Stable-isotope probing coupled with high-throughput sequencing reveals bacterial taxa capable of degrading aniline at three contaminated sites with contrasting pH

Pyraclostrobin repeated treatment altered the degradation behavior in soil and negatively affected soil bacterial communities and functions

This study investigated the degradation dynamics of the fungicide pyraclostrobin in three apple orchard soils, along with the responses of soil bacterial community compositions, functions, co-occurrence patterns, and soil nitrogen cycling, under repeated treatment strategies in laboratory conditions. The degradation half-lives of pyraclostrobin varied across the soil types, ranging from 15.7 to 43.4 days, in the following order: Anyang soil > Qingdao soil > Yangling soil. Repeated pyraclostrobin treatment affected degradation behaviors across the different soils. Pyraclostrobin significantly inhibited soil microbial activity and reduced soil bacterial diversity, with more pronounced negative effects observed at high-concentration treatment. Pyraclostrobin clearly changed soil bacterial community structures, significantly enriching potentially degradative bacterial genera such as Methylibium and Nocardioides, which showed increases in the relative abundances of 3.0-181.8 % compared with control. Additionally, pyraclostrobin reduced the complexity of soil bacterial networks and modified the diversity of functional modules. Notably, repeated treatment severely disrupted soil nitrogen cycling, with the absolute abundances of amoA, amoB, nifH, nirK, and nirS in high-concentration treatment decreasing by up to 19.4-91.8 % compared with control. Collectively, pyraclostrobin repeated application altered the degradation behavior, inhibited soil microbial activities, modified soil bacterial community structures and co-occurrence patterns, and seriously disrupted soil nitrogen cycling.

Metatranscriptomes of activated sludge microbiomes from saline wastewater treatment plant

The activated sludge microbiome (ASM) drives the biological wastewater treatment process in wastewater treatment plants. It has been established in the literature that the ASM is characterized by a high degree of taxonomic and metabolic diversity. However, meta-omics datasets have been derived from domestic wastewater treatment plants with little attention to saline wastewater treatment plants (SWWTP). Existing knowledge of how activated sludge microorganisms impact water quality, interrelate within habitat networks, and respond to environmental perturbations remains limited. Here we present datasets of the metatranscriptomes of SWWTP in The Netherlands, coupled with process data. The dataset represents a two-year and four-month time series of data collected from 2014 to 2017, with samples taken at approximately monthly intervals from the facultative zone in the activated sludge process of an SWWTP. In total, 32 activated sludge samples were analyzed. This dataset can be used to enhance understanding of the unique microbiome composition in SWWTPs, its dynamic responses to environmental variables, and the metabolic functions within the ASM.

Integrated microbiology and metabolomics analysis reveal responses of cotton rhizosphere microbiome and metabolite spectrum to conventional seed coating agents

Fludioxonil (FL) and metalaxyl-M·fludioxonil·azoxystrobin (MFA) are conventional seed coating agents for controlling cotton seedling diseases. However, their effects on seed endophytic and rhizosphere microecology are still poorly understood. This study aimed to assess the effects of FL and MFA on cotton seed endophytes, rhizosphere soil enzymatic activities, microbiome and metabolites. Both seed coating agents significantly changed seed endophytic bacterial and fungal communities. Growing coated seeds in the soils originating from the Alar (AL) and Shihezi (SH) region inhibited soil catalase activity and decreased both bacterial and fungal biomass. Seed coating agents increased rhizosphere bacterial alpha diversity for the first 21 days but decreased fungal alpha diversity after day 21 in the AL soil. Seed coating reduced the abundance of a number of beneficial microorganisms but enriched some potential pollutant-degrading microorganisms. Seed coating agents may have affected the complexity of the co-occurrence network of the microbiome in the AL soil, reducing connectivity, opposite to what was observed in the SH soil. MFA had more pronounced effects on soil metabolic activities than FL. Furthermore, there were strong links between soil microbial communities, metabolites and enzymatic activities. These findings provide valuable information for future research and development on application of seed coatings for disease management.

Insights into autotrophic carbon fixation strategies through metagonomics in the sediments of seagrass beds

Seagrass beds contributes up to 10% ocean carbon storage. Carbon fixation in seagrass bed greatly affect global carbon cycle. Currently, six carbon fixation pathways are widely studied: Calvin, reductive tricarboxylic acid (rTCA), Wood-Ljungdahl (WL), 3-hydroxypropionate (3HP), 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) and dicarboxylate/4-hydroxybutyrate (DC/4-HB). Despite the knowledges about carbon fixation increase, the carbon fixation strategies in seagrass bed sediment remain unexplored. We collected seagrass bed sediment samples from three sites with different characteristics in Weihai, a city in Shandong, China. The carbon fixation strategies were investigated through metagenomics. The results exhibited that five pathways were present, of which Calvin and WL were the most dominant. The community structure of microorganisms containing the key genes of these pathways were further analyzed, and those dominant microorganisms with carbon fixing potential were revealed. Phosphorus significantly negatively corelated with those microorganisms. This study provides an insight into the strategies of carbon fixation in seagrass bed sediments.

Elucidation of aniline adsorption-desorption mechanism on various organo-mineral complexes

Complexes formed by organic matter and clay minerals, which are active components of soil systems, play an important role in the migration and transformation of pollutants in nature. In this study, humic-acid-montmorillonite (HA-MT) and humic-acid-kaolin (HA-KL) complexes were prepared, and their structures before and after the adsorption of aniline were analyzed. The aniline adsorption-desorption characteristics of complexes with different clay minerals and varying HA contents were explored using the static adsorption-desorption equilibrium method. Compared with the pristine clay minerals, the flaky and porous structure of the complexes and the aromaticity were enhanced. The adsorption of aniline on the different clay mineral complexes was nonlinear, and the adsorption capacity increased with increasing HA content. Additionally, the adsorption capacity of HA-MT was higher than that of HA-KL. After adsorption, the specific surface area of the complexes decreased, the surfaces became more complicated, and the aromaticity decreased because aniline is primarily adsorption onto the complexes via aromatic rings. Aniline was adsorbed onto the complexes via spontaneous exothermic physical adsorption. The amount of aniline desorbed from the complexes increased with increasing HA content, and a lag in desorption was observed, with a greater lag for HA-KL than for HA-MT.

Comparing the indigenous microorganism system in typical petroleum-contaminated groundwater

The environmental conditions at a contaminated site will impact on the indigenous microbial communities, with implications for the removal of pollutants. An analysis of the characteristics of microbial communities in petroleum-contaminated groundwater can give insights into the relationships between microbial community and environmental factors, and provide guidance about how microbes can be used to remediate and regulate petroleum-contaminated groundwater. This study focuses on two petroleum-contaminated sites in northeast China, the physico-chemical-biological changes in petroleum-contaminated groundwater were analyzed, the response relationship between hydro-chemical indicators and microbial communities was characterized, and the bioindicator that can reflect the petroleum contamination status were established for environmental monitoring and management. The results showed that Proteobacteria was the dominant bacteria in petroleum-contaminated groundwater, with a relative abundance of 42.45%-91.19%. pH, TDS, DO, NO3-, NO2-, SO42-, NH4+, Al, and Mn have significant effects on microbial community. The effect of petroleum pollutants on microbial communities is not only related to the concentration and composition of the pollutants themselves, but also could indirectly affect microbial communities by changing the content of inorganic electron acceptor components such as iron, manganese, sulfate and nitrate in groundwater, and this indirect effect is significantly greater than the direct impact of pollutants on microbial communities. In petroleum-contaminated groundwater, the dominant genera (Polaromonas, Caulobacter) and microbial metabolic functions (methanol oxidation, methylotrophy, ureolysis, and reductive biosynthesis) of the indigenous microbial community can be used as bioindicators to indicate petroleum contamination status. The higher abundance of these bioindicators in petroleum-contaminated groundwater, the more serious petroleum pollution in groundwater.

Effect of Cucurbit[7]uril on Adsorption of Aniline Derivatives at Quartz

The adsorption behavior of small molecules at solid–liquid interfaces have become an important research topic in recent years. For example, small molecules of aniline pollutants will adsorb on solid surfaces with a massive discharge of industrial wastewater and are difficult to separate. Therefore, their adsorption and desorption on solid surfaces have become an important scientific problem. In this study, the interactions of cucurbit[7]uril (Q[7]) with 4,4′-diaminodiphenylmethane (MDA) and benzidine (AN) are studied using 1H NMR, UV-Vis spectrometry and fluorescence spectroscopy. The results show that Q[7] forms an inclusion complex with MDA and AN. According to the results of Quartz Crystal Microbalance with Dissipation (QCM-D), MDA adsorbs onto a quartz surface and forms a viscous adsorption layer on it. The AN adsorbs on the quartz surface and forms a rigid adsorption film on it. Q[7] can reduce the adsorption of MDA on the quartz surface and increases the adsorption of AN on it. Through the dynamic adsorption experiments, we find that Q[7] has a desorption effect on MDA molecules adsorbed on the quartz surface. An Atomic Force Microscope (AFM) is used to measure the morphological changes in the adsorption film before and after Q[7] makes contact with the quartz surface, and it proves that Q[7] has a desorption effect on MDA molecules adsorbed on the surface.

Diversity of endophytic bacteria in wild rice (Oryza meridionalis) and potential for promoting plant growth and degrading phthalates

Phthalates (PAEs) accumulated in agricultural soils and rice have increased human exposure risks. Microbial degradation could efficiently reduce the residue of organic pollutants in soil and crop plants. Here, we hypothesized that endophytic bacteria from wild rice have the potential for degradation of PAEs and plant growth promoting. The endophytic bacterial community and functional diversity in wild rice (Oryza meridionalis) were analyzed for the first time, and the potential for PAE degradation and plant growth promoting by endophytes were investigated. The results of Illumina high-throughput sequencing revealed that abundant endophytes inhabited in wild rice with Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria being the dominant phyla. Endophytic bacterial diversity and complexity were confirmed by isolation and clustering of isolates. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that endophytes exerted diverse functions such as plant growth promoting, xenobiotics biodegradation, pollution remediation and bacterial chemotaxis. Pure culture experiment showed that 30 isolated endophytic strains exhibited in vitro plant growth promoting activities, and rice plants inoculated with these strains confirmed their growth promoting abilities. Some endophytic strains were capable of efficiently degrading PAEs, with the highest removal percentage of di-n-butyl phthalate (DBP) up to 96.1% by Bacillus amyloliquefaciens strain L381 within 5 days. Synthetic community F and strain L381 rapidly removed DBP from soil (removing 91.0%-99.2% within 10 d and from rice plant slurry (removing 93.4%-99.2% within 5 d). These results confirmed the hypothesis and demonstrated the diversity of endophytic bacteria in wild rice with diverse functions, especially for plant growth promoting and removing PAEs. These multifunctional endophytic bacteria provided good alternatives to reduce PAE accumulation in crops and increase yield.