Potential impact of soil microbial heterogeneity on the persistence of hydrocarbons in contaminated subsurface soils

An in situ reactive zone approach using calcium peroxide for the remediation of benzene and chlorobenzene in groundwater: A field study

There is a gap in understanding the different contributions of biodegradation and free radical oxidation using calcium peroxide (CaO2) for the remediation of mixed contaminants of benzene and chlorobenzene in groundwater. In this study, the remedial efficiency and mechanisms of benzene and chlorobenzene co-contaminants using CaO2 were explored by an integrated approach of field study and laboratory validation. It was found that in the field demonstration program, the radius of influence for each injection point using Geoprobe direct-push was larger than the designed value of 0.75 m in the reactive zones created by CaO2 supplemented with a buffer solution (Area A) and CaO2 only (Area B). Both benzene and chlorobenzene were remediated to meet the cleanup goals within 5 months. The benzene and chlorobenzene concentration rebounds observed in monitoring wells were treated effectively with sustained effect of reagents. The laboratory validation experiments verified CaO2 with a buffer solution could maintain the pH values within the range of 6.05-7.69, and higher DO concentrations for prolonged period. The contributions of biodegradation for benzene were 43.47% and 42.02% in CaO2 group and CaO2 adjusted with buffer solutions group, respectively, while those for chlorobenzene were 16.87% and 19.61%. In addition, it was demonstrated in the laboratory that the application of CaO2 supplemented with a buffer solution had the best remediation efficiency for benzene and chlorobenzene, due to the contributions from both the free radicals HO• and the biodegradation of co-contaminants by the native microbial consortium. Furthermore, the intermediate byproducts, including phenol, 2-chlorophenol and pyruvate, were detected in groundwater collected in the field, and the biodegradation and oxidative degradation pathways of benzene and chlorobenzene with the application of CaO2 were proposed. The microbial composition analyses for groundwater samples revealed that multiple functional bacteria, which are capable of degrading benzene and chlorobenzene, were enriched. The findings of the current study take one step further for the understanding of the fundamentals of CaO2 as a slow oxygen releasing reagent, as well as its engineering applications for the remediation of organic contaminants in soil and groundwater.

Application of soil amendments mitigates phytotoxic effects on Solanum melongena L. and Lycopersicon esculentum L. seedlings exposed to chlorpyrifos and dimethoate pesticides

This field study was done to study the effects of pesticides chlorpyrifos and dimethoate singly and in combination with soil amendments like chemical fertilizer (CF), farmyard manure (FM), and 50% CF + 50% FM (CM) on various indices of growth, physio-biochemical parameters of brinjal, and their residual effect in tomato seedlings. As compared to the control, the decrease of 9.5 and 5.5%, 8.9 and 5.0% in fresh weight, dry weight respectively was recorded in the pesticide-only treatment in the brinjal crop. Pesticides when applied in combination with soil amendments depicted the highest growth of 105.4 and 118.2%, 104.1 and 115.1% in pesticides + CF treatment, 72.7 and 85.1%, 68.1 and 78.1% in pesticides + CM treatment, and 64.4 and 74.0%, 62.7 and 65.7% in pesticides + FM treatment compared to control. In tomato seedlings, the pesticides + CF treatment exhibited the lowest growth indices (25.5 and 31.9%, 26.4 and 28.8%) across the combined treatments while pesticide-only treatment depicted minimum growth compared to the control. In the case of photosynthesis rate and antioxidant activity, the combined treatments showed the trend as pesticides + CF > pesticides + CM > pesticides + FM in the brinjal crop; however, the trend became somewhat reversed in the tomato crop. The results indicated that soil-amended practices modulated pesticide-induced damage by upregulating photosynthetic performance, chlorophyll a fluorescence, and antioxidant balancing which might be associated with the mitigation of ROS-induced pesticide toxicity, and the effect was more pronounced with CM. Furthermore, our study was supported by non-metric-multidimensional scaling (NMDS)-constructed ordination plots by showing spatial patterns in different variables. The study might help in taking management decision to design mitigation actions for government and non-government agency at the farmers' level.

Application of nanofiber carriers for sampling of microbial biomass from contaminated groundwater

Sampling of microbial biomass is crucial for understanding and controlling remediation processes ongoing at contaminated sites in general, particularly when molecular genetic analyses are employed. In this study, fiber-based carriers with a nanofiber layer were developed and tested as a method to sample microbial biomass in groundwater for molecular genetic analysis. Nanofiber carriers, varying in the shape and the linear density of nanofibers, were examined throughout a 27-month monitoring period in groundwater contaminated with benzene, toluene, ethylbenzene and xylene isomers (BTEX), and chlorinated ethenes. The effect of carrier shape and nanofiber layer density on the microbial surface colonization and composition of the microbial biofilm was determined using real-time PCR and next-generation sequencing (NGS) analysis. Differences in microbial community composition between nanofiber carriers, groundwater, and soil samples were also analyzed to assess the applicability of carriers for biomass sampling at contaminated sites. The nanofiber carriers showed their applicability as a sampling tool, particularly because of their easy manipulation that facilitates DNA isolation. The majority of taxa (Proteobacteria, Firmicutes, and Bacteroidetes) present on the carrier surfaces were also detected in the groundwater. Moreover, the microbial community on all nanofiber carriers reflected the changes in the chemical composition of groundwater. Although the carrier characteristics (shape, nanofiber layer) did not substantially influence the microbial community on the carrier surface, the circular and planar carriers with a nanofiber layer displayed faster microbial surface colonization. However, the circular carrier was the most suitable for biomass sampling in groundwater because of its high contact area and because it does not require pre-treatment prior to DNA extraction.

Response of the microbial community to phosphate-solubilizing bacterial inoculants on Ulmus chenmoui Cheng in Eastern China

Phosphate-solubilizing bacteria (PSB) have beneficial effects on plant health and soil composition. To date, studies of PSB in soil have largely been performed under field or greenhouse conditions. However, less is known about the impact of introducing indigenous PSB in the field, including their effects on the local microbial community. In this study, we conducted greenhouse and field experiments to explore the effects of the addition of indigenous PSB on the growth of Chenmou elm (Ulmus chenmoui) and on the diversity and composition of the bacterial community in the soil. We obtained four bacterial isolates with the highest phosphate-solubilizing activity: UC_1 (Pseudomonas sp.), UC_M (Klebsiella sp.), UC_J (Burkholderia sp.), and UC_3 (Chryseobacterium sp.). Sequencing on the Illumina MiSeq platform showed that the inoculated PSB did not become the dominant strains in the U. chenmoui rhizosphere. However, the soil bacterial community structure was altered by the addition of these PSB. The relative abundance of Chloroflexi decreased significantly in response to PSB application in all treatment groups, whereas the populations of several bacteria, including Proteobacteria and Bacteroidetes, increased. Network analysis indicated that Chloroflexi was the most strongly negatively correlated with Proteobacteria, whereas Proteobacteria was strongly positively correlated with Bacteroidetes. Our findings indicate that inoculation with PSB (UC_1, UC_M, UC_J, and UC_3) can improve the growth of U. chenmoui and regulate its rhizosphere microbial community. Therefore, inoculation with these bacterial strains could promote the efficient cultivation and production of high-quality plant materials.

Benefits of organic manure combined with biochar amendments to cotton root growth and yield under continuous cropping systems in Xinjiang, China

Organic manure and biochar amendments have been used in agriculture to improve soil fertility and enhance crop productivity. Plant roots play an important role in the functionality of individual plants, and although the addition of organic manure and biochar reportedly affect roots, it remains unclear how root morphology and physiology respond. We conducted a field experiment to test the hypothesis that organic manure combined with biochar amendment could also enhance the productivity of continuous cropping systems in Xinjiang cotton plantations. Different levels of organic manure and biochar were applied. Organic manure and biochar significantly affected root morphology and physiology by improving soil nutrients. In the absence of biochar, organic manure amendment increased Root TTC reducing capacity, glutamine synthetase and nitrate reductase activity. Furthermore, morphological and physiological parameters peaked with 6% organic manure combined with 1% biochar. A significant increase in root physiology was recognized with an increase in soil nutrient content at the bud stage and a negative relationship between root physiology and soil total K content at the harvesting stage. Thus, our results indicate that organic manure combined with biochar positively influenced cotton roots, and therefore should be used to improve root health in continuous cropping systems.

The Emergence of Different Functionally Equivalent PAH Degrading Microbial Communities from a Single Soil in Liquid PAH Enrichment Cultures and Soil Microcosms Receiving PAHs with and without Bioaugmentation

Polycyclic aromatic hydrocarbon (PAHs) are common soil contaminants of concern due to their toxicity toward plants, animals and microorganisms. The use of indigenous or added microbes (bioaugmentation) is commonly used for bioremediation of PAHs. In this work, the biodegradation rates and changes in the bacterial community structure were evaluated. The enrichment culture was useful for unambiguously identifying members of the soil bacterial community associated with PAH degradation and yielded a low diversity community. No significant difference in the rate of PAH degradation was observed between the microcosm receiving only PAHs or PAHs and bioaugmentation. Moreover, identical matches to the bioaugmentation inoculum were only observed at the initial stages of PAH degradation on day 8. After 22 days of incubation, the substantial degradation of all PAHs had occurred in both microcosms and the PAH contaminated soil had statistically significant increases in Alphaproteobacteria. There were also increases in Betaproteobacteria. In contrast, the PAH contaminated and bioaugmented soil was not enriched in PAH degrading Proteobacteria genera and, instead, an increase from 1.6% to 8% of the population occurred in the phylum Bacteroidetes class Flavobacteria, with Flavobacterium being the only identified genus. In addition, the newly discovered genus Ohtaekwangia increased from 0% to 3.2% of the total clones. These results indicate that the same soil microbial community can give rise to different PAH degrading consortia that are equally effective in PAH degradation efficiency. Moreover, these results suggest that the lack of efficacy of bioaugmentation in soils can be attributed to a lack of persistence of the introduced microbes, yet nonetheless may alter the microbial community that arises in response to PAH contamination in unexpected ways.

Microbial diversity changes with rhizosphere and hydrocarbons in contrasting soils

In the ecotoxicological assessment of petroleum hydrocarbon-contaminated soil, microbial community profile is important aspect due to their involvement in soil functions. However, soil physicochemical properties and the inhabiting plants could dictate the microbial composition. A question remains unanswered is, how an integrated approach may be utilized to account for various contrasting soil properties, plant types (reference vs. native) and the nature of the hydrocarbon contamination. In this study, we utilized bacterial DNA profiling techniques to investigate the relationship between soil properties, contaminant and plant species. Results identified that Proteobacteria and Actinobacteria were the most abundant bacteria of the 45 phyla identified in the hydrocarbon-contaminated soil. The bulk and rhizosphere microbiome showed that the contaminated soil originally had quite distinct bacterial communities compared to the artificially contaminated soil (mine soil = 95 genera vs. other soils = 2-29 genera). In these cases, not significantly but the native plant slightly increased bacterial diversity and relative abundance in the same soils. Also, within each site, the bacterial community was significantly altered with the hydrocarbon concentration. In this instance, the influence of the contaminant was strong and also with the soil pH and organic matter. These results would significantly contribute to the novel insights on the molecular technique-based hydrocarbon toxicity assessment and the development of the further integrative approach with other microbial community and their metabolic profile in the contaminated sites.

Biostimulation of Indigenous Microbial Community for Bioremediation of Petroleum Refinery Sludge

Nutrient deficiency severely impairs the catabolic activity of indigenous microorganisms in hydrocarbon rich environments (HREs) and limits the rate of intrinsic bioremediation. The present study aimed to characterize the microbial community in refinery waste and evaluate the scope for biostimulation based in situ bioremediation. Samples recovered from the wastewater lagoon of Guwahati refinery revealed a hydrocarbon enriched [high total petroleum hydrocarbon (TPH)], oxygen-, moisture-limited, reducing environment. Intrinsic biodegradation ability of the indigenous microorganisms was enhanced significantly (>80% reduction in TPH by 90 days) with nitrate amendment. Preferred utilization of both higher- (>C30) and middle- chain (C20-30) length hydrocarbons were evident from GC-MS analysis. Denaturing gradient gel electrophoresis and community level physiological profiling analyses indicated distinct shift in community’s composition and metabolic abilities following nitrogen (N) amendment. High throughput deep sequencing of 16S rRNA gene showed that the native community was mainly composed of hydrocarbon degrading, syntrophic, methanogenic, nitrate/iron/sulfur reducing facultative anaerobic bacteria and archaebacteria, affiliated to γ- and δ-Proteobacteria and Euryarchaeota respectively. Genes for aerobic and anaerobic alkane metabolism (alkB and bssA), methanogenesis (mcrA), denitrification (nirS and narG) and N₂ fixation (nifH) were detected. Concomitant to hydrocarbon degradation, lowering of dissolve O₂ and increase in oxidation-reduction potential (ORP) marked with an enrichment of N₂ fixing, nitrate reducing aerobic/facultative anaerobic members [e.g., Azovibrio, Pseudoxanthomonas and Comamonadaceae members] was evident in N amended microcosm. This study highlighted that indigenous community of refinery sludge was intrinsically diverse, yet appreciable rate of in situ bioremediation could be achieved by supplying adequate N sources.