Metagenomic insights into the diversity of 2,4-dichlorophenol degraders and the cooperation patterns in a bacterial consortium

Elucidating the role of the genus Pseudomonas involved in coumarin degradation

Coumarin, a synthetic chemical and phytotoxin, exhibits hepatotoxicity and carcinogenicity, posing threats to both human health and environmental safety. Microbial degradation effectively mitigates environmental contamination. In this study, a coumarin-degrading bacterial consortium designated as XDS-7 with Pseudomonas as the key degrader was obtained. However, there is a lack of comprehensive perspective on the key role of the genus Pseudomonas involved in coumarin degradation. We employed the consortium XDS-7 as a model system to investigate the critical role of the genus Pseudomonas involved in coumarin degradation. Metagenomic binning analysis indicated that bin 14 (Pseudomonas sp.) contains the full complement of genes required for coumarin degradation. A coumarin-degrading bacterium, Pseudomonas sp. strain X4, was isolated from consortium XDS-7 using a traditional enrichment method supplemented with chloramphenicol. Genomic analysis demonstrated that strain X4 carries a suite of genes to completely degrade coumarin. Bioinformatics analysis revealed that putative coumarin-degrading bacteria are widely distributed across diverse bacteria of the genus Pseudomonas. In addition, strain X4 completely removed 100 mg kg-1 of coumarin from contaminated soil within 48 h and 100 mg L-1 of coumarin from contaminated wastewater within 4 h. This study will greatly enhance our understanding and utilization of these valuable bioresources.

Efficient photocatalytic in-situ Fenton degradation of 2,4-dichlorophenol via anthraquinone-modified carbon nitride for 2e- oxygen reduction

Constructing a photocatalytic in-situ Fenton system (PISFs) is a promising strategy to address the need for continuous hydrogen peroxide (H2O2) addition and the low efficiency of H2O2 activation for hydroxyl radical generation in the traditional Fenton reaction. In this study, we constructed a photocatalytic in-situ Fenton system using anthraquinone-modified carbon nitride (AQ-C3N4) for efficient pollutant degradation. The resultant AQ-C3N4 not only enhanced the production of H2O2 but also increased the generation of hydroxyl radical (·OH). Experimental results demonstrated that, the apparent rate constant for the degradation of 2,4-Dichlorophenol (2,4-DCP) by AQ-C3N4-PISFs was 0.145 min-1, which is 2.74 times higher than that of C3N4 under visible light. Density functional theory (DFT) calculations indicate that AQ modification promotes electron-hole separation while increasing the adsorption energy of O2. Independent gradient model (IGM) analysis based on Hirshfeld Partition revealed that van der Waals interactions between AQ-C3N4 and 2,4-DCP promoted the degradation process. This work provides new ideas to overcome the problems of continuous addition of H2O2 and low utilization of ·OH that exist in conventional Fenton system.

Response of Soil Bacteria to Short-Term Nitrogen Addition in Nutrient-Poor Areas

Increasing nitrogen (N) addition induces soil nutrient imbalances and is recognized as a major regulator of soil microbial communities. However, how soil bacterial abundance, diversity, and community composition respond to exogenous N addition in nutrient-poor and generally N-limited regions remains understudied. In this study, we investigated the effects of short-term exogenous N additions on soil bacterial communities using quantitative polymerase chain reaction (PCR) and Illumina Miseq sequencing in an in situ N addition field experiment. The results showed that a low nitrogen addition increased the observed species (Sobs) of the bacterial community, and with the increased nitrogen addition, the Sobs of bacteria gradually decreased, especially the unique OTUs. The relative abundance of Proteobacteria, Actinobacteria, and Gemmatimonadetes increased with increasing nitrogen addition, whereas the relative abundance of Chloroflexi and Firmicutes decreased. Soil properties play an important role in bacterial community structure at phylum or genus levels. Short-term nitrogen addition increased the proportion of nodes from Actinobacteria and Proteobacteria in the co-occurrence network and enhanced the stability of the microbial network. Actinobacteria may play an important role in constructing the network. Our study aims to explore the effects of nitrogen addition on the diversity, composition, and structure of soil bacterial communities in nutrient-poor areas caused by ecological disturbances.

Application of earthworm can enhance biological power generation and accelerate sulfamethoxazole removal in agricultural soils

Microbial degradation plays a crucial role in removing sulfonamides from soil, enhancing sulfamethoxazole (SMX) remediation. To further augment SMX removal efficiency and mitigate the transmission risk associated with antibiotic resistance genes (ARGs), this study proposes a novel approach that integrates micro-animals, microorganisms, and microbial fuel cell (MFC) technology. The results showed that earthworm-MFC synergy substantially reduces SMX content and ARGs abundance in soil. The introduction of earthworms enhances humus content, facilitating electron transfer within MFC and consequently improving current generation. Furthermore, electrical stimulation applied to earthworms led to increased protein secretion and enhanced antioxidant system activity, thereby accelerating SMX degradation. Earthworms also foster MFC-associated bacterial growth and SMX-degrading bacteria proliferation, augmenting MFC treatment efficacy. This synergistic effect significantly augmented the overall efficacy of MFC treatment for antibiotics. Overall, integrating earthworm activity with MFC technology effectively optimizes electricity generation and enhances pollutant removal.

Widespread distribution of the DyP-carrying bacteria involved in the aflatoxin B1 biotransformation in Proteobacteria and Actinobacteria

Aflatoxin is one of the most notorious mycotoxins, of which aflatoxin B1 (AFB1) is the most harmful and prevalent. Microbes play a crucial role in the environment for the biotransformation of AFB1. In this study, a bacterial consortium, HS-1, capable of degrading and detoxifying AFB1 was obtained. Here, we combined multi-omics and cultivation-based techniques to elucidate AFB1 biotransformation by consortium HS-1. Co-occurrence network analysis revealed that the key taxa responsible for AFB1 biotransformation in consortium HS-1 mainly belonged to the phyla Proteobacteria and Actinobacteria. Moreover, metagenomic analysis showed that diverse microorganisms, mainly belonging to the phyla Proteobacteria and Actinobacteria, carry key functional enzymes involved in the initial step of AFB1 biotransformation. Metatranscriptomic analysis indicated that Paracoccus-related bacteria were the most active in consortium HS-1. A novel bacterium, Paracoccus sp. strain XF-30, isolated from consortium HS-1, contains a novel dye-decolorization peroxidase (DyP) enzyme capable of effectively degrading AFB1. Taxonomic profiling by bioinformatics revealed that DyP, which is involved in the initial biotransformation of AFB1, is widely distributed in metagenomes from various environments, primarily taxonomically affiliated with Proteobacteria and Actinobacteria. The in-depth examination of AFB1 biotransformation in consortium HS-1 will help us to explore these crucial bioresources more sensibly and efficiently.

Remediation of isoproturon-contaminated soil by Sphingobium sp. strain YBL2: Bioaugmentation, detoxification and community structure

The widely used phenylurea herbicide isoproturon (IPU) and its residues can inhibit the growth of subsequently planted crops. However, reports on bioremediation of IPU-contaminated soil are scarce. In this study, Sphingobium sp. strain YBL2-gfp (a derivative of the IPU-degrading Sphingobium sp. strain YBL2 isolated by our lab) was constructed to bioremediate IPU-contaminated soil. In pot experiments, strain YBL2-gfp colonized the roots of wheat and eliminated IPU residues in the soil within 21 d, effectively alleviating its toxicity and restoring wheat growth. IPU treatment reduced the richness and diversity of soil bacteria, while inoculation YBL2-gfp mainly affected richness with less impact on diversity. The high concentrations of IPU and inoculation of YBL2-gfp alone reduced the soil microbial community connections, while bioaugmentation treatment enhanced the soil microbial community connections. Additionally, strain YBL2-gfp stimulated the metabolic capacity of the indigenous microbes, promoting the degradation of IPU and reducing the negative impact of high concentrations of IPU on microbial community. Taken together, this study offers relatively comprehensive insights into the practical application of bioaugmentation, demonstrating that strain YBL2 has the potential to remediate IPU-contaminated soils.

High levels of cadmium altered soil archaeal activity, assembly, and co-occurrence network in volcanic areas

Soil microbial communities are essential to biogeochemical cycles. However, the responses of microorganisms in volcanic soil with high heavy metal levels remain poorly understood. Here, two areas with high levels of cadmium (Cd) from the same volcano were investigated to determine their archaeal composition and assembly. In this study, the Cd concentrations (0.32-0.38 mg/ kg) in the volcanic soils exceeded the standard risk screening values (GB15618-2018) and correlated with archaeal communities strongly (P < 0.05). Moreover, the area with elevated levels of Cd (periphery) exhibited a greater diversity of archaeal species, albeit with reduced archaeal activity, compared to the area with lower levels of Cd (center). Besides, stochastic processes mainly governed the archaeal communities. Furthermore, the co-occurrence network was simplest in the periphery. The proportion of positive links between taxa increased positively with Cd concentration. Moreover, four keystone taxa (all from the family Nitrososphaeraceae) were identified from the archaeal networks. In its entirety, this study has expanded our comprehension of the variations of soil archaeal communities in volcanic areas with elevated cadmium levels and serves as a point of reference for the agricultural development of volcanic soils in China.