Integrative approaches for assessing the ecological sustainability ofin situbioremediation

Comparative genomics reveal unique markers to monitor by routine PCR assay bioinoculant of Sphingobium indicum B90A in hexachlorocyclohexane (HCH) contaminated soils

Bioinoculants of Sphingobium indicum B90A have been used to decontaminate hexachlorocyclohexane (HCH)-contaminated soils in the past. There is no selective or convenient method available to track the added B90A in HCH-contaminated soils in the presence of several native sphingomonads. Here, we describe a method, BioMarkTrack, for tracking B90A bioinoculant by simple amplification of the B90A specific biomarker genes. Whole-genome sequence data of 120 different genera of sphingomonads (Sphingobium, Novosphingobium, Sphingomonas, Sphingopyxis, and Sphingosinicella) were retrieved from the NCBI database and annotated. Intra- and inter-genus similarity searches, including the genome of B90A as a reference was conducted. 122 unique gene sequences were identified in strain B90A, out of which 45 genes were selected that showed no similarity with the NCBI non-redundant (NR) database or gene sequences in the publicly available database. Primers were designed for amplification of 4 biomarkers. To validate the biomarkers B90A tracking efficacy in bioaugmented soils, a microcosm study was conducted in which sterile garden and HCH-contaminated dumpsite soils were amended with strain B90A. Amplification of the biomarker was observed both in sterile garden soil and HCH-contaminated dumpsite soil but not in control (lacking B90A) samples. Further, the primer set was used to track B90A in a bioremediation field trial soil, demonstrating the convenience and efficiency of the simple PCR-based method, which can be employed for tracking B90A in bioaugmented soils. The approach as presented here can be employed on different bioinoculants to identify unique biomarkers and then tracking these organisms during bioremediation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-024-01321-7.

A comprehensive study on diesel oil bioremediation under microcosm conditions using a combined microbiological, enzymatic, mass spectrometry, and metabarcoding approach

This study aims at the application of a marine fungal consortium (Aspergillus sclerotiorum CRM 348 and Cryptococcus laurentii CRM 707) for the bioremediation of diesel oil-contaminated soil under microcosm conditions. The impact of biostimulation (BS) and/or bioaugmentation (BA) treatments on diesel-oil biodegradation, soil quality, and the structure of the microbial community were studied. The use of the fungal consortium together with nutrients (BA/BS) resulted in a TPH (Total Petroleum Hydrocarbon) degradation 42% higher than that obtained by natural attenuation (NA) within 120 days. For the same period, a 72 to 92% removal of short-chain alkanes (C12 to C19) was obtained by BA/BS, while only 3 to 65% removal was achieved by NA. BA/BS also showed high degradation efficiency of long-chain alkanes (C20 to C24) at 120 days, reaching 90 and 92% of degradation of icosane and heneicosane, respectively. In contrast, an increase in the levels of cyclosiloxanes (characterized as bacterial bioemulsifiers and biosurfactants) was observed in the soil treated by the consortium. Conversely, the NA presented a maximum of 37% of degradation of these alkane fractions. The 5-ringed PAH benzo(a)pyrene, was removed significantly better with the BA/BS treatment than with the NA (48 vs. 38 % of biodegradation, respectively). Metabarcoding analysis revealed that BA/BS caused a decrease in the soil microbial diversity with a concomitant increase in the abundance of specific microbial groups, including hydrocarbon-degrading (bacteria and fungi) and also an enhancement in soil microbial activity. Our results highlight the great potential of this consortium for soil treatment after diesel spills, as well as the relevance of the massive sequencing, enzymatic, microbiological and GC-HRMS analyses for a better understanding of diesel bioremediation.

In vitro assays reveal inherently insecticide-tolerant termite symbionts

Introduction: Termite symbionts are well known for conferring a myriad of benefits to their hosts. Bacterial symbionts are repeatedly associated with increased fitness, nutritional supplementation, pathogen protection, and proper development across insect taxa. In addition, several recent studies link bacterial symbionts to reduced insecticide efficacy. This has important implications both in pest control management and environmental bioremediation efforts. Insects' guts may be a valuable resource for microbes with broad application given their unique niches and metabolic diversity. Though insecticide resistance in termites is considered unlikely due to their life history, the close association of termites with a multitude of bacteria raises the question: is there potential for symbiont-mediated pesticide tolerance in termites? Methods and results: We identified a candidate that could grow in minimal medium containing formulated pesticide. This bacterial isolate was then subjected to continuous culture and subsequently demonstrated improved performance in the presence of pesticide. Isolates subjected to continuous culture were then grown at a range of concentrations from 1-10X the formulation rate. After constant exposure for several generations, isolates grew significantly better. Conclusion: Here we demonstrate that naïve insect hosts can harbor symbionts with inherent insecticide tolerance capable of rapid adaptation to increasing insecticide concentrations overtime. This has broad implications for both pest control and environmental cleanup of residual pesticides.

Bioengineered microbial strains for detoxification of toxic environmental pollutants

Industrialization and other anthropogenic human activities pose significant environmental risks. As a result of the hazardous pollution, numerous living organisms may suffer from undesirable diseases in their separate habitats. Bioremediation, which removes hazardous compounds from the environment using microbes or their biologically active metabolites, is one of the most successful remediation approaches. According to the United Nations Environment Program (UNEP), deteriorating soil health negatively impacts food security and human health over time. Soil health restoration is critical right now. Microbes are widely known for their importance in cleaning up toxins present in the soil, such as heavy metals, pesticides, and hydrocarbons. However, the capacity of local bacteria to digest these pollutants is limited, and the process takes an extended time. Genetically modified organisms (GMOs), whose altered metabolic pathways promote the over-secretion of a variety of proteins favorable to the bioremediation process, can speed up the breakdown process. The need for remediation procedures, degrees of soil contamination, site circumstances, broad adoptions, and numerous possibilities occurring at various cleaning stages are all studied in detail. Massive efforts to restore contaminated soils have also resulted in severe issues. This review focuses on the enzymatic removal of hazardous pollutants from the environment, such as pesticides, heavy metals, dyes, and plastics. There are also in-depth assessments of present discoveries and future plans for efficient enzymatic degradation of hazardous pollutants.

Field scale biodegradation of total petroleum hydrocarbons and soil restoration by Ecopiles: microbiological analysis of the process

Ecopiling is a method for biodegradation of hydrocarbons in soils. It derives from Biopiles, but phytoremediation is added to biostimulation with nitrogen fertilization and bioaugmentation with local bacteria. We have constructed seven Ecopiles with soil heavily polluted with hydrocarbons in Carlow (Ireland). The aim of the study was to analyze changes in the microbial community during ecopiling. In the course of 18 months of remediation, total petroleum hydrocarbons values decreased in 99 and 88% on average for aliphatics and aromatics, respectively, indicating a successful biodegradation. Community analysis showed that bacterial alfa diversity (Shannon Index), increased with the degradation of hydrocarbons, starting at an average value of 7.59 and ending at an average value of 9.38. Beta-diversity analysis, was performed using Bray-Curtis distances and PCoA ordination, where the two first principal components (PCs) explain the 17 and 14% of the observed variance, respectively. The results show that samples tend to cluster by sampling time instead of by Ecopile. This pattern is supported by the hierarchical clustering analysis, where most samples from the same timepoint clustered together. We used DSeq2 to determine the differential abundance of bacterial populations in Ecopiles at the beginning and the end of the treatment. While TPHs degraders are more abundant at the start of the experiment, these populations are substituted by bacterial populations typical of clean soils by the end of the biodegradation process. Similar results are found for the fungal community, indicating that the microbial community follows a succession along the process. This succession starts with a TPH degraders or tolerant enriched community, and finish with a microbial community typical of clean soils.

Field Test of In Situ Groundwater Treatment Applying Oxygen Diffusion and Bioaugmentation Methods in an Area with Sustained Total Petroleum Hydrocarbon (TPH) Contaminant Flow

Contamination of groundwater by petroleum hydrocarbons is a widespread environmental problem in many regions. Contamination of unsaturated and saturated zones could also pose a significant risk to human health. The main purpose of the study was to assess the efficiency of biodegradation of total petroleum hydrocarbon (TPH) in situ, in an area with loam and sandy loam soils, and to identify features and characteristics related to groundwater treatment in an area with a persistent flow of pollutants. We used methods of biostimulation (oxygen as stimulatory supplement) and bioaugmentation to improve water quality. Oxygen was added to the groundwater by diffusion through silicone tubing. The efficiency of groundwater treatment was determined by detailed monitoring. Implementation of the applied measure resulted in an average reduction in TPH concentration of 73.1% compared with the initial average concentration (4.33 mg/L), and in the local area, TPH content was reduced by 95.5%. The authors hope that this paper will contribute to a better understanding of the topic of groundwater treatment by in situ biodegradation of TPH. Further studies on this topic are particularly needed to provide more data and details on the efficiency of groundwater treatment under adverse geological conditions.

Bioremediation of lignin derivatives and phenolics in wastewater with lignin modifying enzymes: Status, opportunities and challenges

Lignin modifying enzymes from fungi and bacteria are potential biocatalysts for sustainable mitigation of different potentially toxic pollutants in wastewater. Notably, the paper and pulp industry generates enormous amounts of wastewater containing high amounts of complex lignin-derived chlorinated phenolics and sulfonated pollutants. The presence of these compounds in wastewater is a critical issue from environmental and toxicological perspectives. Some chloro-phenols are harmful to the environment and human health, as they exert carcinogenic, mutagenic, cytotoxic, and endocrine-disrupting effects. In order to address these most urgent concerns, the use of oxidative lignin modifying enzymes for bioremediation has come into focus. These enzymes catalyze modification of phenolic and non-phenolic lignin-derived substances, and include laccase and a range of peroxidases, specifically lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), and dye-decolorizing peroxidase (DyP). In this review, we explore the key pollutant-generating steps in paper and pulp processing, summarize the most recently reported toxicological effects of industrial lignin-derived phenolic compounds, especially chlorinated phenolic pollutants, and outline bioremediation approaches for pollutant mitigation in wastewater from this industry, emphasizing the oxidative catalytic potential of oxidative lignin modifying enzymes in this regard. We highlight other emerging biotechnical approaches, including phytobioremediation, bioaugmentation, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based technology, protein engineering, and degradation pathways prediction, that are currently gathering momentum for the mitigation of wastewater pollutants. Finally, we address current research needs and options for maximizing sustainable biobased and biocatalytic degradation of toxic industrial wastewater pollutants.

Characterization of sediment microbial communities at two sites with low hydrocarbon pollution in the southeast Gulf of Mexico

Background

Coastal ecosystems are prone to hydrocarbon pollution due to human activities, and this issue has a tremendous impact on the environment, socioeconomic consequences, and represents a hazard to humans. Bioremediation relies on the ability of bacteria to metabolize hydrocarbons with the aim of cleaning up polluted sites.

Methods

The potential of naturally occurring microbial communities as oil degraders was investigated in Sisal and Progreso, two port locations in the southeast Gulf of Mexico, both with a low level of hydrocarbon pollution. To do so, we determined the diversity and composition of bacterial communities in the marine sediment during the dry and rainy seasons using 16S rRNA sequencing. Functional profile analysis (PICRUTSt2) was used to predict metabolic functions associated with hydrocarbon degradation.

Results

We found a large bacterial taxonomic diversity, including some genera reported as hydrocarbon-degraders. Analyses of the alpha and beta diversity did not detect significant differences between sites or seasons, suggesting that location, season, and the contamination level detected here do not represent determining factors in the structure of the microbial communities. PICRUTSt2 predicted 10 metabolic functions associated with hydrocarbon degradation. Most bacterial genera with potential hydrocarbon bioremediation activity were generalists likely capable of degrading different hydrocarbon compounds. The bacterial composition and diversity reported here represent an initial attempt to characterize sites with low levels of contamination. This information is crucial for understanding the impact of eventual rises in hydrocarbon pollution.

Aquatic Macrophytes in Constructed Wetlands: A Fight against Water Pollution

There is growing concern among health institutions worldwide to supply clean water to their populations, especially to more vulnerable communities. Although sewage treatment systems can remove most contaminants, they are not efficient at removing certain substances that can be detected in significant quantities even after standard treatments. Considering the necessity of perfecting techniques that can remove waterborne contaminants, constructed wetland systems have emerged as an effective bioremediation solution for degrading and removing contaminants. In spite of their environmentally friendly appearance and efficiency in treating residual waters, one of the limiting factors to structure efficient artificial wetlands is the choice of plant species that can both tolerate and remove contaminants. For sometimes, the chosen plants composing a system were not shown to increase wetland performance and became a problem since the biomass produced must have appropriated destination. We provide here an overview of the use and role of aquatic macrophytes in constructed wetland systems. The ability of plants to remove metals, pharmaceutical products, pesticides, cyanotoxins and nanoparticles in constructed wetlands were compared with the removal efficiency of non-planted systems, aiming to evaluate the capacity of plants to increase the removal efficiency of the systems. Moreover, this review also focuses on the management and destination of the biomass produced through natural processes of water filtration. The use of macrophytes in constructed wetlands represents a promising technology, mainly due to their efficiency of removal and the cost advantages of their implantation. However, the choice of plant species composing constructed wetlands should not be only based on the plant removal capacity since the introduction of invasive species can become an ecological problem.

Bacterially assembled biopolyester nanobeads for removing cadmium from water

Cadmium (Cd)-contaminated waterbodies are a worldwide concern for the environment, impacting human health. To address the need for efficient, sustainable and cost-effective remediation measures, we developed innovative Cd bioremediation agents by engineering Escherichia coli to assemble poly(3-hydroxybutyric acid) (PHB) beads densely coated with Cd-binding peptides. This was accomplished by translational fusion of Cd-binding peptides to the N- or C-terminus of a PHB synthase that catalyzes PHB synthesis and mediates assembly of Cd2 or Cd1 coated PHB beads, respectively. Cd1 beads showed greater Cd adsorption with 441 nmol Cd mg^-1 bead mass when compared to Cd2 beads (334 nmol Cd mg^-1 bead-mass) and plain beads (238 nmol Cd mg^-1 bead-mass). The Cd beads were not ecotoxic and did attenuate Cd-spiked solutions toxicity. Overall, the bioengineered beads provide a means to remediate Cd-contaminated sites, can be cost-effectively produced at large scale, and offer a biodegradable and safe alternative to synthetic ecotoxic treatments.

Microbial genetic potential for xenobiotic metabolism increases with depth during biofiltration

Water infiltration into the subsurface can result in pronounced biogeochemical depth gradients. In this study, we assess metabolic potential and properties of the subsurface microbiome during water infiltration by analyzing sediments from spatially-segmented columns. Past work in these laboratory set-ups demonstrated that removal efficiencies of trace organic pollutants were enhanced by limited availability of biodegradable dissolved organic carbon (BDOC) associated with higher humic ratios and deeper sediment regions. Distinct differences were observed in the microbial community when contrasting shallow versus deeper profile sediments. Metagenomic analyses revealed that shallow sediments contained an enriched potential for bacterial growth and division processes. In contrast, deeper sediments harbored a significant increase in genes associated with the metabolism of secondary metabolites and the biotransformation of xenobiotic water pollutants. Metatranscripts further supported this trend, with increased potential for metabolic attributes associated with the biotransformation of xenobiotics and antibiotic resistance within deeper sediments. Furthermore, increasing ratios of humics in feed solutions correlated to enhanced expression of genes associated with xenobiotic biodegradation. These results provide genetic support for the interplay of dissolved organic carbon limitation and enhanced trace organic biotransformation by the subsurface microbiome.

Immobilization of metribuzin degrading bacterial consortium MB3R on biochar enhances bioremediation of potato vegetated soil and restores bacterial community structure

Metribuzin (MB) is a triazinone herbicide used for the eradication of weeds in agriculture. Presence of its residues in agricultural soil can potentially harm the establishment of subsequent crops and structure of soil microbial populations. In this study, remediation potential of an MB degrading bacterial consortium MB3R immobilized on biochar was evaluated in potato vegetated soil. In potato vegetated soil augmented with MB3R alone and MB3R immobilized on biochar, 82 and 96% MB degradation was recorded respectively as compared to only 29.3% in un-augmented soil. Kinetic parameters revealed that MB3R immobilized biochar is highly proficient as indicated by significant increase in the rate of biodegradation and decrease in half-life of MB. Enhanced plant growth was observed when augmented with bacterial consortium either alone or immobilized on biochar. Presence of herbicide negatively affected the soil bacterial community structure. However, MB3R immobilized on biochar proved to be helpful for restoration of soil bacterial community structure affected by MB. This is the very first report that reveals improved remediation of contaminated soil and restoration of soil bacterial populations by use of the MB degrading bacterial consortium immobilized on biochar.

Biodegradation of recalcitrant compounds and phthalates by culturable bacteria isolated from Liometopum apiculatum microbiota

Liometopum apiculatum is a species of ants widely distributed in arid and semi-arid ecosystems where there is a relative food shortage compared with tropical ecosystems. L. apiculatum has established an ecological balance involving symbiotic interactions, which have allowed them to survive through mechanisms that are still unknown. Therefore, the aim of this study was to explore the metabolic potential of isolated bacteria from L. apiculatum using enzymatic activity assay and substrate assimilation. Results revealed a complex bacteria consortium belonging to Proteobacteria, Firmicutes, and Actinobacteria phylum. Most of the isolated bacteria showed activities associated with biopolymers degradation, from them Exiguobacterium and B. simplex showed the highest amylolytic activity (27 U/mg protein), while A. johnsonii and B. pumulis showed the highest cellulolytic and xylanolytic activities (1 and 2.9 U/mg protein, respectively). By other hand, some microorganisms such as S. ficaria, E. asburiae, P. agglomerans, A. johnsonii, S. rubidaea, S. marcescens, S. warneri, and M. hydrocarbonoxydans were able to grow up to 1000 mg/L of phthalates esters. These results not only revealed the important contribution of the symbionts in L apiculatum ants feeding habits, but also have shown a promising source of enzymes with potential biotechnological applications such as lignocellulosic biomass hydrolysis and bioremediation processes.

Co-treatment of an oily sludge and aged contaminated soil: permanganate oxidation followed by bioremediation

The bioremediation of an oily sludge (321 ± 30 mg of polycyclic aromatic hydrocarbons/kg_{DRY SLUDGE} and 13420 ± 1300 mg of aliphatic hydrocarbons/kg_{DRY SLUDGE}) by mixture with contaminated soil (23 ± 2 mg of polycyclic aromatic hydrocarbons/kg_{DRY SOIL} and 98 ± 10 mg of aliphatic hydrocarbons/kg_{DRY SOIL}) was studied. Furthermore, the effect of oxidative pretreatments (persulfate and permanganate) on the performance of the global process was examined. The treatments reached contamination levels lower than the original residues, indicating the presence of synergic processes between a highly contaminated sludge and soil with a selected hydrocarbon-degrading community. Pretreatment with permanganate significantly improved biodegradation, possibly due to the increase in bioavailability and biodegradability of petroleum hydrocarbons. Two months of incubation was enough to reach the complete elimination of polycyclic aromatic hydrocarbons and 92% elimination of aliphatic hydrocarbons. Monitoring using five parameters (concentration of total petroleum hydrocarbons, total cultivable heterotrophic bacteria count, lipase and dehydrogenase activities, and polycyclic aromatic hydrocarbon-degrading bacteria count) as an approach for a preliminary scanning of the effectiveness of a treatment is proposed based on principal components analysis.

Petroleum-Tolerant Rhizospheric Bacteria: Isolation, Characterization and Bioremediation Potential

Petroleum is an important energy source. Due to its intensive exploration, accidents resulting in oil spills on soil are frequent, which creates consequences to ecosystems and human health. Rhizodegradation is an efficient technique that promotes the decontamination of polluted environments through the selection and use of rhizosphere microorganisms from phytoremediation plants. The aim of this study was to isolate, identify and characterize bacteria capable of degrading petroleum from the rhizosphere of Panicum aquaticum Poir., a plant that grows in petroleum contaminated soils. Three bacteria were isolated and characterized at the morphological (Gram staining), molecular (16S rRNA gene sequence analysis) and biochemical level. These bacteria were identified as new strains of Bacillus thurigiensis, Bacillus pumilus and Rhodococcus hoagii, which have been reported as potential bioremediators in the literature. All three bacteria were able to use petroleum hydrocarbons as the sole carbon source during in vitro degradation assays. Gas chromatography analysis of these assays indicated reductions of petroleum hydrocarbons between 23% and 96% within 48 h. Among the isolated bacteria, Rhodococcus hoagii presented the highest efficiency of petroleum consumption, reaching 87% of degradation after only 24 h of cultivation, which corresponds to a higher and faster degradation than previously reported, confirming the potential use of Rhodococcus hoagii for petroleum biodegradation.

Soil phenanthrene phytoremediation capacity in bacteria-assisted Spartina densiflora

Polycyclic aromatic hydrocarbons (PAH) have become a threat for the conservation of wetlands worldwide. The halophyte Spartina densiflora has shown to be potentially useful for soil phenanthrene phytoremediation, but no studies on bacteria-assisted hydrocarbon phytoremediation have been carried out with this halophyte. In this work, three phenanthrene-degrading endophytic bacteria were isolated from S. densiflora tissues and used for plant inoculation. Bacterial bioaugmentation treatments slightly improved S. densiflora growth, photosynthetic and fluorescence parameters. But endophyte-inoculated S. densiflora showed lower soil phenanthrene dissipation rates than non-inoculated S. densiflora (30% below) or even bulk soil (23% less). Our work demonstrates that endophytic inoculation on S. densiflora under greenhouse conditions with the selected PAH-degrading strains did not significantly increase inherent phenanthrene soil dissipation capacity of the halophyte. It would therefore be advisable to provide effective follow-up of bacterial colonization, survival and metabolic activity during phenanthrene soil phytoremediation.

Remediation of textile bleaching effluent by bacterial augmented horizontal flow and vertical flow constructed wetlands: A comparison at pilot scale

Fabric bleaching is one of the most widely used processes of the textile industry that also produces a significant amount of highly polluted wastewater. Previously, expensive and chemically extensive conventional remediation systems were used to treat bleaching effluent. Despite this, the potential of constructed wetlands (CWs) as a treatment system remains un-investigated. Furthermore, most research on the use of CWs for textile effluents are conducted at laboratory scale and therefore further research at field-scale is timely. This study compares the efficacy of bacterial augmented vertical flow constructed wetlands (VFCWs) and horizontal flow constructed wetlands (HFCWs) for the remediation of textile bleaching wastewater at pilot scale. To this end, CWs macrocosms of 1000 L water capacity were planted with Phragmites australis and inoculated with bacterial strains possessing pollutant degradation and plant growth-promoting traits. The results showed that both variants of CWs were effective in attenuating pollutants from the wastewater; however, the performance of HFCWs exceeded that of the VFCWs for almost every pollutant measure undertaken. For HFCWs, a significant reduction in COD (89%), BOD (91%), TOC (96%), and toxicity was achieved in a period of 72 h during the first month of operation. Bacterial inoculation in CWs further improved the system's performance and these bacteria also exhibited persistence in the rhizoplane (43%), root interior (56%) and shoot interior (29%) of P. australis. This study, therefore, suggests that the bacterial augmented HFCWs is a suitable approach for industrial scale textile bleach wastewater treatment.

Influence of bioaugmentation and biostimulation on PAH degradation in aged contaminated soils: Response and dynamics of the bacterial community

Polycyclic aromatic hydrocarbons (PAHs) represent a group of hazardous compounds that are ubiquitous and persistent. The main aim of this study was to investigate the degradation of PAHs in chronically contaminated, aged and weathered soils obtained from a former gas plant of Australia. Biostimulation and bioaugmentation using individual isolates (Rhodococcus sp. (NH2), Achromobacter sp. (NH13), Oerskovia paurometabola (NH11), Pantoea sp. (NH15), Sejongia sp. (NH20), Microbacterium maritypicum (NH30) and Arthrobacter equi (NH21)) and a consortium of these isolates were tested during mesocosm studies. A significant reduction (99%) in PAH concentration was observed in all the treatments. In terms of the abundance of PAH-degrading genes and microbial community structure during PAH degradation, qPCR results revealed that Gram-positive bacteria were dominant over other bacterial communities in all the treatments. 16S sequencing results revealed that the inoculated organisms did not establish themselves during the treatment. However, substantial bacterial community changes during the treatments were observed, suggesting that the natural community exhibited sufficient resilience and diversity to enable an active, but changing degrading community at all stages of the degradation process. Consequently, biostimulation is proposed as the best strategy to remediate PAHs in aged, weathered and chronically contaminated soils.

Effects of Physico-Chemical Parameters on Actinomycetes Communities during Composting of Agricultural Waste

The objective of this study was to investigate the influence of physico-chemical parameters on Actinomycetes communities and to prioritize those parameters that contributed to Actinomycetes community composition during the composting of agricultural waste. Denaturing gradient gel electrophoresis of polymerase chain reaction (PCR-DGGE) and redundancy analysis (RDA) were used to determine the relationships between those parameters and Actinomycetes community composition. Quantitative PCR (qPCR) and regression analysis were used to monitor the 16S rDNA copy numbers of Actinomycetes and to analyse the correlations between physico-chemical parameters and Actinomyces 16S rDNA gene abundance, respectively. The RDA results showed that moisture content, water soluble carbon (WSC) and pH (p < 0.05) made the main contributions to the temporal variations of Actinomycetes community composition. The output of the regression analysis indicated that moisture content (R2 = 0.407, p < 0.01) showed a negative linear relationship with the Actinomyces 16S rDNA gene abundance.

Enhanced degradation of hydrocarbons by gamma ray induced mutant strain of Pseudomonas putida

Soil contamination due to petroleum hydrocarbons is a ubiquitous environmental problem for which efficient remediation alternatives are required. Application of hydrocarbons degrading bacteria with enhanced degradation potential is such an alternative. The aim of present investigation was to induce mutagenicity in Pseudomonas putida through gamma-ray irradiation for the enhanced degradation of crude oil. A total of mutant 10 bacterial strains (300A-J) were screened for their degradation abilities in vitro; among which the performance of 300-B was outstanding. Subsequently, spiked soil (30 g/kg crude oil) was augmented with the wild-type parent strain and mutant 300-B strain in individual experiments. Bacterial inoculation in both experiments enhanced hydrocarbons degradation; however, degradation was 46.3% higher when 300-B mutant strain was employed. This improved oil degradation was found to have a strong positive correlation with the gene abundance and expression of the mutant strain, suggesting its successful survival and catabolic potential in situ. Concomitantly, a better nutrients assimilation and water utilization was observed in the experiment containing 300-B mutant. Yet preliminary, these findings highlight the importance of gamma ray irradiation towards improved degradation potential of previously isolated hydrocarbons degrading bacteria.

Multi-method assessment of the intrinsic biodegradation potential of an aquifer contaminated with chlorinated ethenes at an industrial area in Barcelona (Spain)

The bioremediation potential of an aquifer contaminated with tetrachloroethene (PCE) was assessed by combining hydrogeochemical data of the site, microcosm studies, metabolites concentrations, compound specific-stable carbon isotope analysis and the identification of selected reductive dechlorination biomarker genes. The characterization of the site through 10 monitoring wells evidenced that leaked PCE was transformed to TCE and cis-DCE via hydrogenolysis. Carbon isotopic mass balance of chlorinated ethenes pointed to two distinct sources of contamination and discarded relevant alternate degradation pathways in the aquifer. Application of specific-genus primers targeting Dehalococcoides mccartyi species and the vinyl chloride-to-ethene reductive dehalogenase vcrA indicated the presence of autochthonous bacteria capable of the complete dechlorination of PCE. The observed cis-DCE stall was consistent with the aquifer geochemistry (positive redox potentials; presence of dissolved oxygen, nitrate, and sulphate; absence of ferrous iron), which was thermodynamically favourable to dechlorinate highly chlorinated ethenes but required lower redox potentials to evolve beyond cis-DCE to the innocuous end product ethene. Accordingly, the addition of lactate or a mixture of ethanol plus methanol as electron donor sources in parallel field-derived anoxic microcosms accelerated dechlorination of PCE and passed cis-DCE up to ethene, unlike the controls (without amendments, representative of field natural attenuation). Lactate fermentation produced acetate at near-stoichiometric amounts. The array of techniques used in this study provided complementary lines of evidence to suggest that enhanced anaerobic bioremediation using lactate as electron donor source is a feasible strategy to successfully decontaminate this site.

Dichloromethane biodegradation in multi-contaminated groundwater: Insights from biomolecular and compound-specific isotope analyses

Dichloromethane (DCM) is a widespread and toxic industrial solvent which often co-occurs with chlorinated ethenes at polluted sites. Biodegradation of DCM occurs under both oxic and anoxic conditions in soils and aquifers. Here we investigated in situ and ex situ biodegradation of DCM in groundwater sampled from the industrial site of Themeroil (France), where DCM occurs as a major co-contaminant of chloroethenes. Carbon isotopic fractionation (ε_C) for DCM ranging from -46 to -22‰ were obtained under oxic or denitrifying conditions, in mineral medium or contaminated groundwater, and for laboratory cultures of Hyphomicrobium sp. strain GJ21 and two new DCM-degrading strains isolated from the contaminated groundwater. The extent of DCM biodegradation (B%) in the aquifer, as evaluated by compound-specific isotope analysis (δ¹³C), ranged from 1% to 85% applying DCM-specific ε_C derived from reference strains and those determined in this study. Laboratory groundwater microcosms under oxic conditions showed DCM biodegradation rates of up to 0.1 mM·day^-1, with concomitant chloride release. Dehalogenase genes dcmA and dhlA involved in DCM biodegradation ranged from below 4 × 10² (boundary) to 1 × 10⁷ (source zone) copies L^-1 across the contamination plume. High-throughput sequencing on the 16S rrnA gene in groundwater samples showed that both contaminant level and terminal electron acceptor processes (TEAPs) influenced the distribution of genus-level taxa associated with DCM biodegradation. Taken together, our results demonstrate the potential of DCM biodegradation in multi-contaminated groundwater. This integrative approach may be applied to contaminated aquifers in the future, in order to identify microbial taxa and pathways associated with DCM biodegradation in relation to redox conditions and co-contamination levels.

Investigation of the population dynamics within a Pseudomonas aeruginosa biofilm using a flow based biofilm model system and flow cytometric evaluation of cellular physiology

In this study a flow based biofilm model system was used to simulate the formation of Pseudomonas aeruginosa biofilms on a stainless steel surface. To investigate the complexity of biofilm-associated P. aeruginosa populations a combination of microscopic observations and flow cytometric analysis (FCM) was adopted. Biofilm-associated P. aeruginosa cells were evaluated (1) under optimal vs reduced nutrient-availability at the initial adhesion stage, and (2) irrespective of nutrient-availability within a mature biofilm. Microscopic estimation of the extent of attachment revealed more effective colonization upon optimal vs starvation conditions. FCM allowed an in situ evaluation of P. aeruginosa vitality, using cellular redox potential measurements to discriminate active, mid-active and non-active sub-populations. Samples from recently attached cells and mature biofilms showed significant differences in the percentages of bacterial cells from the defined sub-populations. The approach demonstrated that distribution of individual P. aeruginosa sub-populations was influenced by the stage of the biofilm life-cycle and nutrient availability.

Subcellular distribution and biotransformation of phenanthrene in pakchoi after inoculation with endophytic Pseudomonas sp. as probed using HRMS coupled with isotope-labeling

Contamination of food-crops with polycyclic aromatic hydrocarbons (PAHs) poses a grave concern to food safety, especially when PAHs are internalized. We have demonstrated in our previous study that inoculation of crop with a phenanthrene-degrading endophytic Pseudomonas sp. Ph6-gfp could overcome this problem. Here, the subcellular distribution and biotransformation mechanism of phenanthrene in pakchoi (Brassica chinensis L.) seedlings with inoculation of Ph6-gfp were further investigated both in vitro and in vivo. The possible biotransformation products of phenanthrene were identified by high-resolution mass spectrometry (HRMS) coupled with ¹³C₂-phenanthrene labeling. Results indicated that Ph6-gfp colonized pakchoi interior and reduced the content of phenanthrene in different cell compartments. Notably, the inoculation hindered the subcellular distribution of phenanthrene from intercellular space to subcellular fractions (i.e., cell wall, cell membrane, cell solution, and cell organelles), likely resulting from the interception and biodegradation of phenanthrene by the bacterium between the cell wall and intercellular space. Additionally, the conjugation reactions of phenanthrene-metabolites and endogenous plant compounds were enhanced as a result of the inoculation. We propose that endophytic degradation, plant metabolism, and conjugation reaction are the three possible biotransformation mechanisms that could account for the changes in phenanthrene inside the plant cell compartments. This is the first observation of endophytic bacteria (EB)-enhanced biotransformation and conjugation of phenanthrene in pakchoi at the subcellular level, which drive novel insights in regulating food-crop contamination with endophytes in PAH-contaminated matrices.

Insight Into the Variation of Bacterial Structure in Atrazine-Contaminated Soil Regulating by Potential Phytoremediator: Pennisetum americanum (L.) K. Schum

Although plants of the genus Pennisetum can accelerate the removal of atrazine from its rhizosphere, the roles played by this plant in adjusting the soil environment and soil microorganism properties that might contribute to pollutant removal are incompletely understood. We selected Pennisetum americanum (L.) K. Schum (P. americanum) as the test plant and investigated the interaction between P. americanum and atrazine-contaminated soil, focusing on the adjustment of the soil biochemical properties as well as bacterial functional and community diversity in the rhizosphere using Biolog EcoPlates and high-throughput sequencing of the 16S rRNA gene. The results demonstrate that the rhizosphere soil of P. americanum exhibited higher catalase activity, urease activity and water soluble organic carbon (WSOC) content, as well as a suitable pH for microorganisms after a 28-day incubation. The bacterial functional diversity indices (Shannon and McIntosh) for rhizosphere soil were 3.17 ± 0.04 and 6.43 ± 0.86 respectively, while these indices for non-rhizosphere soil were 2.95 ± 0.06 and 3.98 ± 0.27. Thus, bacteria in the P. americanum rhizosphere exhibited better carbon substrate utilization than non-rhizosphere bacteria. Though atrazine decreased the richness of the soil bacterial community, rhizosphere soil had higher bacterial community traits. For example, the Shannon diversity indices for rhizosphere and non-rhizosphere soil were 5.821 and 5.670 respectively. Meanwhile, some bacteria, such as those of the genera Paenibacillus, Rhizobium, Sphingobium, and Mycoplana, which facilitate soil nutrient cycling or organic pollutants degradation, were only found in rhizosphere soil after a 28-day remediation. Moreover, redundancy analysis suggests that the soil biochemical properties that were adjusted by the test plant exhibited correlations with the bacterial community composition and functional diversity. These results suggest that the soil environment and bacterial properties could be adjusted by P. americanum during phytoremediation of atrazine-contaminated soil.

Biodegradation of di-n-butyl phthalate (DBP) by a novel endophytic Bacillus megaterium strain YJB3

Phthalic acid esters (PAEs) are a group of recalcitrant and hazardous organic compounds that pose a great threat to both ecosystem and human beings. A novel endophytic strain YJB3 that could utilize a wide range of PAEs as the sole carbon and energy sources for cell growth was isolated from Canna indica root tissue. It was identified as Bacillus megaterium based on morphological characteristics and 16S rDNA sequence homology analysis. The degradation capability of the strain YJB3 was investigated by incubation in mineral salt medium containing di-n-butyl-phthalate (DBP), one of important PAEs under different environmental conditions, showing 82.5% of the DBP removal in 5days of incubation under the optimum conditions (acetate 1.2g·L^-1, inocula 1.8%, and temperature 34.2°C) achieved by two-step sequential optimization technologies. The DBP metabolites including mono-butyl phthalate (MBP), phthalic acid (PA), protocatechuic acid (PCA), etc. were determined by GC-MS. The PCA catabolic genes responsible for the aromatic ring cleavage of PCA in the strain YJB3 were excavated by whole-genome sequencing. Thus, a degradation pathway of DBP by the strain YJB3 was proposed that MBP was formed, followed by PA, and then the intermediates were further utilized till complete degradation. To our knowledge, this is the first study to show the biodegradation of PAEs using endophyte. The results in the present study suggest that the strain YJB3 is greatly promising to act as a competent inoculum in removal of PAEs in both soils and crops.

Formulation and stabilization of an Arthrobacter strain with good storage stability and 4-chlorophenol-degradation activity for bioremediation

Chlorophenols are widespread and of environmental concern due to their toxic and carcinogenic properties. Development of less costly and less technically challenging remediation methods are needed; therefore, we developed a formulation based on micronized vermiculite that, when air-dried, resulted in a granular product containing the 4-chlorophenol (4-CP)-degrading Gram-positive bacterium Arthrobacter chlorophenolicus A6. This formulation and stabilization method yielded survival rates of about 60% that remained stable in storage for at least 3 months at 4 °C. The 4-CP degradation by the formulated and desiccated A. chlorophenolicus A6 cells was compared to that of freshly grown cells in controlled-environment soil microcosms. The stabilized cells degraded 4-CP equally efficient as freshly grown cells in two different set-ups using both hygienized and non-treated soils. The desiccated microbial product was successfully employed in an outdoor pot trial showing its effectiveness under more realistic environmental conditions. No significant phytoremediation effects on 4-CP degradation were observed in the outdoor pot experiment. The 4-CP degradation kinetics from both the microcosms and the outdoor pot trial were used to generate a predictive model of 4-CP biodegradation potentially useful for larger-scale operations, enabling better bioremediation set-ups and saving of resources. This study also opens up the possibility of formulating and stabilizing also other Arthrobacter strains possessing different desirable pollutant-degrading capabilities.

N-acyl-homoserine lactone dynamics during biofilm formation of a 1,2,4-trichlorobenzene mineralizing community on clay

In Gram-negative bacteria, quorum sensing systems are based on the N-acyl-homoserine lactone (AHL) molecule. The objective of this study was to investigate the role of quorum sensing systems during biofilm formation by a microbial community while degrading the pollutant. Our model system included 1,2,4-trichlorobenzene (1,2,4-TCB) and its mineralizing Gram-negative bacterial community to investigate the relationships between AHL dynamics, cell growth and pollutant degradation. Biomineralization of 1,2,4-TCB was monitored for both the planktonic bacterial community with and without sterile clay particles in liquid cultures. The bacterial growth and production of AHLs were quantified by fluorescent in situ hybridization and immunoassay analysis, respectively. A rapid production of AHLs which occurred coincided with the biofilm formation and the increase of mineralization rate of 1,2,4-TCB in liquid cultures. There is a positive correlation between the cell density of Bodertella on the clay particles and mineralization rate of 1,2,4-TCB. 3-oxo-C_12:1-HSL appears to be the dominant AHL with the highest intensity and rapidly degraded by the bacterial community via two main consecutive reactions (lactone hydrolysis and decarboxylic reaction). These findings suggest that the integrated AHLs and their degraded products play a crucial role in biofilm formation and biomineralization of 1,2,4-TCB in culture.

Organohalide Respiration with Chlorinated Ethenes under Low pH Conditions

Bioremediation at chlorinated solvent sites often leads to groundwater acidification due to electron donor fermentation and enhanced dechlorination activity. The microbial reductive dechlorination process is robust at circumneutral pH, but activity declines at groundwater pH values below 6.0. Consistent with this observation, the activity of tetrachloroethene (PCE) dechlorinating cultures declined at pH 6.0 and was not sustained in pH 5.5 medium, with one notable exception. Sulfurospirillum multivorans dechlorinated PCE to cis-1,2-dichloroethene (cDCE) in pH 5.5 medium and maintained this activity upon repeated transfers. Microcosms established with soil and aquifer materials from five distinct locations dechlorinated PCE-to-ethene at pH 5.5 and pH 7.2. Dechlorination to ethene was maintained following repeated transfers at pH 7.2, but no ethene was produced at pH 5.5, and only the transfer cultures derived from the Axton Cross Superfund (ACS) microcosms sustained PCE dechlorination to cDCE as a final product. 16S rRNA gene amplicon sequencing of pH 7.2 and pH 5.5 ACS enrichments revealed distinct microbial communities, with the dominant dechlorinator being Dehalococcoides in pH 7.2 and Sulfurospirillum in pH 5.5 cultures. PCE-to-trichloroethene- (TCE-) and PCE-to-cDCE-dechlorinating isolates obtained from the ACS pH 5.5 enrichment shared 98.6%, and 98.5% 16S rRNA gene sequence similarities to Sulfurospirillum multivorans. These findings imply that sustained Dehalococcoides activity cannot be expected in low pH (i.e., ≤ 5.5) groundwater, and organohalide-respiring Sulfurospirillum spp. are key contributors to in situ PCE reductive dechlorination under low pH conditions.

Efficient phytoremediation of organic contaminants in soils using plant-endophyte partnerships

Soil pollution with organic contaminants is one of the most intractable environmental problems today, posing serious threats to humans and the environment. Innovative strategies for remediating organic-contaminated soils are critically needed. Phytoremediation, based on the synergistic actions of plants and their associated microorganisms, has been recognized as a powerful in situ approach to soil remediation. Suitable combinations of plants and their associated endophytes can improve plant growth and enhance the biodegradation of organic contaminants in the rhizosphere and/or endosphere, dramatically expediting the removal of organic pollutants from soils. However, for phytoremediation to become a more widely accepted and predictable alternative, a thorough understanding of plant-endophyte interactions is needed. Many studies have recently been conducted on the mechanisms of endophyte-assisted phytoremediation of organic contaminants in soils. In this review, we highlight the superiority of organic pollutant-degrading endophytes for practical applications in phytoremediation, summarize alternative strategies for improving phytoremediation, discuss the fundamental mechanisms of endophyte-assisted phytoremediation, and present updated information regarding the advances, challenges, and new directions in the field of endophyte-assisted phytoremediation technology.

Effects of Sulfate Reduction on Trichloroethene Dechlorination by Dehalococcoides-Containing Microbial Communities

In order to elucidate interactions between sulfate reduction and dechlorination, we systematically evaluated the effects of different concentrations of sulfate and sulfide on reductive dechlorination by isolates, constructed consortia, and enrichments containing Dehalococcoides sp. Sulfate (up to 5 mM) did not inhibit the growth or metabolism of pure cultures of the dechlorinator Dehalococcoides mccartyi 195, the sulfate reducer Desulfovibrio vulgaris Hildenborough, or the syntroph Syntrophomonas wolfei In contrast, sulfide at 5 mM exhibited inhibitory effects on growth of the sulfate reducer and the syntroph, as well as on both dechlorination and growth rates of D. mccartyi Transcriptomic analysis of D. mccartyi 195 revealed that genes encoding ATP synthase, biosynthesis, and Hym hydrogenase were downregulated during sulfide inhibition, whereas genes encoding metal-containing enzymes involved in energy metabolism were upregulated even though the activity of those enzymes (hydrogenases) was inhibited. When the electron acceptor (trichloroethene) was limiting and an electron donor (lactate) was provided in excess to cocultures and enrichments, high sulfate concentrations (5 mM) inhibited reductive dechlorination due to the toxicity of generated sulfide. The initial cell ratio of sulfate reducers to D. mccartyi (1:3, 1:1, or 3:1) did not affect the dechlorination performance in the presence of sulfate (2 and 5 mM). In contrast, under electron donor limitation, dechlorination was not affected by sulfate amendments due to low sulfide production, demonstrating that D. mccartyi can function effectively in anaerobic microbial communities containing moderate sulfate concentrations (5 mM), likely due to its ability to outcompete other hydrogen-consuming bacteria and archaea.IMPORTANCE Sulfate is common in subsurface environments and has been reported as a cocontaminant with chlorinated solvents at various concentrations. Inconsistent results for the effects of sulfate inhibition on the performance of dechlorination enrichment cultures have been reported in the literature. These inconsistent findings make it difficult to understand potential mechanisms of sulfate inhibition and complicate the interpretation of bioremediation field data. In order to elucidate interactions between sulfate reduction and reductive dechlorination, this study systematically evaluated the effects of different concentrations of sulfate and sulfide on reductive dechlorination by isolates, constructed consortia, and enrichments containing Dehalococcoides sp. This study provides a more fundamental understanding of the competition mechanisms between reductive dechlorination by Dehalococcoides mccartyi and sulfate reduction during the bioremediation process. It also provides insights on the significance of sulfate concentrations on reductive dechlorination under electron donor/acceptor-limiting conditions during in situ bioremediation applications. For example, at a trichloroethene-contaminated site with a high sulfate concentration, proper slow-releasing electron donors can be selected to generate an electron donor-limiting environment that favors reductive dechlorination and minimizes the sulfide inhibition effect.

Plant-bacteria partnerships for the remediation of persistent organic pollutants

High toxicity, bioaccumulation factor and widespread dispersal of persistent organic pollutants (POPs) cause environmental and human health hazards. The combined use of plants and bacteria is a promising approach for the remediation of soil and water contaminated with POPs. Plants provide residency and nutrients to their associated rhizosphere and endophytic bacteria. In return, the bacteria support plant growth by the degradation and detoxification of POPs. Moreover, they improve plant growth and health due to their innate plant growth-promoting mechanisms. This review provides a critical view of factors that affect absorption and translocation of POPs in plants and the limitations that plant have to deal with during the remediation of POPs. Moreover, the synergistic effects of plant-bacteria interactions in the phytoremediation of organic pollutants with special reference to POPs are discussed.

Effects of Funnelliformis mosseae inoculation on alleviating atrazine damage in Canna indica L. var. flava Roxb

Atrazine residue in the environment continually damages plants and therefore requires immediate attention and effective development of methods for its decontamination. The effects of Funnelliformis mosseae inoculation on growth and physiology in atrazine-treated Canna indica L. var. flava Roxb. were investigated. At atrazine concentrations up to 15 mg L^-1, the growth of C. indica plants were negatively affected. Inoculation with F. mosseae alleviated the atrazine inhibition of plant growth and biomass. Furthermore, the chlorophyll content and root function increased under F. mosseae inoculation, and the oxidative stress of malondialdehyde, peroxidase, and superoxide dismutase activities induced by atrazine were also alleviated by F. mosseae inoculation. The removal rate of atrazine by untreated C. indica was significant, with removal rates of 20.5-55.3% by the end of a 14-day experiment; however, F. mosseae inoculation increased the removal rate to 35.6-75.1%. In conclusion, F. mosseae inoculation can alleviate the damage induced by atrazine in C. indica. Accordingly, C. indica inoculated with F. mosseae has excellent potential to be used in phytoremediation in habitats polluted by high atrazine concentrations.

The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective

Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHCs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites. Bacterially driven PHC bioremediation is attributed to the presence of diverse suites of metabolic genes for aliphatic and aromatic hydrocarbons, along with a broader suite of physiological properties including biosurfactant production, biofilm formation, chemotaxis to hydrocarbons, and flexibility in cell-surface hydrophobicity. In soils impacted by PHC contamination, microbial bioremediation generally relies on the addition of high-energy electron acceptors (e.g., oxygen) and fertilization to supply limiting nutrients (e.g., nitrogen, phosphorous, potassium) in the face of excess PHC carbon. As an alternative, the addition of plants can greatly improve bioremediation rates and outcomes as plants provide microbial habitats, improve soil porosity (thereby increasing mass transfer of substrates and electron acceptors), and exchange limiting nutrients with their microbial counterparts. In return, plant-associated microorganisms improve plant growth by reducing soil toxicity through contaminant removal, producing plant growth promoting metabolites, liberating sequestered plant nutrients from soil, fixing nitrogen, and more generally establishing the foundations of soil nutrient cycling. In a practical and applied sense, the collective action of plants and their associated microorganisms is advantageous for remediation of PHC contaminated soil in terms of overall cost and success rates for in situ implementation in a diversity of environments. Mechanistically, there remain biological unknowns that present challenges for applying bio- and phyto-remediation technologies without having a deep prior understanding of individual target sites. In this review, evidence from traditional and modern omics technologies is discussed to provide a framework for plant-microbe interactions during PHC remediation. The potential for integrating multiple molecular and computational techniques to evaluate linkages between microbial communities, plant communities and ecosystem processes is explored with an eye on improving phytoremediation of PHC contaminated sites.

Insights into the degradation capacities of Amycolatopsis tucumanensis DSM 45259 guided by microarray data

The analysis of catabolic capacities of microorganisms is currently often achieved by cultivation approaches and by the analysis of genomic or metagenomic datasets. Recently, a microarray system designed from curated key aromatic catabolic gene families and key alkane degradation genes was designed. The collection of genes in the microarray can be exploited to indicate whether a given microbe or microbial community is likely to be functionally connected with certain degradative phenotypes, without previous knowledge of genome data. Herein, this microarray was applied to capture new insights into the catabolic capacities of copper-resistant actinomycete Amycolatopsis tucumanensis DSM 45259. The array data support the presumptive ability of the DSM 45259 strain to utilize single alkanes (n-decane and n-tetradecane) and aromatics such as benzoate, phthalate and phenol as sole carbon sources, which was experimentally validated by cultivation and mass spectrometry. Interestingly, while in strain DSM 45259 alkB gene encoding an alkane hydroxylase is most likely highly similar to that found in other actinomycetes, the genes encoding benzoate 1,2-dioxygenase, phthalate 4,5-dioxygenase and phenol hydroxylase were homologous to proteobacterial genes. This suggests that strain DSM 45259 contains catabolic genes distantly related to those found in other actinomycetes. Together, this study not only provided new insight into the catabolic abilities of strain DSM 45259, but also suggests that this strain contains genes uncommon within actinomycetes.

Changes in fatty acid composition of Stenotrophomonas maltophilia KB2 during co-metabolic degradation of monochlorophenols

The changes in the cellular fatty acid composition of Stenotrophomonas maltophilia KB2 during co-metabolic degradation of monochlorophenols in the presence of phenol as well as its adaptive mechanisms to these compounds were studied. It was found that bacteria were capable of degrading 4-chlorophenol (4-CP) completely in the presence of phenol, while 2-chlorophenol (2-CP) and 3-chlorophenol (3-CP) they degraded partially. The analysis of the fatty acid profiles indicated that adaptive mechanisms of bacteria depended on earlier exposure to phenol, which isomer they degraded, and on incubation time. In bacteria unexposed to phenol the permeability and structure of their membranes could be modified through the increase of hydroxylated and cyclopropane fatty acids, and straight-chain and hydroxylated fatty acids under 2-CP, 3-CP and 4-CP exposure, respectively. In the exposed cells, regardless of the isomer they degraded, the most important changes were connected with the increase of the contribution of branched fatty acid on day 4 and the content of hydroxylated fatty acids on day 7. The changes, particularly in the proportion of branched fatty acids, could be a good indicator for assessing the progress of the degradation of monochlorophenols by S. maltophilia KB2. In comparison, in phenol-degrading cells the increase of cyclopropane and straight-chain fatty acid content was established. These findings indicated the degradative potential of the tested strain towards the co-metabolic degradation of persistent chlorophenols, and extended the current knowledge about the adaptive mechanisms of these bacteria to such chemicals.

Degradation of phenanthrene by Novosphingobium sp. HS2a improved plant growth in PAHs-contaminated environments

At the same time that the European Union (EU) policy recommend to direct efforts towards reductions of heavy metals, polycyclic aromatic hydrocarbons (PAHs) and mining residues, there is the need to increase the cultivable areas within Europe to cope with the increasing demands for food and energy crops. Bioremediation is a good technique for the restoration of contaminated soils; however, it has not been used extensively because of the variability of the outcome. This variability is frequently due to a bad establishment of foreign degrading populations in soil. We have demonstrated that Novosphingobium sp. HS2aR (i) is able to compete with other root colonizers and with indigenous bacteria, (ii) is able to establish in high numbers in the contaminated environments and (iii) is able to remove more than 90 % of the extractable phenanthrene in artificially contaminated soils. Furthermore, we have demonstrated that the capacity to remove phenanthrene is linked to the ability to promote plant growth in contaminated environments. The fact that the presence of Novosphingobium sp. HS2aR improves the growth of plants in contaminated soil suggests that it may be a useful strain for utilization in amelioration of soil quality while improving the growth of economically important energy crops, thus adding value to the bioremediation strategy.

A novel bioremediation strategy for petroleum hydrocarbon pollutants using salt tolerant Corynebacterium variabile HRJ4 and biochar

The present work aimed to develop a novel strategy to bioremediate the petroleum hydrocarbon contaminants in the environment. Salt tolerant bacterium was isolated from Dagang oilfield, China and identified as Corynebacterium variabile HRJ4 based on 16S rRNA gene sequence analysis. The bacterium had a high salt tolerant capability and biochar was developed as carrier for the bacterium. The bacteria with biochar were most effective in degradation of n-alkanes (C16, C18, C19, C26, C28) and polycyclic aromatic hydrocarbons (NAP, PYR) mixture. The result demonstrated that immobilization of C. variabile HRJ4 with biochar showed higher degradation of total petroleum hydrocarbons (THPs) up to 78.9% after 7-day of incubation as compared to the free leaving bacteria. The approach of this study will be helpful in clean-up of petroleum-contamination in the environments through bioremediation process using eco-friendly and cost effective materials like biochar.

Metabolomics Analysis Reveals the Participation of Efflux Pumps and Ornithine in the Response of Pseudomonas putida DOT-T1E Cells to Challenge with Propranolol

Efflux pumps are critically important membrane components that play a crucial role in strain tolerance in Pseudomonas putida to antibiotics and aromatic hydrocarbons that result in these toxicants being expelled from the bacteria. Here, the effect of propranolol on P. putida was examined by sudden addition of 0.2, 0.4 and 0.6 mg mL^-1 of this β-blocker to several strains of P. putida, including the wild type DOT-T1E and the efflux pump knockout mutants DOT-T1E-PS28 and DOT-T1E-18. Bacterial viability measurements reveal that the efflux pump TtgABC plays a more important role than the TtgGHI pump in strain tolerance to propranolol. Mid-infrared (MIR) spectroscopy was then used as a rapid, high-throughput screening tool to investigate any phenotypic changes resulting from exposure to varying levels of propranolol. Multivariate statistical analysis of these MIR data revealed gradient trends in resultant ordination scores plots, which were related to the concentration of propranolol. MIR illustrated phenotypic changes associated with the presence of this drug within the cell that could be assigned to significant changes that occurred within the bacterial protein components. To complement this phenotypic fingerprinting approach metabolic profiling was performed using gas chromatography mass spectrometry (GC-MS) to identify metabolites of interest during the growth of bacteria following toxic perturbation with the same concentration levels of propranolol. Metabolic profiling revealed that ornithine, which was only produced by P. putida cells in the presence of propranolol, presents itself as a major metabolic feature that has important functions in propranolol stress tolerance mechanisms within this highly significant and environmentally relevant species of bacteria.

Bioaugmentation strategy employing a microbial consortium immobilized in chitosan beads for oil degradation in mesocosm scale

A bacterial consortium composed by four metagenomic clones and Bacillus subtilis strain CBMAI 707, all derived from petroleum reservoirs, was entrapped in chitosan beads and evaluated regarding hydrocarbon degradation capability. Experiments were carried out in mesocosm scale (3000L) with seawater artificially polluted with crude oil. At different time intervals, mesocosms were sampled and subjected to GC-FID and microbiological analyses, as total and heterotrophic culturable bacterial abundance (DAPI and CFU count), biological oxygen demand (BOD) and taxonomic diversity (massive sequencing of 16S rRNA genes). The results obtained showed that degradation of n-alkane hydrocarbons was similar between both treatments. However, aromatic compound degradation was more efficient in bioaugmentation treatment, with biodegradation percentages reaching up to 99% in 30days. Community dynamics was different between treatments and the consortium used in the bioaugmentation treatment contributed to a significant increase in aromatic hydrocarbon degradation.

Metabolic Fingerprinting of Pseudomonas putida DOT-T1E Strains: Understanding the Influence of Divalent Cations in Adaptation Mechanisms Following Exposure to Toluene

Pseudomonas putida strains can adapt and overcome the activity of toxic organic solvents by the employment of several resistant mechanisms including efflux pumps and modification to lipopolysaccharides (LPS) in their membranes. Divalent cations such as magnesium and calcium play a crucial role in the development of solvent tolerance in bacterial cells. Here, we have used Fourier transform infrared (FT-IR) spectroscopy directly on cells (metabolic fingerprinting) to monitor bacterial response to the absence and presence of toluene, along with the influence of divalent cations present in the growth media. Multivariate analysis of the data using principal component-discriminant function analysis (PC-DFA) showed trends in scores plots, illustrating phenotypic alterations related to the effect of Mg(2+), Ca(2+) and toluene on cultures. Inspection of PC-DFA loadings plots revealed that several IR spectral regions including lipids, proteins and polysaccharides contribute to the separation in PC-DFA space, thereby indicating large phenotypic response to toluene and these cations. Finally, the saturated fatty acid ratio from the FT-IR spectra showed that upon toluene exposure, the saturated fatty acid ratio was reduced, while it increased in the presence of divalent cations. This study clearly demonstrates that the combination of metabolic fingerprinting with appropriate chemometric analysis can result in practicable knowledge on the responses of important environmental bacteria to external stress from pollutants such as highly toxic organic solvents, and indicates that these changes are manifest in the bacterial cell membrane. Finally, we demonstrate that divalent cations improve solvent tolerance in P. putida DOT‑T1E strains.

The effect of Funnelliformis mosseae inoculation on the phytoremediation of atrazine by the aquatic plant Canna indica L. var. flava Roxb

Funnelliformis mosseaeinoculation exhibited a beneficial effect on the phytoremediation of atrazine in water by the aquatic plantCanna indicaL.

Metabolic analysis of the response of Pseudomonas putida DOT-T1E strains to toluene using Fourier transform infrared spectroscopy and gas chromatography mass spectrometry

INTRODUCTION

An exceptionally interesting stress response of Pseudomonas putida strains to toxic substances is the induction of efflux pumps that remove toxic chemical substances from the bacterial cell out to the external environment. To exploit these microorganisms to their full potential a deeper understanding of the interactions between the bacteria and organic solvents is required. Thus, this study focuses on investigation of metabolic changes in P. putida upon exposure to toluene.

OBJECTIVE

Investigate observable metabolic alterations during interactions of three strains of P. putida (DOT-T1E, and its mutants DOT-T1E-PS28 and DOT-T1E-18) with the aromatic hydrocarbon toluene.

METHODS

The growth profiles were measured by taking optical density (OD) measurement at 660 nm (OD₆₆₀) at various time points during incubation. For fingerprinting analysis, Fourier-transform infrared (FT-IR) spectroscopy was used to investigate any phenotypic changes resulting from exposure to toluene. Metabolic profiling analysis was performed using gas chromatography-mass spectrometry (GC-MS). Principal component-discriminant function analysis (PC-DFA) was applied to the FT-IR data while multiblock principal component analysis (MB-PCA) and N-way analysis of variance (N-way ANOVA) were applied to the GC-MS data.

RESULTS

The growth profiles demonstrated the effect of toluene on bacterial cultures and the results suggest that the mutant P. putida DOT-T1E-18 was more sensitive (significantly affected) to toluene compared to the other two strains. PC-DFA on FT-IR data demonstrated the differentiation between different conditions of toluene on bacterial cells, which indicated phenotypic changes associated with the presence of the solvent within the cell. Fifteen metabolites associated with this phenotypic change, in P. putida due to exposure to solvent, were from central metabolic pathways. Investigation of MB-PCA loading plots and N-way ANOVA for condition | strain × time blocking (dosage of toluene) suggested ornithine as the most significant compound that increased upon solvent exposure.

CONCLUSION

The combination of metabolic fingerprinting and profiling with suitable multivariate analysis revealed some interesting leads for understanding the mechanism of Pseudomonas strains response to organic solvent exposure.

Spatial and temporal dynamics of organohalide-respiring bacteria in a heterogeneous PCE-DNAPL source zone

Effective treatment of sites contaminated with dense non-aqueous phase liquids (DNAPLs) requires detailed understanding of the microbial community responses to changes in source zone strength and architecture. Changes in the spatial and temporal distributions of the organohalide-respiring Dehalococcoides mccartyi (Dhc) strains and Geobacter lovleyi strain SZ (GeoSZ) were examined in a heterogeneous tetrachloroethene- (PCE-) DNAPL source zone within a two-dimensional laboratory-scale aquifer flow cell. As part of a combined remedy approach, flushing with 2.3 pore volumes (PVs) of 4% (w/w) solution of the nonionic, biodegradable surfactant Tween® 80 removed 55% of the initial contaminant mass, and resulted in a PCE-DNAPL distribution that contained 51% discrete ganglia and 49% pools (ganglia-to-pool ratio of 1.06). Subsequent bioaugmentation with the PCE-to-ethene-dechlorinating consortium BDI-SZ resulted in cis-1,2-dichloroethene (cis-DCE) formation after 1 PV (ca. 7 days), while vinyl chloride (VC) and ethene were detected 10 PVs after bioaugmentation. Maximum ethene yields (ca. 90 μM) within DNAPL pool and ganglia regions coincided with the detection of the vcrA reductive dehalogenase (RDase) gene that exceeded the Dhc 16S rRNA genes by 2.0±1.3 and 4.0±1.7 fold in the pool and ganglia regions, respectively. Dhc and GeoSZ cell abundance increased by up to 4 orders-of-magnitude after 28 PVs of steady-state operation, with 1 to 2 orders-of-magnitude increases observed in close proximity to residual PCE-DNAPL. These observations suggest the involvement of these dechlorinators the in observed PCE dissolution enhancements of up to 2.3 and 6.0-fold within pool and ganglia regions, respectively. Analysis of the solid and aqueous samples at the conclusion of the experiment revealed that the highest VC (≥155 μM) and ethene (≥65 μM) concentrations were measured in zones where Dhc and GeoSZ were predominately attached to the solids. These findings demonstrate dynamic responses of organohalide-respiring bacteria in a heterogeneous DNAPL source zone, and emphasize the influence of source zone architecture on bioremediation performance.

Diversity of alkane hydroxylase genes on the rhizoplane of grasses planted in petroleum-contaminated soils

The study investigated the diversity and genotypic features of alkane hydroxylase genes on rhizoplanes of grasses planted in artificial petroleum-contaminated soils to acquire new insights into the bacterial communities responsible for petroleum degradation in phytoremediation. Four types of grass (Cynodon dactylon, two phenotypes of Zoysia japonica, and Z. matrella) were used. The concentrations of total petroleum hydrocarbon effectively decreased in the grass-planted systems compared with the unplanted system. Among the representative alkane hydroxylase genes alkB, CYP153, almA and ladA, the first two were detected in this study, and the genotypes of both genes were apparently different among the systems studied. Their diversity was also higher on the rhizoplanes of the grasses than in unplanted oil-contaminated soils. Actinobacteria-related genes in particular were among the most diverse alkane hydroxylase genes on the rhizoplane in this study, indicating that they are one of the main contributors to degrading alkanes in oil-contaminated soils during phytoremediation. Actinobacteria-related alkB genes and CYP153 genes close to the genera Parvibaculum and Aeromicrobium were found in significant numbers on the rhizoplanes of grasses. These results suggest that the increase in diversity and genotype differences of the alkB and CYP153 genes are important factors affecting petroleum hydrocarbon-degrading ability during phytoremediation.

Tetrachloromethane-Degrading Bacterial Enrichment Cultures and Isolates from a Contaminated Aquifer

Abstract: The prokaryotic community of a groundwater aquifer exposed to high concentrations of tetrachloromethane (CCl₄) for more than three decades was followed by terminal restriction fragment length polymorphism (T-RFLP) during pump-and-treat remediation at the contamination source. Bacterial enrichments and isolates were obtained under selective anoxic conditions, and degraded 10 mg·L⁻¹ CCl₄, with less than 10% transient formation of chloroform. Dichloromethane and chloromethane were not detected. Several tetrachloromethane-degrading strains were isolated from these enrichments, including bacteria from the Klebsiella and Clostridium genera closely related to previously described CCl₄ degrading bacteria, and strain TM1, assigned to the genus Pelosinus, for which this property was not yet described. Pelosinus sp. TM1, an oxygen-tolerant, Gram-positive bacterium with strictly anaerobic metabolism, excreted a thermostable metabolite into the culture medium that allowed extracellular CCl₄ transformation. As estimated by T-RFLP, phylotypes of CCl₄-degrading enrichment cultures represented less than 7%, and archaeal and Pelosinus strains less than 0.5% of the total prokaryotic groundwater community.