination (aerobic biodegradation). The significantly longer dissipation half-lives of γ-HCH at the coldest site suggests that the fate of POPs in frozen regions (e.g. polar regions) needs more attention. Overall, the fate of more volatile chemicals (e.g. γ-HCH) might be more responsive to the climate change.

Bioremediation characteristics, influencing factors of dichlorodiphenyltrichloroethane (DDT) removal by using non-indigenous Paracoccus sp

The marine bacterium able to consume DDT as the nutrient source was isolated from sea water which was identified as Paracoccus sp. DDT-21 based on 16 S rDNA gene sequence and Gram negative rod, obligate aerobic, non-motile biochemical characteristics. The isolate can degrade over 80% of the DDT, at a concentration of 50 mg/L in MSM in 72 h. Time and pollutant (DDT) dependent growth studies indicated that the isolate Paracoccus sp., DDT-21 significantly degrade the DDT and tolerates under DDT stress up to 50 mg/L. The DDT degradation capability of the strain Paracoccus sp. DDT-21 was found to be 5 ˃ 10 ˃ 15 ˃ 25 ˃ 50 mg/L DDT. The high concentrations (75 and 100 mg/L) of DDT showed significant decrease in DDT degradation. The optimal DDT degradation (∼90.0%) was observed at 6 g/L of yeast extract, 6% of glucose in pH 7.0 at 35 °C with 72 h of incubation as constant. Furthermore, four metabolites were observed by GC-MS analysis such as, DDE, DDD, DDMU, and DDA. The obtained results indicate that the isolate Paracoccus sp. DDT-21 is a promising candidate for the removal and/or detoxification of DDT in the environment.

Beneficial microbiomes for bioremediation of diverse contaminated environments for environmental sustainability: present status and future challenges

Over the past few decades, the rapid development of agriculture and industries has resulted in contamination of the environment by diverse pollutants, including heavy metals, polychlorinated biphenyls, plastics, and various agrochemicals. Their presence in the environment is of great concern due to their toxicity and non-biodegradable nature. Their interaction with each other and coexistence in the environment greatly influence and threaten the ecological environment and human health. Furthermore, the presence of these pollutants affects the soil quality and fertility. Physicochemical techniques are used to remediate such environments, but they are less effective and demand high costs of operation. Bioremediation is an efficient, widespread, cost-effective, and eco-friendly cleanup tool. The use of microorganisms has received significant attention as an efficient biotechnological strategy to decontaminate the environment. Bioremediation through microorganisms appears to be an economically viable and efficient approach because it poses the lowest risk to the environment. This technique utilizes the metabolic potential of microorganisms to clean up contaminated environments. Many microbial genera have been known to be involved in bioremediation, including Alcaligenes, Arthrobacter, Aspergillus, Bacillus, Burkholderia, Mucor, Penicillium, Pseudomonas, Stenotrophomonas, Talaromyces, and Trichoderma. Archaea, including Natrialba and Haloferax, from extreme environments have also been reported as potent bioresources for biological remediation. Thus, utilizing microbes for managing environmental pollution is promising technology, and, in fact, the microbes provide a useful podium that can be used for an enhanced bioremediation model of diverse environmental pollutants.

Whole genome strategies and bioremediation insight into dehalogenase-producing bacteria

An integral approach to decoding both culturable and uncultured microorganisms' metabolic activity involves the whole genome sequencing (WGS) of individual/complex microbial communities. WGS of culturable microbes, amplicon sequencing, metagenomics, and single-cell genome analysis are selective techniques integrating genetic information and biochemical mechanisms. These approaches transform microbial biotechnology into a quick and high-throughput culture-independent evaluation and exploit pollutant-degrading microbes. They are windows into enzyme regulatory bioremediation pathways (i.e., dehalogenase) and the complete bioremediation process of organohalide pollutants. While the genome sequencing technique is gaining the scientific community's interest, it is still in its infancy in the field of pollutant bioremediation. The techniques are becoming increasingly helpful in unraveling and predicting the enzyme structure and explore metabolic and biodegradation capabilities.

Isolation, Biochemical and Genomic Characterization of Glyphosate Tolerant Bacteria to Perform Microbe-Assisted Phytoremediation

The large-scale use of the herbicide glyphosate leads to growing ecotoxicological and human health concerns. Microbe-assisted phytoremediation arises as a good option to remove, contain, or degrade glyphosate from soils and waterbodies, and thus avoid further spreading to non-target areas. To achieve this, availability of plant-colonizing, glyphosate-tolerant and -degrading strains is required and at the same time, it must be linked to plant-microorganism interaction studies focusing on a substantive ability to colonize the roots and degrade or transform the herbicide. In this work, we isolated bacteria from a chronically glyphosate-exposed site in Argentina, evaluated their glyphosate tolerance using the minimum inhibitory concentration assay, their in vitro degradation potential, their plant growth-promotion traits, and performed whole genome sequencing to gain insight into the application of a phytoremediation strategy to remediate glyphosate contaminated agronomic soils. Twenty-four soil and root-associated bacterial strains were isolated. Sixteen could grow using glyphosate as the sole source of phosphorous. As shown in MIC assay, some strains tolerated up to 10000 mg kg^–1 of glyphosate. Most of them also demonstrated a diverse spectrum of in vitro plant growth-promotion traits, confirmed in their genome sequences. Two representative isolates were studied for their root colonization. An isolate of Ochrobactrum haematophilum exhibited different colonization patterns in the rhizoplane compared to an isolate of Rhizobium sp. Both strains were able to metabolize almost 50% of the original glyphosate concentration of 50 mg l^–1 in 9 days. In a microcosms experiment with Lotus corniculatus L, O. haematophilum performed better than Rhizobium, with 97% of glyphosate transformed after 20 days. The results suggest that L. corniculatus in combination with to O. haematophilum can be adopted for phytoremediation of glyphosate on agricultural soils. An effective strategy is presented of linking the experimental data from the isolation of tolerant bacteria with performing plant-bacteria interaction tests to demonstrate positive effects on the removal of glyphosate from soils.

Mass spectrometry-based identification of bacteria isolated from industrially contaminated site in Salamanca (Mexico) and evaluation of their potential for DDT degradation

Longstanding industrial deposits of 1-chloro-4-[2,2,2-trichloro-1-(4-chlorophenyl)ethyl]benzene (DDT) impose environmental threat in Salamanca city, located in central Mexico. Native bacteria from this location were isolated and identified, and their potential utility for DDT biodegradation was examined. Twenty-five isolates were obtained, and cell lysates were analyzed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) with Biotyper^TR; twenty-one organisms were identified at species level, and the other four were assigned to genus. The most abundant species corresponded to Bacillus (44%) and Pseudomonas genera (20%). Eight bacteria could grow in the presence of 200 mg/L of DDT. Two-week exposure of Lysinibacillus fusiformis, Bacillus mycoides, Bacillus pumilus, and Bacillus cereus to DDT 50 mg/L and 200 mg/L, caused percentage pesticide degradation in the range 41-48% and 26-31%, respectively. Other four bacteria presented lower degradation rates. Gas chromatography-mass spectrometry (GC-MS) analysis of the spent media revealed that eight isolates assisted the conversion of DDT, DDD (1,1-dichloro-2,2-bis-(4-chlorophenyl)ethane), and DDE (1,1-dichloro-2,2-bis-(4-chlorophenyl)ethylene) to DDMU (1,1-(2-chloro-1,1-ethenediyl)-bis-(4-chlorobenzene)); however, DDNU (2,2-bis(4-chlorophenyl)ethylene), DBP (4,4'-dichlorobenzophenone(bis(4-chlorophenyl)methanone)) and DBH (bis(4-chlorophenyl)methanol) were found only for L. fusiformis, B. mycoides, B. cereus, B. marisflavi, and B. megaterium. Within the context of DDT biodegradation, the first three were the most promising isolates and further studies will be aimed at setting the experimental conditions for efficient mineralization of DDT congeners.

Monitoring of DDT in Agricultural Soils under Organic Farming in Poland and the Risk of Crop Contamination

The analysis of 142 agricultural soil samples collected in organic farms across Poland with the intent to evaluate the level of DDT contamination resulted in more than 80% of the soils containing DDT. The ΣDDT (sum of all metabolites and isomers) concentration ranged between 0.005 and 0.383 mg/kg ΣDDT, with an average value of 0.064 mg/kg ΣDDT. However, the majority of plant samples collected from the crops growing on the sampled soils did not contain detectable DDT residues. The high DDT pollution levels detected in samples from four voivodeships (regions) among those monitored have been hypothesised to be linked to horticultural productions occurring to the sampled fields and typical of those regions, particularly in big-sized farms, during the period of DDT application, as well as the number of pesticides landfills present in these voivodeships. The elaboration of the o,p'-DDT/p,p'-DDT and DDT/(DDE + DDD) ratios to appraise the source or the period of contamination suggested that the contamination originated from past use of DDT rather than from impurities of more recent applications of other formulated substances. Such outcome thus suggests that the risk of contamination of organic products is likely derived from general environmental pollution levels rather than from the use of unauthorised substances in organic farming productions. Data from a trial with artificial contamination of soils indicated that using the DDT/(DDE + DDD) ratio in the presence of a low level of contamination could be less reliable than in highly contaminated soils.

Optimization of microbial assisted phytoremediation of soils contaminated with pesticides

580 microbial strains were isolated from the rhizosphere of the plants Cucurbita pepo L. and Xanthium strumarium grown on soil contaminated with dichlorodiphenyltrichloroethane (DDT) and its metabolites. During the cultivation, two bacterial strains were selected because of their ability to grow on media containing 0.5-5.0 mg L^-1 of dichlorodiphenyldichloroethylene (DDE) as the sole carbon source. They were identified as Bacillus vallismortis and Bacillus aryabhattai. Both of these species were shown to have a high capacity for the utilization of DDE - more than 90% of which was consumed after 21 days of cultivation. Laboratory experiments were carried out then to assess the possibility of using these strains for the decontamination of organochlorine pesticides (OCPs) contaminated soils. Inoculation of C. pepo and X. strumarium with our isolates B. vallismortis and B. aryabhattai resulted in a reduction of the pollutant stress to the plants as shown by an increase both in aboveground and in root biomass. The microorganisms enhanced the uptake and phytostabilization potential of C. pepo and X. strumarium and can be applied for the treatment of DDE contaminated soils.

Cu–Fe Incorporated Graphene-Oxide Nanocomposite as Highly Efficient Catalyst in the Degradation of Dichlorodiphenyltrichloroethane (DDT) from Aqueous Solution

Abstract

Fe/graphene oxide and Cu–Fe/graphene oxide nanocomposite were synthesized by the atomic implantation method to study the photocatalytic degradation of dichlorodiphenyltrichloroethane (DDT). The synthesized nanocomposites were characterized by the XRD, N2 isotherms, SEM with EDX, TEM and XPS analysis. Characterization results have reported that oxides of Cu and Fe were uniformly distributed on graphene oxide and exited in the form of Cu+ and Fe2+ ions in Cu–Fe/graphene oxide nanocomposite. The high photocatalytic DDT removal efficiency 99.7% was obtained for Cu–Fe/graphene oxide under the optimal condition of 0.2 g/L catalyst, 15 mg/L H2O2 and pH 5. It was attributed to the reduction of Fe3+ to Fe2+ by Cu+ ions and –OH radicals formation. However, it was dropped to 90.4% in the recycling study by leaching of iron and without a change in phase structure and morphology.

Graphic Abstract

Phytoremediation and Bioremediation of Pesticide-Contaminated Soil

Management and destruction of obsolete pesticides and the remediation of pesticide-contaminated soil are significant global issues with importance in agriculture, environmental health and quality of life. Pesticide use and management have a history of problems because of insufficient knowledge of proper planning, storage, and use. This manuscript reviews recent literature with an emphasis on the management of obsolete pesticides and remediation of pesticide-contaminated soil. The rhizosphere of plants is a zone of active remediation. Plants also take up contaminated water and remove pesticides from soil. The beneficial effects of growing plants in pesticide-contaminated soil include pesticide transformation by both plant and microbial enzymes. This review addresses recent advances in the remediation of pesticide-contaminated soil with an emphasis on processes that are simple and can be applied widely in any country.

The genome of Alcaligenes aquatilis strain BU33N: Insights into hydrocarbon degradation capacity

Environmental contamination with hydrocarbons though natural and anthropogenic activities is a serious threat to biodiversity and human health. Microbial bioremediation is considered as the effective means of treating such contamination. This study describes a biosurfactant producing bacterium capable of utilizing crude oil and various hydrocarbons as the sole carbon source. Strain BU33N was isolated from hydrocarbon polluted sediments from the Bizerte coast (northern Tunisia) and was identified as Alcaligenes aquatilis on the basis of 16S rRNA gene sequence analysis. When grown on crude oil and phenanthrene as sole carbon and energy sources, isolate BU33N was able to degrade ~86%, ~56% and 70% of TERHc, n-alkanes and phenanthrene, respectively. The draft genome sequence of the A. aquatilis strain BU33N was assembled into one scaffold of 3,838,299 bp (G+C content of 56.1%). Annotation of the BU33N genome resulted in 3,506 protein-coding genes and 56 rRNA genes. A large repertoire of genes related to the metabolism of aromatic compounds including genes encoding enzymes involved in the complete degradation of benzoate were identified. Also genes associated with resistance to heavy metals such as copper tolerance and cobalt-zinc-cadmium resistance were identified in BU33N. This work provides insight into the genomic basis of biodegradation capabilities and bioremediation/detoxification potential of A. aquatilis BU33N.

Evidence of non-DDD pathway in the anaerobic degradation of DDT in tropical soil

DDT transformation to DDD in soil is the most commonly reported pathway under anaerobic conditions. A few instances of DDT conversion to products other than DDD/DDE have been reported under aerobic conditions and hardly any under anaerobic conditions. In particular, few reports exist on the anaerobic degradation of DDT in African tropical soils, despite DDT contamination arising from obsolete pesticide stockpiles in the continent as well as new contamination from DDT use for mosquito and tsetse fly control. Moreover, the development of possible remediation strategies for contaminated sites demands adequate understanding of different soil processes and their effect on DDT persistence, hence necessitating the study. The aim of this work was to study the effect of simulated anaerobic conditions and slow-release carbon sources (compost) on the dissipation of DDT in two tropical clay soils (paddy soil and field soil) amenable to periodic flooding. The results showed faster DDT dissipation in the field soil but higher metabolite formation in the paddy soil. To explain this paradox, the levels of dissolved organic carbon and carbon mineralization (CH₄ and CO₂) were correlated with p,p-DDT and p,p-DDD concentrations. It was concluded that DDT underwent reductive degradation (DDD pathway) in the paddy soil and both reductive (DDD pathway) and oxidative degradation (non-DDD pathway) in the field soil.

Antimicrobial Resistance in Stenotrophomonas spp

Bacteria of the genus Stenotrophomonas are found throughout the environment, in close association with soil, sewage, and plants. Stenotrophomonas maltophilia, the first member of this genus, is the predominant species, observed in soil, water, plants, animals, and humans. It is also an opportunistic pathogen associated with the increased number of infections in both humans and animals in recent years. In this article, we summarize all Stenotrophomonas species (mainly S. maltophilia) isolated from animals and food products of animal origin and further distinguish all isolates based on antimicrobial susceptibility and resistance phenotypes. The various mechanisms of both intrinsic and acquired antimicrobial resistance, which were mainly identified in S. maltophilia isolates of nosocomial infections, have been classified as follows: multidrug efflux pumps; resistance to β-lactams, aminoglycosides, quinolones, trimethoprim-sulfamethoxazole, and phenicols; and alteration of lipopolysaccharide and two-component regulatory systems. The dissemination, coselection, and persistence of resistance determinants among S. maltophilia isolates have also been elaborated.

Ecological risk assessment of pesticide mixtures in the alluvial aquifers of central Italy: Toward more realistic scenarios for risk mitigation

In this study we used the data of an extensive pesticide monitoring survey that took place in 11 alluvial aquifers of central Italy from 2010 to 2015 to explore 4 different scenarios of risk. The Scenarios 1 and 2 were used to depict the risk of failing to meet the good groundwater chemical status as defined by the Water Framework Directive. The Scenarios 3 and 4 were used to assess for the first time the ecological risk in groundwater bodies, defined as the likelihood of hazard to the groundwater communities stably residing in the 11 alluvial aquifers that may be affected by pesticide contamination. The ecological risk was assessed through a new procedure called GERAp (Groundwater Ecological Risk Assessment due to pesticides). The main results of this study highlighted that: 1) the Scenario 1 provided information of little use for risk managers; 2) more realistic information was provided by using the highest concentrations measured in the six-year monitoring period and considering the ecological risk in a combined scenario (Scenarios 2 and 4); 3) the achievement of the good chemical status by 2027 in 3 aquifers will be likely much more difficult than in the others because the ecosystem services, such as pesticide biodegradation, are likely less efficient in the 3 groundwater bodies; 4) some pesticides that were banned in Europe in 2009 should be kept monitored in the next surveys because they showed a persistent occurrence in the 11 aquifers; 5) DDT forms, Dieldrin and Heptachlor are expected to damage groundwater communities at concentrations that are lower than the present legal limits.

Dissemination of antibiotic resistance genes and human pathogenic bacteria from a pig feedlot to the surrounding stream and agricultural soils

The dissemination of antibiotic resistance genes (ARGs), human pathogenic bacteria (HPB), and antibiotic-resistant HPB (ARHPB) from animal feedlot to nearby environment poses a potentially high risk to environmental ecology and public health. Here, a metagenomic analysis was employed to explore the dissemination of ARGs, HPB, and ARHPB from a pig feedlot to surrounding stream and agricultural soils. In total, not detectable (ND)-1,628.4 μg/kg of antibiotic residues, 18 types of ARGs, 48 HPB species, and 216 ARB isolates were detected in all samples. Antibiotic residues from pig feedlot mainly migrated into stream sediments and greenhouse soil. The dominant ARGs and HPB species from pig feedlot spread into stream sediments (tetracycline resistance genes, Clostridium difficile, and Mycobacterium tuberculosis), stream water (multidrug resistance (MDR) genes, Shigella flexneri, and Bordetella pertussis), and greenhouse soil (MDR genes, Bacillus anthracis, and Brucella melitensis). It is concerning that 54.4% of 216 ARB isolates from all samples were potential ARHPB species, and genome sequencing and functional annotation of 4 MDR HPB isolates showed 9 ARG types. Our findings revealed the potential migration and dissemination of antibiotic residues, ARGs, HPB, and ARHPB from pig feedlot to surrounding stream and agricultural soils via pig sewage discharge and manure fertilization.

Biodegradability and ecological safety assessment of Stenotrophomonas sp. DDT-1 in the DDT-contaminated soil

The biodegradability and ecological safety assessment of the previously isolated DDT-degrading bacterial strain Stenotrophomonas sp. DDT-1 were investigated in the DDT-contaminated soil under laboratory and field conditions. Under laboratory conditions, the degradation rates of fresh p,p'-DDT in soil were enhanced by 2.0-3.0-fold with the introduction of the strain DDT-1 compared to those of the control treatments. A similar enhancement in the dissipation of DDTs (p,p'-DDT, p,p'-DDE, p,p'-DDD, and o,p'-DDT) in the aged DDT-contaminated field plot soils resulted from the inoculation with this strain. Meanwhile, the degradation rates of DDTs increased by 2.9-5.5- and 2.8-7.6-fold in the inoculated greenhouse and open field soils, respectively, after field demonstration application of strain DDT-1 preparation. Moreover, no significant differences in the soil enzyme activity, microbial functional diversity, and bacterial community structure were observed between the inoculated and un-inoculated field soils, but several soil microbial genera exhibited some fluctuations in abundance. It is concluded that strain DDT-1 could accelerate the removal of DDTs residues in field soils, and furthermore, its inoculation was ecologically safe.

GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas

The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT). The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM. We demonstrate the practical utility of the software by analyzing 170 Stenotrophomonas genome sequences available in RefSeq and 10 new complete genomes of Mexican environmental S. maltophilia complex (Smc) isolates reported herein. A combination of core-genome and PGM analyses was used to revise the molecular systematics of the genus. An unsupervised learning approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a core-genome average nucleotide identity (cgANIb) of 95.9% that are perfectly consistent with strongly supported clades on the core- and pan-genome trees. In addition, we identified 16 misclassified RefSeq genome sequences, 14 of them labeled as S. maltophilia, demonstrating the broad utility of the software for phylogenomics and geno-taxonomic studies. The code, a detailed manual and tutorials are freely available for Linux/UNIX servers under the GNU GPLv3 license at https://github.com/vinuesa/get_phylomarkers. A docker image bundling GET_PHYLOMARKERS with GET_HOMOLOGUES is available at https://hub.docker.com/r/csicunam/get_homologues/, which can be easily run on any platform.

Bioinformatics Analysis and Characterization of Highly Efficient Polyvinyl Alcohol (PVA)-Degrading Enzymes from the Novel PVA Degrader Stenotrophomonas rhizophila QL-P4

Polyvinyl alcohol (PVA) is used widely in industry, and associated environmental pollution is a serious problem. Herein, we report a novel, efficient PVA degrader, Stenotrophomonas rhizophila QL-P4, isolated from fallen leaves from a virgin forest in the Qinling Mountains. The complete genome was obtained using single-molecule real-time (SMRT) technology and corrected using Illumina sequencing. Bioinformatics analysis revealed eight PVA/vinyl alcohol oligomer (OVA)-degrading genes. Of these, seven genes were predicted to be involved in the classic intracellular PVA/OVA degradation pathway, and one (BAY15_3292) was identified as a novel PVA oxidase. Five PVA/OVA-degrading enzymes were purified and characterized. One of these, BAY15_1712, a PVA dehydrogenase (PVADH), displayed high catalytic efficiency toward PVA and OVA substrate. All reported PVADHs only have PVA-degrading ability. Most importantly, we discovered a novel PVA oxidase (BAY15_3292) that exhibited higher PVA-degrading efficiency than the reported PVADHs. Further investigation indicated that BAY15_3292 plays a crucial role in PVA degradation in S. rhizophila QL-P4. Knocking out BAY15_3292 resulted in a significant decline in PVA-degrading activity in S. rhizophila QL-P4. Interestingly, we found that BAY15_3292 possesses exocrine activity, which distinguishes it from classic PVADHs. Transparent circle experiments further proved that BAY15_3292 greatly affects extracellular PVA degradation in S. rhizophila QL-P4. The exocrine characteristics of BAY15_3292 facilitate its potential application to PVA bioremediation. In addition, we report three new efficient secondary alcohol dehydrogenases (SADHs) with OVA-degrading ability in S. rhizophila QL-P4; in contrast, only one OVA-degrading SADH was reported previously.IMPORTANCE With the widespread application of PVA in industry, PVA-related environmental pollution is an increasingly serious issue. Because PVA is difficult to degrade, it accumulates in aquatic environments and causes chronic toxicity to aquatic organisms. Biodegradation of PVA, as an economical and environment-friendly method, has attracted much interest. To date, effective and applicable PVA-degrading bacteria/enzymes have not been reported. Herein, we report a new efficient PVA degrader (S. rhizophila QL-P4) that has five PVA/OVA-degrading enzymes with high catalytic efficiency, among which BAY15_1712 is the only reported PVADH with both PVA- and OVA-degrading abilities. Importantly, we discovered a novel PVA oxidase (BAY15_3292) that is not only more efficient than other reported PVA-degrading PVADHs but also has exocrine activity. Overall, our findings provide new insight into PVA-degrading pathways in microorganisms and suggest S. rhizophila QL-P4 and its enzymes have the potential for application to PVA bioremediation to reduce or eliminate PVA-related environmental pollution.

Biodegradation of the veterinary antibiotics enrofloxacin and ceftiofur and associated microbial community dynamics

Fluoroquinolones and cephalosporins are two classes of veterinary antibiotics arising as pollutants of emerging concern. In this work, the microbial degradation of two representative antibiotics of both these classes, enrofloxacin (ENR) and ceftiofur (CEF), is reported. Biodegradation of the target antibiotics was investigated by supplementing the culture medium with ENR and CEF, individually and in mixture. Microbial inocula were obtained from rhizosphere sediments of plants derived from experimental constructed wetlands designed for the treatment of livestock wastewaters contaminated with trace amounts of these antibiotics. Selected microbial inocula were acclimated during a period of 5months, where the antibiotics were supplemented every three weeks at the concentration of 1mgL^-1, using acetate as a co-substrate. After this period, the acclimated consortia were investigated for their capacity to biodegrade 2 and 3mgL^-1 of ENR and CEF. Complete removal of CEF from the inoculated culture medium was always observed within 21days, independently of its concentration or the concomitant presence of ENR. Biodegradation of ENR decreased with the increase in its concentration in the culture medium, with defluorination percentages decreasing from ca. 65 to 4%. Ciprofloxacin and norfloxacin were detected as biodegradation intermediates of ENR in the microbial cultures supplemented with this antibiotic, indicating that defluorination of at least part of ENR in these cultures is not an immediate catabolic step. Abiotic mechanisms showed high influence in the removal of CEF, affecting less ENR degradation. The acclimation process with the target antibiotics led to significant shifts in the structure and diversity of the microbial communities, predominantly selecting microorganisms belonging to the phyla Proteobacteria (e.g. Achromobacter, Variovorax and Stenotrophomonas genera) and Bacteroidetes (e.g. Dysgonomonas, Flavobacterium and Chryseobacterium genera). The results presented in this study indicate that biodegradation can be an important mechanism for the environmental removal of the tested compounds.

Complete genome sequence of Stenotrophomonas sp. KACC 91585, an efficient bacterium for unsaturated fatty acid hydration

Hydroxy fatty acids (HFAs) such as 10-hydroxystearic acid (10-HSA) and 10-hydroxy-12(Z)-octadecenoic acid (10-HOD), which are similar to ricinoleic acid, are important starting materials and intermediates for the industrial manufacture of many commodities. Stenotrophomonas sp. KACC 91585, which was isolated from lake sediment, is an efficient bacterium for unsaturated fatty acid hydration that produces 10-HSA and 10-HOD from oleic acid and linoleic acid, respectively, with high conversion rates. The complete genome of this strain is 4,541,729bp with 63.83% GC content and devoid of plasmids. Sets of genes involved in the fatty acid biosynthesis and modification as well as modified lipids were identified in the genome, and these genes were concerned with HFA production. This genome sequence provides molecular information and elucidation for HFA production, and will be used as an efficient biocatalyst source for the biotechnological production of HFA.

The Environmental Issues of DDT Pollution and Bioremediation: a Multidisciplinary Review

DDT (1,1,1-trichloro-2,2-bis(4-chlorophenyl) ethane) is probably the best known and most useful organochlorine insecticide in the world which was used since 1945 for agricultural purposes and also for vector-borne disease control such as malaria since 1955, until its banishment in most countries by the Stockholm convention for ecologic considerations. However, the World Health Organization allowed its reintroduction only for control of vector-borne diseases in some tropical countries in 2006. Due to its physicochemical properties and specially its persistence related with a half-life up to 30 years, DDT linked to several health and social problems which are due to its accumulation in the environment and its biomagnification properties in living organisms. This manuscript compiles a multidisciplinary review to evaluate primarily (i) the worldwide contamination of DDT and (ii) its (eco) toxicological impact onto living organisms. Secondly, several ways for DDT bioremediation from contaminated environment are discussed. For this, reports on DDT biodegradation capabilities by microorganisms and ways to enhance bioremediation strategies to remove DDT are presented. The different existing strategies for DDT bioremediation are evaluated with their efficiencies and limitations to struggle efficiently this contaminant. Finally, rising new approaches and technological bottlenecks to promote DDT bioremediation are discussed.

Characterization and genome functional analysis of a novel metamitron-degrading strain Rhodococcus sp. MET via both triazinone and phenyl rings cleavage

A novel bacterium capable of utilizing metamitron as the sole source of carbon and energy was isolated from contaminated soil and identified as Rhodococcus sp. MET based on its morphological characteristics, BIOLOG GP2 microplate profile, and 16S rDNA phylogeny. Genome sequencing and functional annotation of the isolate MET showed a 6,340,880 bp genome with a 62.47% GC content and 5,987 protein-coding genes. In total, 5,907 genes were annotated with the COG, GO, KEGG, Pfam, Swiss-Prot, TrEMBL, and nr databases. The degradation rate of metamitron by the isolate MET obviously increased with increasing substrate concentrations from 1 to 10 mg/l and subsequently decreased at 100 mg/l. The optimal pH and temperature for metamitron biodegradation were 7.0 and 20–30 °C, respectively. Based on genome annotation of the metamitron degradation genes and the metabolites detected by HPLC-MS/MS, the following metamitron biodegradation pathways were proposed: 1) Metamitron was transformed into 2-(3-hydrazinyl-2-ethyl)-hydrazono-2-phenylacetic acid by triazinone ring cleavage and further mineralization; 2) Metamitron was converted into 3-methyl-4-amino-6(2-hydroxy-muconic acid)-1,2,4-triazine-5(4H)-one by phenyl ring cleavage and further mineralization. The coexistence of diverse mineralization pathways indicates that our isolate may effectively bioremediate triazinone herbicide-contaminated soils.