Improved RDX detoxification with starch addition using a novel nitrogen-fixing aerobic microbial consortium from soil contaminated with explosives

Chitin amendments eliminate the negative impacts of continuous cropping obstacles on soil properties and microbial assemblage

Continuous cropping of soybean leads to soil environment deterioration and soil-borne disease exacerbation, which in turn limits the sustainability of agricultural production. Chitin amendments are considered promising methods for alleviating soybean continuous cropping obstacles; however, the underlying mechanisms of soil sickness reduction remain unclear. In this study, soil amendments with pure and crude chitin at different addition dosages were employed to treat diseased soil induced by continuous cropping of soybean for five years. Chitin amendments, especially crude chitin, remarkably increased soil pH, available phosphorus (AP), potassium (AK) and nitrate nitrogen ( NO 3 - -N) contents, and improved soybean plant growth and soil microbial activities (FDA). Additionally, chitin application significantly enriched the relative abundances of the potential biocontrol bacteria Sphingomonas, Streptomyces, and Bacillus and the fungi Mortierella, Purpureocillium, and Metarhizium while depleted those of the potential plant pathogens Fusarium, Cylindrocarpon and Paraphoma. Moreover, chitin amendments induced looser pathogenic subnetwork structures and less pathogenic cooperation with other connected microbial taxa in the rhizosphere soils. The structural equation model (SEM) revealed that pure and crude chitin amendments promoted soybean plant growth by indirectly regulating soil pH-mediated soil microbial activities and potentially beneficial microbes, respectively. Therefore, the reduction strategies for continuous cropping obstacles by adding pure and crude chitin were distinct; pure chitin amendments showed general disease suppression, while crude chitin exhibited specific disease suppression. Overall, chitin amendments could suppress potential plant pathogens and improve soil health, thereby promoting soybean growth, which provides new prospects for cultivation practices to control soybean continuous cropping obstacles.

Agriterribacter soli sp. nov., isolated from herbicide-contaminated soil

A Gram-stain-negative, non-spore-forming and rod-shaped bacterium, designated strain NS-102T, was isolated from herbicide-contaminated soil sampled in Nanjing, PR China, and its taxonomic status was investigated by a polyphasic approach. Cell growth of strain NS-102T occurred at 16–42 °C (optimum, 30 °C), at pH 5.0–8.0 (optimum, pH 6.0) and in the presence of 0–3.5 % (w/v) NaCl (optimum, without addition of NaCl). The 16S rRNA gene sequence of strain NS-102T shows high similarity to that of Agriterribacter humi YJ03T (96.9 % similarity), followed by Terrimonas terrae T16R-129T (93.8 %) and Terrimonas pekingensis QHT (93.6 %). Average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between the draft genomes of strain NS-102T and A. humi YJ03T were 72.5, 69.4 and 18.6%, respectively. The only respiratory quinone was MK-7, and phosphatidylethanolamine and unidentified lipids were the major polar lipids. The major cellular fatty acids of strain NS-102T contained high amounts of iso-C15 : 0 (24.6 %), iso-C17 : 03-OH (24.1 %), iso-C15 : 0 G (16.6 %) and summed feature 3 (C16 : 1  ω6c and/or C16 : 1  ω7c) (15.6 %). The G+C content of the total DNA was determined to be 40.0 mol%. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain NS-102T represents a novel species of the genus Agriterribacter , for which the name Agriterribacter soli sp. nov. is proposed. The type strain is NS-102T (=CCTCC AB 2017249T=KCTC 62322T).

A sketch of microbiological remediation of explosives-contaminated soil focused on state of art and the impact of technological advancement on hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) degradation

When high-energy explosives such as hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX), 2,4,6-trinitrotoluene (TNT) are discharged into the surrounding soil and water during production, testing, open dumping, military, or civil activities, they leave a toxic footprint. The US Environmental Protection Agency has labeled RDX as a potential human carcinogen that must be degraded from contaminated sites quickly. Bioremediation of RDX is an exciting prospect that has received much attention in recent years. However, a lack of understanding of RDX biodegradation and the limitations of current approaches have hampered the widespread use of biodegradation-based strategies for RDX remediation at contamination sites. Consequently, new bioremediation technologies are required to enhance performance. In this review, we explore the requirements for in-silico analysis for producing biological models of microbial remediation of RDX in soil. On the other hand, potential gene editing methods for getting the host with target gene sequences responsible for the breakdown of RDX are also reported. Microbial formulations and biosensors for detection and bioremediation are also briefly described. The biodegradation of RDX offers an alternative remediation method that is both cost-effective and ecologically acceptable. It has the potential to be used in conjunction with other cutting-edge technologies to further increase the efficiency of RDX degradation.

In-vessel composting of HMX and RDX contaminated sludge using microbes isolated from contaminated site

Current study was carried out with an objective to remediate highly contaminated sludge with HMX and RDX obtained from an explosive manufacturing facility in North India employing indigenous microbes, Arthrobacter subterraneus (isolate no. S2-TSB-17) and Bacillus sonorensis (isolate no. S8-TSB-4) which were isolated from the same contaminated site. In-vessel composting of the explosive contaminated sludge was performed in 12 different bioreactors using cow manure and garden waste as bulking agents. 78.5% degradation of HMX was observed in reactor no. 2 with Bacillus sonorensis having combination of 10% sludge, 70% cow manure and 20% garden waste on 80th day. Two secondary metabolites Bis(hydroxymethyl)nitramine and methylene dinitramine were identified while studying the degradation pathway. Similarly, degradation of 91.2% was observed for RDX in reactor no. 11 with consortia of Arthrobacter subterraneus and Bacillus sonorensis on 80th day. During the study, release of significant nitrate and nitrite ions were observed. It has already been established that RDX and HMX degradation leads to release of nitrite/nitrate ions. The highest nitrite (reactor no. 11) and nitrate (reactor no. 2) release observed were 24.02 ± 0.05 mg/kg and 30.65 ± 0.99 mg/kg on 50th and 70th day, respectively. Scanning electron microscopic studies confirmed the attachment and presence of microbes with solid surface and no deformation in structure was observed in the microbial cells due to contamination stress. Findings of the study concluded that in-vessel composting assisted with native bacterial species can be a potential technology for the treatment of explosive contaminated sludge at the contaminated sites.

Applications of food waste-derived black soldier fly larval frass as incorporated compost, side-dress fertilizer and frass-tea drench for soilless cultivation of leafy vegetables in biochar-based growing media

Black soldier fly (BSF) larval bioconversion can recycle nutrients in organic wastes into larval biomass and frass. While the frass has been commonly marketed as a soil amendment, its usefulness in soilless cultivation remains largely unexplored. Growth experiments were conducted to investigate the effectiveness of surplus food-derived and okara-derived BSF larval frass as an incorporated compost, side-dress fertilizer and frass-tea drench for the cultivation of pak choi and lettuce in waste-wood derived biochar growing media. Pak choi yields from treatments with surplus food-derived frass and biochar at a 10:90 (v/v) ratio and inorganic fertilizer were comparable to those of the control which consisted of soil, peat-based compost and inorganic fertilizer. However, yields decreased with increasing frass incorporation rates owing to high salinity and potentially low oxygen conditions in the growing media. When used as a fertilizer on biochar-coir growing media, the direct application of frass as a side-dress fertilizer was 1.6-6.8 times more effective in promoting lettuce growth than the application as a frass-tea drench. Frass fertilizers derived from surplus food outperformed those derived from okara by 1.3-5.3 times. Lettuce yields were not significantly different between the treatment with surplus food-derived frass applied as a side-dress fertilizer and the control of liquid inorganic fertilizer. Variations in fertilizing potential were attributed to nutrient availability and the presence of plant growth promoting microbes in the growing media. BSF larval frass derived from food waste shows promise in partially replacing unsustainable agricultural inputs for leafy vegetable cultivation, including soil and inorganic fertilizers.

Degradation of high energetic material hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by a microbial consortium using response surface methodological approach

Soil and water get polluted with hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) during its manufacturing, storage and use for civil and military purposes. RDX has toxic effects on living and non-living environment and is a recalcitrant compound. Therefore, the remediation of this compound is necessary. Microbial degradation of RDX can be a suitable and sustainable option to reduce its deleterious impact on the environment. Therefore, the optimization for degradation of energetic munition compound RDX employing the consortium of native bacterial species, isolated from an actual contaminated site, was performed. The experiment was planned with three independent variables (initial RDX concentration, inoculum size of microbes, and duration of the experiment) and three dependent variables (percentage removal of RDX, optical density, and nitrite release). Both independent and dependent variables were analyzed by the response surface methodology (RSM) using the Box–Behnken design. The statistical analysis using analysis of variance (ANOVA) depicted a high regression coefficient, R2 = 0.9881 with the statistically significant p-value fitted into a quadratic regression model for percentage removal of RDX. Results showed an initial RDX concentration of 40 mg/L, inoculation size 6 mL and a time duration of 12 days was optimal for the reduction of RDX up to 80.4%.

Isolation and identification of a novel bacterium, Pseudomonas sp. ZyL-01, involved in the biodegradation of CL-20

Hexanitrohexaazaisowurtzitane (CL-20) is a compound with a polycyclic cage and an N-nitro group that has been shown to play an unfavorable role in environmental fate, biosafety, and physical health. The aim of this study was to isolate the microbial community and to identify a single microbial strain that can degrade CL-20 with desirable efficiency. Metagenomic sequencing methods were performed to investigate the dynamic changes in the composition of the community diversity. The most varied genus among the microbial community was Pseudomonas, which increased from 1.46% to 44.63% during the period of incubation (MC0-MC4). Furthermore, the new strain was isolated and identified from the activated sludge by bacterial morphological and 16s rRNA sequencing analyses. The CL-20 concentrations decreased by 75.21 μg/mL and 74.02 μg/mL in 48 h by MC4 and Pseudomonas sp. ZyL-01, respectively. Moreover, ZyL-01 could decompose 98% CL-20 of the real effluent in 14 day's incubation with the glucose as carbon source. Finally, a draft genome sequence was obtained to predict possible degrading enzymes involved in the biodegradation of CL-20. Specifically, 330 genes that are involved in energy production and conversion were annotated by Gene Ontology functional enrichment analysis, and some of these candidates may encode enzymes that are responsible for CL-20 degradation. In summary, our studies indicate that microbes might be a valuable biological resource for the treatment of environmental contamination caused by CL-20 and that Pseudomonas sp. ZyL-01 might be a promising candidate for eradicating CL-20 to achieve a more biosafe environment and improve public health.

A Sporolactobacillus-, Clostridium-, and Paenibacillus- Dominant Microbial Consortium Improved Anaerobic RDX Detoxification by Starch Addition

In the present study, an anaerobic microbial consortium for the degradation of hexahydro-1,3,5- trinitro-1,3,5-triazine (RDX) was selectively enriched with the co-addition of RDX and starch under nitrogen-deficient conditions. Microbial growth and anaerobic RDX biodegradation were effectively enhanced by the co-addition of RDX and starch, which resulted in increased RDX biotransformation to nitroso derivatives at a greater specific degradation rate than those for previously reported anaerobic RDX-degrading bacteria (isolates). The accumulation of the most toxic RDX degradation intermediate (MNX [hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine]) was significantly reduced by starch addition, suggesting improved RDX detoxification by the co-addition of RDX and starch. The subsequent MiSeq sequencing that targeted the bacterial 16S rRNA gene revealed that the Sporolactobacillus, Clostridium, and Paenibacillus populations were involved in the enhanced anaerobic RDX degradation. These results suggest that these three bacterial populations are important for anaerobic RDX degradation and detoxification. The findings from this work imply that the Sporolactobacillus, Clostridium, and Paenibacillus dominant microbial consortium may be valuable for the development of bioremediation resources for RDX-contaminated environments.

Enhancing hexahydro-1, 3, 5-trinitro-1, 3, 5-triazine (RDX) remediation through water-dispersible Microbacterium esteraromaticum granules

In the current manuscript, we explored the remediation potential of Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by Gram-positive Microbacterium esteraromaticum 12849. The strain detoxified 70.9 and 63.93% RDX in minimal nutrient medium and soil, respectively. Subsequently, the strain 12849 was formulated in form of water-dispersible granules (WDG) using talcum powder and alginic acid as inert ingredients. During the microcosm study, WDG exhibited 8.98% enhanced RDX degradation in contrast to the unformulated Microbacterium esteraromaticum. The LC-MS analysis revealed the presence of two intermediates, namely N-methyl-N, N'-dinitromethanediamine, and methylenedintramine, during the RDX degradation by strain 12849 in soil. Interestingly, no significant difference was observed in the rate of RDX degradation by strain 12849 due to the formulation process. The first-order kinetics was seen in RDX degradation with a degradation coefficient of 0.04 and 0.0339 day^-1 by formulated and unformulated strain, respectively. The current investigation implies M. esteraromaticum as a potential microbe for RDX degradation and opens up the possibility of exploiting it in its effective WDG form for explosive contaminated sites.

Effects of antibiotics on microbial community structure and microbial functions in constructed wetlands treated with artificial root exudates

In the rhizosphere, plant root exudates can mediate the toxicity of antibiotics on microorganisms, yet the mechanisms are poorly understood. To simulate the antibiotic contamination of global rivers and lakes, the current study investigated the effects of two antibiotics (ofloxacin at 8.69 × 10⁴ ng L^-1 and tetracycline at 8.62 × 10⁴ ng L^-1) and their binary combination (8.24 × 10⁴ ng L^-1 ofloxacin and 7.11 × 10⁴ ng L^-1 tetracycline) on bacterial communities in micro-polluted constructed wetlands with and without artificial root exudates. The two antibiotics had no significant effects on the removal of excess carbon and nitrogen from the microcosms treated with and without exudates. Furthermore, with regard to bacterial community structure, antibiotic exposure increased the bacterial richness of bulk and exudate treated microcosms (P < 0.05). However, a significant increase (P < 0.05) in bacterial diversity elicited by ofloxacin and antibiotic mixture exposure was only observed in microcosms with exudates. In exudate treated microcosms, ofloxacin promoted the relative abundance of Arthrobacter spp., which are ofloxacin-resistant bacterial species, which significantly varied from what was observed in microcosms free of exudates. Moreover, tetracycline, ofloxacin and their combination all significantly increased the relative abundance of nitrogen cycling bacteria Rhizobacter spp. and Rhizobium spp., and decreased the relative abundance of antibiotic-resistant bacteria Pseudomonas spp. Simultaneously, with regard to bacterial community functions, the functional profiles (Kyoto Encyclopedia of Genes and Genomes) showed that the pathways of amino acid and carbohydrate metabolism were enhanced by antibiotics in microcosms with exudates. The findings illustrate that antibiotics not only alter the bacterial structure and composition but also change their functional properties in constructed wetlands, and these interruption effects could be affected by root exudates of plants, which may further reveal the ecological implication of plants in constructed wetlands.

Application of humic acid changes the microbial communities and inhibits the expression of tetracycline resistance genes in 4-chlorophenol wastewater treatment

The occurrence and spread of antibiotic resistance genes (ARGs) are concerns that have threatened public health for many years. However, the effects of humic acid (HA) application on the expression of ARGs in chlorophenols wastewater treatment are rarely reported. In this study, we investigated the sludge performance, including the removal of pollutants, changes in the microbial communities, and the expression of tetracycline resistance genes (TRGs), to explore the function of HA in 4-chlorophenol (4-CP) wastewater treatment at different HA concentrations. The results showed that HA application did not significantly stimulate the removal of pollutants, other than the removal of PO₄^3--P. High-throughput sequencing analysis indicated that the application of HA influenced the microbial communities and changed the expression level of TRGs. Quantitative real-time PCR analysis showed that the expression of numerous TRGs (tetC, tetG, tetW, tetX, and intI1) was significantly inhibited by the application of HA (25 mg L^-1) during 4-CP wastewater treatment. In summary, HA application played an important role in treating chlorophenols wastewater and reducing the expression of TRGs. This work aimed to provide an efficient method of reducing the expression level of ARGs in industrial wastewater treatment, which has inevitable environmental significance.

Microbial Enrichment Culture Responsible for the Complete Oxidative Biodegradation of 3-Amino-1,2,4-triazol-5-one (ATO), the Reduced Daughter Product of the Insensitive Munitions Compound 3-Nitro-1,2,4-triazol-5-one (NTO)

3-Nitro-1,2,4-triazol-5-one (NTO) is one of the main ingredients of many insensitive munitions, which are being used as replacements for conventional explosives. As its use becomes widespread, more research is needed to assess its environmental fate. Previous studies have shown that NTO is biologically reduced to 3-amino-1,2,4-triazol-5-one (ATO). However, the final degradation products of ATO are still unknown. We have studied the aerobic degradation of ATO by enrichment cultures derived from the soil. After multiple transfers, ATO degradation was monitored in closed bottles through measurements of inorganic carbon and nitrogen species. The results indicate that the members of the enrichment culture utilize ATO as the sole source of carbon and nitrogen. As ATO was mineralized to CO₂, N₂, and NH₄⁺, microbial growth was observed in the culture. Co-substrates addition did not increase the ATO degradation rate. Quantitative polymerase chain reaction analysis revealed that the organisms that enriched using ATO as carbon and nitrogen source were Terrimonas spp., Ramlibacter-related spp., Mesorhizobium spp., Hydrogenophaga spp., Ralstonia spp., Pseudomonas spp., Ectothiorhodospiraceae, and Sphingopyxis. This is the first study to report the complete mineralization of ATO by soil microorganisms, expanding our understanding of natural attenuation and bioremediation of the explosive NTO.

Effects of decabromodiphenyl ether and planting on the abundance and community composition of nitrogen-fixing bacteria and ammonia oxidizers in mangrove sediments: A laboratory microcosm study

While nitrogen (N) fixation and ammonia oxidation by microorganisms are two important N cycling processes, little is known about how the microbes that drive these two processes respond when sediments are contaminated with persistent organic pollutants. In this study, we carried out a laboratory microcosm experiment to examine the effects of decabromodiphenyl ether (BDE-209), either on its own or combined with a common mangrove species, Avicennia marina, on the abundance, diversity, and community composition of N-fixing bacteria (NFB) and ammonia-oxidizing archaea (AOA) and bacteria (AOB) in mangrove sediments. The sediments were very N-limited after one year. The rates of N fixation and NFB abundance were significantly higher in the sediments that contaminated by BDE-209, especially in the planted sediment, indicating that both BDE-209 and planting stimulated N fixation in N-limited mangrove sediments. In contrast, the potential nitrification rate and abundance of AOA and AOB decreased significantly under BDE-209 and planting, and the inhibitory effects were stronger in the sediment with both planting and BDE-209 than in the sediments with either BDE-209 or planting. The results from pyrosequencing showed that the richness and diversity of NFB increased, while those of AOA and AOB decreased, in the sediments treated with BDE-209 only and with BDE-209 combined with planting. The community compositions of NFB, AOA, and AOB in the sediments shifted significantly because of BDE-209, either alone or particularly when combined with planting, as shown by the increases in some NFB from the Proteobacteria phylum and decreases in AOA in the Nitrosopumilus genus and AOB in the Nitrosospira genus, respectively.

1,3-Dinitrobenzene reductive degradation by alkaline ascorbic acid - Reaction mechanisms, degradation pathways and reagent optimization

Nitro-aromatic compounds (NACs) such as 1,3-dinitrobenzene (1,3-DNB) contain the nitrogroup (-NO₂), in which the N with a +III oxidation state accepts electrons. Water soluble ascorbic acid (AsA) at elevated pH produces electron transfer and governs the electron-donating pathway. The influence of the NaOH/AsA molar ratio on the degradation of 1,3-DNB was investigated. Using 0.21-2 M NaOH and 20-100 mM AsA, nearly complete 1,3-DNB removals (90-100%) were achieved within 0.5 h. On the basis of intermediates identified using GC/MS, the reduction pathways of 1,3-DNB can be categorized into step-by-step electron transfer, and condensation routes. A higher NaOH/AsA molar ratio would result in relatively higher AsA decomposition, promote the condensation route into the formation of azo- and azoxy-compounds, and ultimately reduce 1,3-DNB to 1,3-phenylenediamine. Contaminated soil flushing using 500 mM NaOH/100 mM AsA revealed that 1,3-DNB was completely degraded within 2 h. Based on these test results, the alkaline AsA treatment method is a potential remediation process for NACs contaminated soils.

Improved TNT detoxification by starch addition in a nitrogen-fixing Methylophilus-dominant aerobic microbial consortium

In this study, a novel aerobic microbial consortium for the complete detoxification of 2,4,6-trinitrotoluene (TNT) was developed using starch as a slow-releasing carbon source under nitrogen-fixing conditions. Aerobic TNT biodegradation coupled with microbial growth was effectively stimulated by the co-addition of starch and TNT under nitrogen-fixing conditions. The addition of starch with TNT led to TNT mineralization via ring cleavage without accumulation of any toxic by-products, indicating improved TNT detoxification by the co-addition of starch and TNT. Pyrosequencing targeting the bacterial 16S rRNA gene suggested that Methylophilus and Pseudoxanthomonas population were significantly stimulated by the co-addition of starch and TNT and that the Methylophilus population became predominant in the consortium. Together with our previous study regarding starch-stimulated RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) degradation (Khan et al., J. Hazard. Mater. 287 (2015) 243-251), this work suggests that the co-addition of starch with a target explosive is an effective way to stimulate aerobic explosive degradation under nitrogen-fixing conditions for enhancing explosive detoxification.