nlong Yu

Metagenomic analysis reveals potential biodegradation pathways of persistent pesticides in freshwater and marine sediments

The abundance and diversity of biodegradation genes (BDGs) and potential degradation pathways of dichlorodiphenyltrichloroethane (DDT), hexachlorocyclohexane (HCH), and atrazine (ATZ) in freshwater and marine sediments were investigated by metagenomic analysis using 6 datasets (16Gb in total). The datasets were derived using Illumina high-throughput sequencing and were based on BLAST against self-established databases of BDGs, DDT degradation genes (DDGs), HCH degradation genes (HDGs), and ATZ degradation genes (ADGs). The results showed that the abundance and diversity of BDGs, DDGs, HDGs, and ADGs varied with sample source and locations. The lip and mnp genes, which encode for peroxidase, and the carA gene, which encodes for laccase, were detected as the dominant genes for degradation of organic pollutants. The hdt, hdg, and atzB genes, which encode for hydratase, dehalogenase, and ethylaminohydrolase, were found to be the most abundant genes involved in DDT, HCH, and ATZ degradation, respectively. The identified 69 genera capable of degrading organic pollutants were mostly affiliated with Proteobacteria (49.3%) and Actinobacteria (21.7%). Four genera, including Plesiocystis, Anaerolinea, Jannaschia, and Mycobacterium, were the major biodegradation populations in all sediments. In this study, the nearly complete biodegradation pathways of DDT and ATZ were found, and the partial degradation pathway of HCH was detected in all sediments.

Biochar: A review of its impact on pesticide behavior in soil environments and its potential applications

Biochar is produced from the pyrolysis of carbon-rich plant- and animal-residues under low oxygen and high temperature conditions and has been increasingly used for its positive role in soil compartmentalization through activities such as carbon sequestration and improving soil quality. Biochar is also considered a unique adsorbent due to its high specific surface area and highly carbonaceous nature. Therefore, soil amendments with small amounts of biochar could result in higher adsorption and, consequently, decrease the bioavailability of contaminants to microbial communities, plants, earthworms, and other organisms in the soil. However, the mechanisms affecting the environmental fate and behavior of organic contaminants, especially pesticides in biochar-amended soil, are not well understood. The purpose of this work is to review the role of biochar in primary processes, such as adsorption-desorption and leaching of pesticides. Biochar has demonstrable effects on the fate and effects of pesticides and has been shown to affect the degradation and bioavailability of pesticides for living organisms. Moreover, some key aspects of agricultural and environmental applications of biochar are highlighted.

Exploring bacterial community structure and function associated with atrazine biodegradation in repeatedly treated soils.

Substantial application of the herbicide atrazine in agriculture leads to persistent contamination, which may damage the succeeding crops and pose potential threats to soil ecology and environmental health. Here, the degradation characteristics of atrazine and dynamic change of soil bacterial community structure and function as well as their relations were studied during three repeated treatments at the recommended, double, and five-fold doses. The results showed that the degradation half-life of atrazine obviously decreased with increased treatment frequency. Soil microbial functional diversity displayed a variation trend of suppression-recovery-stimulation, which was associated with increased degradation rate of atrazine. 16S amplicon sequencing was conducted to explore bacterial community structure and correlate the genus to potential atrazine degradation. A total of seven potentially atrazine-degrading bacterial genera were found including Nocardioides, Arthrobacter, Bradyrhizobium, Burkholderia, Methylobacterium, Mycobacterium, and Clostridium. These bacterial genera showed almost complete atrazine degradation pathways including dechlorination, dealkylation, hydroxylation, and ring cleavage. Furthermore, the relative abundance of four of them (i.e., Nocardioides, Arthrobacter, Methylobacterium, and Bradyrhizobium) increased with treatment frequency and atrazine concentration, suggesting that they may participate in atrazine degradation during repeated treatments. Our findings reveal the potential relationship between atrazine degradation and soil bacterial community structure in repeatedly treated soils.

Variations in dissipation rate, microbial function and antibiotic resistance due to repeated introductions of manure containing sulfadiazine and chlortetracycline to soil

Antibiotic persistence following five successive treatments of sulfadiazine (SDZ) and chlortetracycline (CTC), alone and in combination, in manure-amended soil was studied under laboratory conditions. The resulting effects on soil respiration and enzyme activities as well as pollution-induced community tolerance, were also examined. A trend of initial suppression followed by recovery was observed in the dissipation rates of SDZ or CTC during the antibiotic treatments, and combined treatment with both antibiotics did not alter the respective dissipation rates significantly. Soil respiration activity with SDZ and/or CTC treatments was inhibited during the initial two treatments; however, the activity thereafter recovered to or exceeded the level of the individual manure treatment. Initially, soil urease and dehydrogenase activities were not affected; however, after the fifth treatment, these activities were significantly stimulated in the CTC individual and combined treatments compared with their activities in the individual manure treatment. Bacterial community tolerance to SDZ and CTC in manure-amended soil increased significantly (p⩽0.05) with antibiotic treatment frequency.

Metagenomic analysis reveals the prevalence of biodegradation genes for organic pollutants in activated sludge.

The abundance, diversity, and distribution of biodegradation genes (BDGs) and phenol degradation genes (PDGs) in activated sludge (AS) from two wastewater treatment plants (WWTPs) at different sampling times were assessed by metagenomic analysis using a total of 15 datasets derived from Illumina high-throughput sequencing and BLAST comparisons to BDGs and PDGs databases. The results showed that the abundance (0.015-0.030%) and diversity of BDGs in AS varied with the WWTP and the sampling times. The p450 and pmo genes were the most abundant genes in the BDGs and PDGs subgroups, respectively. MG-RAST analysis revealed that 87 detected bacterial genera potentially capable of degrading pollutants were mostly affiliated with Proteobacteria (59.8%), Bacteroidetes (17.2%), and Actinobacteria (9.2%). Mycobacterium, belonging to Actinobacteria, was found to be the most abundant genus (23.4%). This method could be used to monitor an ASs biodegradation ability for organic pollutants and to evaluate its wastewater treatment efficiency.

Plasmid-mediated bioaugmentation for the degradation of chlorpyrifos in soil.

To overcome the poor survival and low activity of the bacteria used for bioremediation, a plasmid-mediated bioaugmentation method was investigated, which could result in a persistent capacity for the degradation of chlorpyrifos in soil. The results indicate that the pDOC plasmid could transfer into soil bacteria, including members of the Pseudomonas and Staphylococcus genera. The soil bacteria acquired the ability to degrade chlorpyrifos within 5 days of the transfer of pDOC. The efficiency of the pDOC transfer in the soil, as measured by the chlorpyrifos degradation efficiency and the most probable number (MPN) of chlorpyrifos degraders, was influenced by the soil temperature, moisture level and type. The best performance for the transfer of pDOC was observed under conditions of 30°C and 60% water-holding capacity (WHC). The results presented in this paper show that the transfer of pDOC can enhance the degradation of chlorpyrifos in various soils, although the degradation efficiency did vary with the soil type. It may be concluded that the introduction of plasmids encoding enzymes that can degrade xenobiotics or donor strains harboring these plasmids is an alternative approach in bioaugmentation.

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

A novel bacterium capable of utilizing 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane (DDT) as the sole carbon and energy source was isolated from a contaminated soil which was identified as Stenotrophomonas sp. DDT-1 based on morphological characteristics, BIOLOG GN2 microplate profile, and 16S rDNA phylogeny. Genome sequencing and functional annotation of the isolate DDT-1 showed a 4,514,569 bp genome size, 66.92% GC content, 4,033 protein-coding genes, and 76 RNA genes including 8 rRNA genes. Totally, 2,807 protein-coding genes were assigned to Clusters of Orthologous Groups (COGs), and 1,601 protein-coding genes were mapped to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The degradation half-lives of DDT increased with substrate concentration from 0.1 to 10.0 mg/l, whereas decreased with temperature from 15 °C to 35 °C. Neutral condition was the most favorable for DDT biodegradation. Based on genome annotation of DDT degradation genes and the metabolites detected by GC-MS, a mineralization pathway was proposed for DDT biodegradation in which it was orderly converted into DDE/DDD, DDMU, DDOH, and DDA via dechlorination, hydroxylation, and carboxylation, and ultimately mineralized to carbon dioxide. The results indicate that the isolate DDT-1 is a promising bacterial resource for the removal or detoxification of DDT residues in the environment.

Effect of vegetation of transgenic Bt rice lines and their straw amendment on soil enzymes, respiration, functional diversity and community structure of soil microorganisms under field conditions.

With the development of transgenic crops, there is an increasing concern about the possible adverse effects of their vegetation and residues on soil environmental quality. This study was carried out to evaluate the possible effects of the vegetation of transgenic Bt rice lines Huachi B6 (HC) and TT51 (TT) followed by the return of their straw to the soil on soil enzymes (catalase, urease, neutral phosphatase and invertase), anaerobic respiration activity, microbial utilization of carbon substrates and community structure, under field conditions. The results indicated that the vegetation of the two transgenic rice lines (HC and TT) and return of their straw had few adverse effects on soil enzymes and anaerobic respiration activity compared to their parent and distant parent, although some transient differences were observed. The vegetation and subsequent straw amendment of Bt rice HC and TT did not appear to have a harmful effect on the richness, evenness and community structure of soil microorganisms. No different pattern of impact due to plant species was found between HC and TT. It could be concluded that the vegetation of transgenic Bt rice lines and the return of their straw as organic fertilizer may not alter soil microbe-mediated functions.

Residual effectiveness of boron fertilizer for oilseed rape in intensively cropped rice-based rotations

Long-term field experiments (3–4 years) were conducted to evaluate the residual effect of boron (B) fertilizer for oilseed rape (Brassica napus L.) in an intensive crop rotation including two rice (Oryza sativa) crops per year. Experiments were conducted on four sites where the soil types were sandy, silty and clayey Inceptisols, and an Ultisol, located in the Zhejiang Province, Southeast China. Application of B fertilizer at rates of 1.1, 1.65 and 3.3 kg B/ha in the first year showed a different residual effect on oilseed yield in successive years, but had only small positive effects on the rice grain yield at two sites. The residual effect of 1.1 kg B/ha remained fully effective in correcting B deficiency in oilseed rape for 2 years in the Inceptisols, whereas the residual effect of 1.65 kg B/ha continued to correct B deficiency for at least 3 years in both the Inceptisols and the Ultisol. Foliar application of B fertilizer generally corrected B deficiency for oilseed rape but showed limited residual effect in the following years after application. The decline in residual values of B from a single fertilizer addition was closely related to the soil and leaf B concentration. Soil available B also decreased dramatically with the advance of rotation, but a larger decrease was found at a depth of 20–40-cm for the Inceptisols and the Ultisol. Thus, a more detailed understanding of the B cycling in the system is now needed to optimize management of B fertilizer.

Changes in soil microbial community structure and function associated with degradation and resistance of carbendazim and chlortetracycline during repeated treatments

The degradation characteristics of carbendazim (CBD) and chlortetracycline (CTC) in individual and combined treatments, and dynamics of soil microbial structural and functional diversity as well as their potential relations were studied during three repeated treatments using different concentrations. The results showed that the degradation half-life of CBD at concentrations of 3mg/kg and 6mg/kg obviously increased, but that of CTC at levels of 1mg/kg and 10mg/kg decreased with increasing treatment frequency. Soil microbial activity and functional diversity displayed the suppression trend in CBD treatment and the suppression-recovery-stimulation trend in CTC and CBD+CTC treatments, which were consistent with the findings of decreased degradation rate of CBD and increased degradation rate of CTC. 16S amplicon sequencing analysis revealed five potentially dominant CTC-resistant microbial genera including Bacillus, Actinobacillus, Pseudomonas, Mycobacterium, and Corynebacterium, which may mainly carry major facilitator superfamily transporter protein, ribosomal protection protein, and other proteins encoded by tetA, tetB, tetC, tetH, tetL, tetM, tetO, tetV, tetW, tetX, tetZ, tet33, and tet39. These five dominant genera may jointly contribute to the elevated bacterial community resistance to CTC. Our findings provided a better understanding of microbial community structure and function changes in repeatedly treated soils with CBD and CTC.