Comparative genomic analysis of 26 Sphingomonas and Sphingobium strains: Dissemination of bioremediation capabilities, biodegradation potential and horizontal gene transfer

Co-exposure of pyraclostrobin and biochar promoted antibiotic resistance genes transfer from soil to lettuce

The widespread presence of antibiotic resistance genes (ARGs) threatens ecological security and human health. In agricultural production, the simultaneous presence of non-antibiotic substances fungicides and biochar utilized for soil remediation has unclear effects on the spread of ARGs in the soil-vegetable systems. Herein, this study conducted a pots experiment and found that biochar significantly reduced pyraclostrobin accumulation in the soil and lettuce roots. Simultaneously, the co-exposure of pyraclostrobin and biochar increased the microbial community alpha diversity and the abundance of ARGs in soil, while promoting the transfer of ARGs from soil to lettuce. Proteobacteria were identified as potential primary carriers of ARGs. Planting lettuce mitigated the effects of pyraclostrobin or/and biochar on ARGs accumulation in soil. Furthermore, MGEs and bacterial community abundance were the most important direct factors increasing ARGs in soil and lettuce. Overall, these findings evaluated the combined effects of non-antibiotic substances fungicides and soil remediation materials biochar on the generation and transmission of ARGs, providing potential strategies for controlling ARGs transfer in soil-vegetable systems.

Antibiotic resistance patterns and cross-family ARG transfer in families Burkholderiaceae and Sphingomonadaceae: A large-scale genome-wide analysis of over 10 K genomes

Members of Burkholderiaceae and Sphingomonadaceae play an active role in pollutant degradation, yet their antibiotic resistance risks are frequently overlooked. This study analyzed 9406 Burkholderiaceae and 2343 Sphingomonadaceae genomes to investigate the distribution, horizontal gene transfer (HGT), and co-occurrence patterns of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs). ARGs were prevalent in Burkholderiaceae (93.2 % of genomes), dominated by bacitracin (89.0 %), multidrug (88.1 %), and beta-lactam (40.5 %) resistance, while Sphingomonadaceae exhibited lower ARG prevalence (11.6 %). Notably, Burkholderia and Caballeronia displayed high multidrug resistance (10.1 ARGs per genome) and frequent ARG-MRG co-occurrence (84.4 %). Strong ARG-MRG-MGE correlations were observed in Burkholderiaceae, suggesting MGEs play a key role in resistance dissemination. Additionally, ARGs correlated with metabolic genes, linking metabolic versatility to resistance. Genes like capO (chloramphenicol oxidase) and blaTEM-116 (beta-lactamase) were shared among distantly related genera, while mcr-5.1 (MCR phosphoethanolamine transferase) co-occurred with MRGs across Cupriavidus species, highlighting HGT and co-selection risks. ARG transfer between Burkholderiaceae, Sphingomonadaceae and clinical pathogens was frequent (114-1306 events/10,000 genome pairs), with sulfonamide resistance dominating (51.3 % of HGT). These findings highlight Burkholderiaceae and Sphingomonadaceae as critical reservoirs of resistance genes and emphasize the need for enhanced surveillance and mitigation strategies to curb the spread of multidrug resistance.

Effects of Paenibacillus polymyxa WZ14 inoculation on phytoextraction efficiency and rhizosphere soil bacterial characteristics in multi-heavy metals contaminated soil

Contaminated soils containing multiple heavy metals, including lead (Pb), cadmium (Cd), and copper (Cu), has been identified as the momentous environmental challenge that requires urgent remediation. This study was first used to explore the effects of Paenibacillus polymyxa WZ14 on the phytoremediation of soils co-contaminated with Cd, Pb, and Cu, focusing on heavy metal bioaccumulation, translocation in Sophora xanthantha and Robinia pseudoacacia L., and soil bacterial community structure. The results demonstrated that the WZ14 strain exhibited strong adaptability and growth potential in heavy-metal-contaminated soil, significantly increasing soil organic carbon, hydrolyzed nitrogen, available phosphorus, and available potassium levels, thereby the total biomass of Sophora xanthantha and Robinia pseudoacacia L. significantly increased by 108.50 % and 61.80 %, respectively. Additionally, With the WZ14 treatment, the total accumulation of Cd, Pb and Cu in Sophora xanthantha significantly increased by 121.31 %, 164.56 %, and 110.17 %, respectively, representing the most effective treatment. Pb and Cu accumulation was largely concentrated in the roots, while Cu distribution was relatively uniform across two plants tissues. 16S rRNA analysis identified that Sphingomonas, Flavisolibacter, Bacillus, and Streptomyces as the key bioindicators of heavy metal contamination, and these four species had positive effects confirmed through the Mantel test and LEfSe analysis. Our findings suggest that the WZ14 strain significantly enhances the phytoremediation capacity of Sophora xanthantha in heavy-metal-contaminated soil, highlighting its potential and feasibility of their combined application for restoring soils contaminated with multiple heavy metals.

A holistic perspective on the efficiency of microbial enzymes in bioremediation process: Mechanism and challenges: A review

Industrial activities, pharmaceutical contaminants, excessive agricultural inputs, and improper waste disposal have contributed to the widespread pollution of soil and water. Traditional remediation techniques, while effective, often generate secondary waste and are economically unfeasible. In contrast, microbial bioremediation offers a sustainable and cost-effective alternative by utilizing microorganisms and their enzymatic systems to degrade and detoxify pollutants. This review investigates the potential of microbial enzymes in remediation strategies for removing heavy metals and pharmaceutical contaminants from polluted environments. It analyzes the fundamental mechanisms by which microorganisms sequester and degrade these pollutants, emphasizing the enzymatic processes that facilitate their breakdown. Furthermore, it explores key microbial factors influencing bioremediation efficiency, including microbial diversity and environmental conditions. Additionally, it examines the challenges associated with scaling these bioremediation strategies for global environmental applications and provides insights for future research and implementation.

Integration of microbiomics and metabolomics reveals energy metabolism imbalance in crucian carp (Carassius auratus) under saline-alkaline exposure

The ecological conditions of freshwater aquaculture are deteriorating by degrees in recent years. Consequently, the comprehensive utilization of saline-alkaline water has garnered increasing societal attention. Here, crucian carp (Carassius auratus) were exposed to 20, 40 mmol/L NaHCO3 for 30 days (T, F group). Metabolomic analyses were conducted using UPLC-QTOF/MS, complemented by biochemical and microbiology profiling to elucidate the damage of the saline environment to the intestinal microbial structure, which in turn interfered with the energy metabolism. It was observed that carbonate alkalinity (CA) exposure not only caused intestine oxidative stress but also changed the levels of several digestive enzymes, including α-amylase (AMS), chymotrypsin (CHY), lipase (LPS). Metabolomic analysis identified 22 different metabolites (DEMs) in T group and 77 DEMs in F group. MetaboAnalyst analysis indicated that these metabolites are primarily involved in energy-related pathways, including the citric acid cycle, galactose metabolism, and glycine, serine, and threonine metabolism. Intestinal microbial diversity and community composition were altered under carbonate alkalinity exposure, with increase in Proteobacteria abundance and decline in Firmicutes, abundance alongside enrichment of Sphingomonas. Herein, saline-alkaline stress disrupted the physiological homeostasis of the crucian carp intestine, leading to microbial dysbiosis and energy metabolic imbalance. This study provides a theoretical foundation for understanding the stress response of the crucian carp intestine and the role of the intestinal microbiome in host resilience under adverse environmental conditions.

Comparative Pan- and Phylo-Genomic Analysis of Ideonella and Thermobifida Strains: Dissemination of Biodegradation Potential and Genomic Divergence

Ideonella and Thermobifida were the most promising bacterial candidates for degrading plastic polymers. A comparative pan- and phylogenomic analysis of 33 Ideonella and Thermobifida strains was done to determine their plastic degradation potential, niche adaptation and speciation. Our study disclosed that more accessory genes in the strains showed phenotypic plasticity, according to the BPGA data. Pan and core genes were employed for the phylogenetic reconstruction. Pathway enrichment analyses scrutinized the functional roles of the core and adaptive-associated genes. KEGG annotation revealed that most genes were associated with the metabolism of amino acids and carbohydrates. The detailed COG analysis disclosed that approximately 40% of the pan genes performed metabolic functions. The unique gene pool consisted of genes chiefly involved in "general function prediction" and "amino acid transport and metabolism". Our in silico study revealed that these strains could assist in agronomic applications in the future since they devour nitrogen compounds and their central metabolic pathways are involved in amino acid metabolism. The rational selection of strains of Ideonella is far more effective at depolymerising plastics than Thermobifida. A greater number of unique genes, 1701 and 692, were identified for Ideonella sakaiensis 201-F6 and Thermobifida alba DSM-43795, respectively. Furthermore, we examined the singletons involved in xenobiotic catabolism. The unique singleton data were used to construct a supertree. To characterize the conserved patterns, we used SMART and MEME to identify domain and transmembrane regions in the unique protein sequences. Therefore, our study unraveled the genomic insights into the ecology-driven speciation of Ideonella and Thermobifida.

Enhancing soil quality in soybean cultivation: Mycorrhizal technology combined with intercropping under high cadmium stress

Cadmium (Cd) contamination presents a serious challenges for sustainable agriculture. This study evaluated the combined impact of arbuscular mycorrhizal fungi (AMF) inoculation and intercropping with Solanum nigrum on soil microbial diversity, enzyme activity, and environmental factors in soybean cultivation under high Cd stress. The combined treatment effectively reduced bioavailable Cd in soil, with the acid-soluble Cd fraction at 19.57 mg/kg and the reducible Cd fraction at 61.35 %, resulting in safe soybean grain Cd levels (2.63 mg/kg, below the 3 mg/kg organic standard). Illumina NovaSeq sequencing analysis revealed that key bacterial taxa, including Bradyrhizobium and PMMR1, were correlated with reduced Cd uptake in grains. Although bacterial α diversity increased, microbial network stability decreased in response to Cd, AMF inoculation, and intercropping. The combined treatment also enhanced soil enzyme activity by regulating the relative abundance of dominant or key genera such as Subgroup_6, Rokubacteriales and Pseudarthrobacter. Notably, catalase activity was 97.25 % higher in the combined treatment compared to monoculture without AMF colonization under high Cd conditions. These findings demonstrate the synergistic potential of AMF inoculation and S. nigrum intercropping as a sustainable approach to mitigate Cd contamination in crops while improving soil health in Cd-contaminated environments.

Metabolomic Analysis of Carotenoids Biosynthesis by Sphingopyxis sp. USTB-05

Carotenoids belonging to the class of tetraterpenoids have extensive applications in medicine, food, nutrition, cosmetics, and feed. Among them, lutein and zeaxanthin can prevent macular degeneration in the elderly, which is very important for protecting vision. Here, we introduce the first metabolomic analysis of Sphingopyxis sp. USTB-05, aiming to shed light on the biosynthesis of carotenoids. Sphingopyxis sp. USTB-05 has the complete methylerythritol 4-phosphate (MEP) pathway and carotenoid biosynthesis pathway, especially involved in the bioconversion of zeaxanthin, violaxanthin, and astaxanthin. Metabolomic profiling identified seven carotenes and six xanthophylls synthesized by Sphingopyxis sp. USTB-05. Zeaxanthin, in particular, was found to be the most abundant, with a content of 37.1 µg/g dry cells. Collectively, the results presented herein greatly enhance our understanding of Sphingopyxis sp. USTB-05 in carotenoids biosynthesis, and thus further accelerate its fundamental molecular investigations and biotechnological applications.

Assessment of bacterial biotransformation of alkylnaphthalene lubricating base oil component 1-butylnaphthalene by LC/ESI-MS(/MS)

Alkylnaphthalene lubricating oils are synthetic Group V base oils that are utilized in wide-ranging industrial applications and which are composed of polyalkyl chain-alkylated naphthalenes. Identification of alkylnaphthalene biotransformation products and determination of their mass spectrometry (MS) fragmentation signatures provides valuable information for predicting their environmental fates and for development of analytical methods to monitor their biodegradation. In this work, laboratory-based environmental petroleomics was applied to investigate the catabolism of the alkylnaphthalene, 1-butylnaphthalene (1-BN), by liquid chromatography electrospray ionization MS data mapping and targeted collision-induced dissociation (CID) analyses. Comparative mapping revealed that numerous catabolites were produced from soil bacterium, Sphingobium barthaii KK22. Targeted CID showed unique patterns of production of even-valued deprotonated fragments that were found to originate from specific classes of bacterial catabolites. Based upon results of CID analyses of catabolites and authentic standards, MS signatures were proposed to occur through formation of distonic radical anions from bacterially-produced alkylphenol biotransformation products. Finally, spectra interpretation was guided by CID results to propose chemical structures for twenty-two 1-BN catabolites resulting in construction of 1-BN biotransformation pathways. Multiple pathways were identified that included aromatic ring-opening, alkyl chain-shortening and production of α,β-unsaturated aldehydes from alkylated phenols. Until now, α,β-unsaturated aldehydes have not been a class of compounds much reported from alkylated polycyclic aromatic hydrocarbon (APAH) and PAH biotransformation. This work provides a new understanding of alkylnaphthalene biotransformation and proposes MS markers applicable to monitoring APAH biotransformation in the form of alkylated phenols, and by extension, α,β-unsaturated aldehydes, and toxic potential during spilled oil biodegradation.

Joint effect of black carbon deriving from wheat straw burning and plastic mulch film debris on the soil biochemical properties, bacterial and fungal communities

Black carbon (BC) formed after straw burning remains in farmland soil and coexists with plastic mulch film (PMF) debris. It is unclear how BC influences soil multifunctionality in the presence of PMF debris. In this study, we determined the joint effects of BC and PMF debris on soil biochemical properties and microbial communities. We conducted a soil microcosm experiment by adding BC formed by direct burning of wheat straw and PMF debris (polyethylene (PE) and biodegradable PMF (BP)) into soil at the dosages of 1 %, and soils were sampled on the 15th, 30th, and 100th day of soil incubation for high-throughput sequencing. The results showed that the degradation of PMF debris was accompanied by the release of microplastics (MPs). BC decreased NH4+-N (PE: 68.63 %; BP: 58.97 %) and NO3--N (PE: 12.83 %; BP: 51.37 %) and increased available phosphorus (AP) (PE: 79.12 %; BP: 26.09 %) in soil containing PMF debris. There were significant differences in enzyme activity among all the treatments. High-throughput sequencing indicated that BC reduced bacterial and fungal richness and fungal diversity in PMF debris-exposed soil, whereas PMF debris and BC resulted in significant changes in the proportion of dominant phyla and genera of bacteria and fungi, which were affected by incubation time. Furthermore, BC affected microorganisms by influencing soil properties, and pH and N content were the main influencing factors. In addition, FAPRPTAX analysis indicated that BC and PMF debris affected soil C and N cycling. These findings provide new insights into the response of soil multifunctionality to BC and PMF debris.

Unveiling genomic features linked to traits of plant growth-promoting bacterial communities from sugarcane

Microorganisms are ubiquitous, and those inhabiting plants have been the subject of several studies. Plant-associated bacteria exhibit various biological mechanisms that enable them to colonize host plants and, in some cases, enhance their fitness. In this study, we describe the genomic features predicted to be associated with plant growth-promoting traits in six bacterial communities isolated from sugarcane. The use of highly accurate single-molecule real-time sequencing technology for metagenomic samples from these bacterial communities allowed us to recover 17 genomes. The taxonomic assignments for the binned genomes were performed, revealing taxa distributed across three main phyla: Bacillota, Bacteroidota, and Pseudomonadota, with the latter being the most representative. Subsequently, we functionally annotated the metagenome-assembled genomes (MAGs) to characterize their metabolic pathways related to plant growth-promoting traits. Our study successfully identified the enrichment of important functions related to phosphate and potassium acquisition, modulation of phytohormones, and mechanisms for coping with abiotic stress. These findings could be linked to the robust colonization of these sugarcane endophytes.

Insights into CO2 and N2O emissions driven by applying biochar and nitrogen fertilizers in upland soil

Biochar and soil carbon sequestration hold promise in mitigating global warming by storing carbon in the soil. However, the interaction between biochar properties, soil carbon-nitrogen cycling, and nitrogen fertilizer application's impact on soil carbon-nitrogen balance remained unclear. Herein, we conducted batch experiments to study the effects and mechanisms of rice straw biochar application (produced at 300, 500, and 700 °C) on net greenhouse gas emissions (CO2, N2O, CH4) in upland soils under different forms of nitrogen fertilizers. The findings revealed that (NH4)2SO4 and urea significantly elevated soil carbon dioxide equivalent emissions, ranging from 28 to 61.7 kg CO2e/ha and 8.2 to 37.7 kg CO2e/ha, respectively. Conversely, KNO3 reduced soil CO2e emissions, ranging from 2.2 to 13.6 kg CO2e/ha. However, none of these three nitrogen forms exhibited a significant effect on CH4 emissions. The pyrolysis temperature of biochar was found negatively correlated with soil CO2 and N2O emissions. The alkaline substances presented in biochar pyrolyzed at 500-700 °C raised soil pH, increased the ratio of Gram-negative to Gram-positive bacteria, and enhanced the relative abundance of Sphingomonadaceae. Moreover, the co-application of KNO3 based nitrogen fertilizer and biochar increased the total carbon/inorganic nitrogen ratio and reduces the relative abundance of Nitrospirae. This series of reactions led to a significant increase in soil DOC content, meanwhile reduced soil CO2 emissions, and inhibited the nitrification process and decreased the emission of soil N2O. This study provided a scientific basis for the rational application of biochar in soil.

The Effects of Exogenous Benzoic Acid on the Physicochemical Properties, Enzyme Activities and Microbial Community Structures of Perilla frutescens Inter-Root Soil

This study analyzed the effects of benzoic acid (BA) on the physicochemical properties and microbial community structure of perilla rhizosphere soil. The analysis was based on high-throughput sequencing technology and physiological and biochemical detection. The results showed that with the increase in BA concentration, soil pH significantly decreased, while the contents of total nitrogen (TN), alkaline nitrogen (AN), available phosphorus (AP), and available potassium (AK) significantly increased. The activities of soil conversion enzymes urease and phosphatase significantly increased, but the activities of catalase and peroxidase significantly decreased. This indicates that BA can increase soil enzyme activity and improve nutrient conversion; the addition of BA significantly altered the composition and diversity of soil bacterial and fungal communities. The relative abundance of beneficial bacteria such as Gemmatimonas, Pseudolabrys, and Bradyrhizobium decreased significantly, while the relative abundance of harmful fungi such as Pseudogymnoascus, Pseudoeurotium, and Talaromyces increased significantly. Correlation analysis shows that AP, AN, and TN are the main physicochemical factors affecting the structure of soil microbial communities. This study elucidates the effects of BA on the physicochemical properties and microbial community structure of perilla soil, and preliminarily reveals the mechanism of its allelopathic effect on the growth of perilla.

Bioaerosols released from multistage biofilter for gaseous benzene removal: Escape behavior and pathogenicity

Biological deodorization systems are widely used to control odors and volatile organic compounds. However, the secondary contamination of bioaerosol emissions is a noteworthy issue in the operation of biofilters for off-gas purification. In this study, a multistage biofilter for benzene treatment was utilized to investigate the bioaerosol emissions under different flow rates and spray intervals. At the outlet of the biofilter, 99-7173 CFU/m3 of bioaerosols were detected, among which pathogens accounted for 8.93-98.73 %. Proteobacteria and Firmicutes dominated bioaerosols at the phylum level. The Mantel test based on the Bray-Curtis distance revealed strong influences of flow rate introduced to the biofilter and biomass colonized on the packing materials (PMs) on bioaerosol emissions. The non-metric multidimensional scaling results suggested a correlation between the bioaerosol community and bacteria on the PMs. Bacillus and Stenotrophomonas were the two main genera stripped from the biofilm on PMs to form the bioaerosols. SourceTracker analysis confirmed that microorganisms from the PMs near outlet contributed an average of 22.3 % to bioaerosols. Pathogenic bacteria carried by bioaerosols included Bacillus, Serratia, Stenotrophomonas, Achromobacter, Enterococcus, and Pseudomonas. Bioaerosols were predicted to cause human diseases, with antimicrobial drug resistance and bacterial infectious disease being the two main pathogenic pathways. Stenotrophomonas sp. LMG 19833, Pseudomonas sp., and Stenotrophomonas sp. were the keystone species in the bioaerosol co-occurrence network. Overall, results of present study promote the insight of bioaerosols, particularly pathogen emissions, and provide a basis for controlling bioaerosol contamination from biofilters.

Adaptive evolution of Sphingopyxis sp. MC4 conferred degradation potential for persistent β- and δ-Hexachlorocyclohexane (HCH) isomers

Hexachlorocyclohexane (HCH), an organochlorine pesticide imposes several harmful impacts on the ecosystem. β- and δ-isomers of HCH are highly toxic, persistent, and recalcitrant to biodegradation, slow and incomplete degradation of β- and δ- isomers have been reported in a few strains. We have isolated a strain designated as Sphingopyxis strain MC4 that can tolerate and degrade high concentrations of α-, β-, γ- and δ-HCH isomers. To date, no other Sphingopyxis strain has been reported to degrade β- and δ-isomers. To understand the underlying genetic makeup contributing to adaptations, the whole genome of strain MC4 was sequenced. Comparative genome analysis showed that strain MC4 harbors the complete pathway (lin genes) required for HCH degradation. Genetic footprints such as presence of lin genes on genomic islands, IS6100 elements in close proximity of lin genes, and synteny in lin flanking regions with other strains reflects the horizontal gene transfer in strain MC4. Positive selection and HGT drive the adaptive evolution of strain MC4 under the pressure of HCH contamination that it experienced in its surrounding niche. In silico analyses showed efficient binding of β- and δ-isomers with enzymes leading to rapid degradation that need further validation by cloning and biochemical experiments.

Complex interactions between diverse mobile genetic elements drive the evolution of metal-resistant bacterial genomes

In this study, we compared the genomes of three metal-resistant bacteria isolated from mercury-contaminated soil. We identified diverse and novel MGEs with evidence of multiple LGT events shaping their genomic structure and heavy metal resistance. Among the three metal-resistant strains, Sphingobium sp SA2 and Sphingopyxis sp SE2 were resistant to multiple metals including mercury, cadmium, copper, zinc and lead. Pseudoxanthomonas sp SE1 showed resistance to mercury only. Whole genome sequencing by Illumina and Oxford Nanopore technologies was undertaken to obtain comprehensive genomic data. The Sphingobium and Sphingopyxis strains contained multiple chromosomes and plasmids, whereas the Pseudoxanthomonas strain contained one circular chromosome. Consistent with their metal resistance profiles, the strains of Sphingobium and Sphingopyxis contained a higher quantity of diverse metal resistance genes across their chromosomes and plasmids compared to the single-metal resistant Pseudoxanthomonas SE1. In all three strains, metal resistance genes were principally associated with various novel MGEs including genomic islands (GIs), integrative conjugative elements (ICEs), transposons, insertion sequences (IS), recombinase in trio (RIT) elements and group II introns, indicating their importance in facilitating metal resistance adaptation in a contaminated environment. In the Pseudoxanthomonas strain, metal resistance regions were largely situated on a GI. The chromosomes of the strains of Sphingobium and Sphingopyxis contained multiple metal resistance regions, which were likely acquired by several GIs, ICEs, numerous IS elements, several Tn3 family transposons and RIT elements. Two of the plasmids of Sphingobium were impacted by Tn3 family transposons and ISs likely integrating metal resistance genes. The two plasmids of Sphingopyxis harboured transposons, IS elements, an RIT element and a group II intron. This study provides a comprehensive annotation of complex genomic regions of metal resistance associated with novel MGEs. It highlights the critical importance of LGT in the evolution of metal resistance of bacteria in contaminated environments.

A new quantitative insight: Interaction of polyethylene microplastics with soil - microbiome - crop

In this study, the interaction between primary/secondary PE MPs and soil - microbiome - crop complex system and PE MPs enrichment behavior in crops were studied by using the self-developed quantitative characterization method of Eu-MPs and in situ zymography. The results demonstrated for the first time the enrichment effect of micron-sized PE (> 10 µm) in crops, manifested as roots>leaves>stems. Primary PE MPs significantly increased soil TN, TC, SOM and β-glu activity and inhibited Phos activity. Age-PE MPs significantly reduced soil TN, TP, β-glu and Phos activities and also have significant inhibitory effects on plant height, stem diameter, and leaf dry weight of maize. Age-PE MPs significantly affected soil microbial diversity, mainly caused by bacterial genera such as UTCFX1, Sphingomonas, Subgroup-6 and Gemmatimonas. Age-PE MPs also affected some metabolism related to microbial community composition and maize growth, including Glycerolipid, Citrate cycle (TCA cycle), C5-Branched dibasic acid, Arginine and proline, Tyrosine metabolism, pentose phosphate pathway, Valine, leucine and isoleucine biosynthesis. These research results indicated that the PE MPs, which are widely present in farmland soils, can affect crop growth, soil microbial community and metabolic function after aging, thus affecting agroecosystems and terrestrial biodiversity.

Bacterial benz(a)anthracene catabolic networks in contaminated soils and their modulation by other co-occurring HMW-PAHs

Polycyclic aromatic hydrocarbons (PAHs) are major environmental pollutants in a number of point source contaminated sites, where they are found embedded in complex mixtures containing different polyaromatic compounds. The application of bioremediation technologies is often constrained by unpredictable end-point concentrations enriched in recalcitrant high molecular weight (HMW)-PAHs. The aim of this study was to elucidate the microbial populations and potential interactions involved in the biodegradation of benz(a)anthracene (BaA) in PAH-contaminated soils. The combination of DNA stable isotope probing (DNA-SIP) and shotgun metagenomics of ¹³C-labeled DNA identified a member of the recently described genus Immundisolibacter as the key BaA-degrading population. Analysis of the corresponding metagenome assembled genome (MAG) revealed a highly conserved and unique genetic organization in this genus, including novel aromatic ring-hydroxylating dioxygenases (RHD). The influence of other HMW-PAHs on BaA degradation was ascertained in soil microcosms spiked with BaA and fluoranthene (FT), pyrene (PY) or chrysene (CHY) in binary mixtures. The co-occurrence of PAHs resulted in a significant delay in the removal of PAHs that were more resistant to biodegradation, and this delay was associated with relevant microbial interactions. Members of Immundisolibacter, associated with the biodegradation of BaA and CHY, were outcompeted by Sphingobium and Mycobacterium, triggered by the presence of FT and PY, respectively. Our findings highlight that interacting microbial populations modulate the fate of PAHs during the biodegradation of contaminant mixtures in soils.

Tomato Plant Microbiota under Conventional and Organic Fertilization Regimes in a Soilless Culture System

Tomato is the main vegetable cultivated under soilless culture systems (SCSs); production of organic tomato under SCSs has increased due to consumer demands for healthier and environmentally friendly vegetables. However, organic tomato production under SCSs has been associated with low crop performance and fruit quality defects. These agricultural deficiencies could be linked to alterations in tomato plant microbiota; nonetheless, this issue has not been sufficiently addressed. Thus, the main goal of the present study was to characterize the rhizosphere and phyllosphere of tomato plants cultivated under conventional and organic SCSs. To accomplish this goal, tomato plants grown in commercial greenhouses under conventional or organic SCSs were tested at 8, 26, and 44 weeks after seedling transplantation. Substrate (n = 24), root (n = 24), and fruit (n = 24) composite samples were subjected to DNA extraction and high-throughput 16S rRNA gene sequencing. The present study revealed that the tomato core microbiota was predominantly constituted by Proteobacteria, Actinobacteria, and Firmicutes. Remarkably, six bacterial families, Bacillaceae, Microbacteriaceae, Nocardioidaceae, Pseudomonadaceae, Rhodobacteraceae, and Sphingomonadaceae, were shared among all substrate, rhizosphere, and fruit samples. Importantly, it was shown that plants under organic SCSs undergo a dysbiosis characterized by significant changes in the relative abundance of Bradyrhizobiaceae, Caulobacteraceae, Chitinophagaceae, Enterobacteriaceae, Erythrobacteraceae, Flavobacteriaceae, Nocardioidaceae, Rhodobacteraceae, and Streptomycetaceae. These results suggest that microbial alterations in substrates, roots, and fruits could be potential factors in contributing to the crop performance and fruit quality deficiencies observed in organic SCSs.

Bioengineered microbial strains for detoxification of toxic environmental pollutants

Industrialization and other anthropogenic human activities pose significant environmental risks. As a result of the hazardous pollution, numerous living organisms may suffer from undesirable diseases in their separate habitats. Bioremediation, which removes hazardous compounds from the environment using microbes or their biologically active metabolites, is one of the most successful remediation approaches. According to the United Nations Environment Program (UNEP), deteriorating soil health negatively impacts food security and human health over time. Soil health restoration is critical right now. Microbes are widely known for their importance in cleaning up toxins present in the soil, such as heavy metals, pesticides, and hydrocarbons. However, the capacity of local bacteria to digest these pollutants is limited, and the process takes an extended time. Genetically modified organisms (GMOs), whose altered metabolic pathways promote the over-secretion of a variety of proteins favorable to the bioremediation process, can speed up the breakdown process. The need for remediation procedures, degrees of soil contamination, site circumstances, broad adoptions, and numerous possibilities occurring at various cleaning stages are all studied in detail. Massive efforts to restore contaminated soils have also resulted in severe issues. This review focuses on the enzymatic removal of hazardous pollutants from the environment, such as pesticides, heavy metals, dyes, and plastics. There are also in-depth assessments of present discoveries and future plans for efficient enzymatic degradation of hazardous pollutants.

A comprehensive review on the potential of microbial enzymes in multipollutant bioremediation: Mechanisms, challenges, and future prospects

Industrialization and other human activity represent significant environmental hazards. Toxic contaminants can harm a comprehensive platform of living organisms in their particular environments. Bioremediation is an effective remediation process in which harmful pollutants are eliminated from the environment using microorganisms or their enzymes. Microorganisms in the environment often create a variety of enzymes that can eliminate hazardous contaminants by using them as a substrate for development and growth. Through their catalytic reaction mechanism, microbial enzymes may degrade and eliminate harmful environmental pollutants and transform them into non-toxic forms. The principal types of microbial enzymes which can degrade most hazardous environmental contaminants include hydrolases, lipases, oxidoreductases, oxygenases, and laccases. Several immobilizations, genetic engineering strategies, and nanotechnology applications have been developed to improve enzyme performance and reduce pollution removal process costs. Until now, the practically applicable microbial enzymes from various microbial sources and their ability to degrade multipollutant effectively or transformation potential and mechanisms are unknown. Hence, more research and further studies are required. Additionally, there is a gap in the suitable approaches considering toxic multipollutants bioremediation using enzymatic applications. This review focused on the enzymatic elimination of harmful contaminants in the environment, such as dyes, polyaromatic hydrocarbons, plastics, heavy metals, and pesticides. Recent trends and future growth for effectively removing harmful contaminants by enzymatic degradation are also thoroughly discussed.

Positive and negative effects of recirculating aquaculture water advanced oxidation: O3 and O3/UV treatments improved water quality but increased antibiotic resistance genes

Recirculating aquaculture systems (RASs) can be efficiently used for aquaculture, and oxidation treatment is commonly used to improve water quality. However, the effects of oxidation treatments on aquaculture water safety and fish yield in RASs are poorly understood. In this study, we tested the effects of O₃ and O₃/UV treatments on aquaculture water quality and safety during culture of crucian carp. O₃ and O₃/UV treatments reduced the dissolved organic carbon (DOC) concentration by ∼40% and destroyed the refractory organic lignin-like features. There was enrichment of ammonia oxidizing (Nitrospira, Nitrosomonas, and Nitrosospira) and denitrifying (Pelomonas, Methyloversatilis, and Sphingomonas) bacteria, and N-cycling functional genes were enriched by 23% and 48%, respectively, after O₃ and O₃/UV treatments. Treatment with O₃ and O₃/UV reduced NH₄⁺-N and NO₂^--N in RASs. O₃/UV treatment increased fish length and weight as well as probiotics in fish intestine. However, high saturated intermediates and tannin-like features induced antibiotic resistance genes (ARGs) in O₃ and O₃/UV treatments, by 52% and ∼28%, respectively, and also enhanced horizontal transfer of ARGs. Overall, the application of O₃/UV achieved better effects. However, understanding the potential biological risks posed by ARGs in RASs and determining the most efficient water treatment strategies to mitigate these risks should be goals of future work.

Polycyclic aromatic hydrocarbon (PAH) biodegradation capacity revealed by a genome-function relationship approach

BACKGROUND

Polycyclic aromatic hydrocarbon (PAH) contamination has been a worldwide environmental issue because of its impact on ecosystems and human health. Biodegradation plays an important role in PAH removal in natural environments. To date, many PAH-degrading strains and degradation genes have been reported. However, a comprehensive PAH-degrading gene database is still lacking, hindering a deep understanding of PAH degraders in the era of big data. Furthermore, the relationships between the PAH-catabolic genotype and phenotype remain unclear.

RESULTS

Here, we established a bacterial PAH-degrading gene database and explored PAH biodegradation capability via a genome-function relationship approach. The investigation of functional genes in the experimentally verified PAH degraders indicated that genes encoding hydratase-aldolase could serve as a biomarker for preliminarily identifying potential degraders. Additionally, a genome-centric interpretation of PAH-degrading genes was performed in the public genome database, demonstrating that they were ubiquitous in Proteobacteria and Actinobacteria. Meanwhile, the global phylogenetic distribution was generally consistent with the culture-based evidence. Notably, a few strains affiliated with the genera without any previously known PAH degraders (Hyphomonas, Hoeflea, Henriciella, Saccharomonospora, Sciscionella, Tepidiphilus, and Xenophilus) also bore a complete PAH-catabolic gene cluster, implying their potential of PAH biodegradation. Moreover, a random forest analysis was applied to predict the PAH-degrading trait in the complete genome database, revealing 28 newly predicted PAH degraders, of which nine strains encoded a complete PAH-catabolic pathway.

CONCLUSIONS

Our results established a comprehensive PAH-degrading gene database and a genome-function relationship approach, which revealed several potential novel PAH-degrader lineages. Importantly, this genome-centric and function-oriented approach can overcome the bottleneck of conventional cultivation-based biodegradation research and substantially expand our current knowledge on the potential degraders of environmental pollutants.

Physicochemical characteristics and microbial communities of rhizosphere in complex amendment-assisted soilless revegetation of gold mine tailings

Amendment-assisted soilless revegetation is a promissing ecological restoration method of mine tailings because of its eco-friendliness and low-cost. However, it is difficult to establish the plant community during ecological restoration because of its nutrient deficiency and heavy metal toxicity. In this study, the complex amendment, consisting of 1% peat, 1% sludge and 4% bentonite, was used to assist tall fescue to revegetate gold mine tailings. The variation in physicochemical characteristics and microbial community diversity and composition of rhizosphere tailings were investigated. The complex amendments significantly promoted tall fescue growth with an increase of 35.33% in shoot length and 27.19% in fresh weight. The improved plant growth was attributed to the reduction in heavy metal accumulation and the variation in the characteristics of rhizosphere tailing microecology. The heavy metal concentrations in plant tissues were decreased by 27.71-53.44% in the amended groups. Compared with the control, the available nitrogen (N), phosphorus (P) and potassium (K) levels in TA (without plant cultivation) and TPA (with plant cultivation) were also enhanced by 36.67-49.09% and 42.21-71.47%, respectively. Besides, the amendments introduced more exclusive operational taxonomic units (OTU) and increased the relative abundance of ecologically beneficial microbes in the rhizosphere. Overall, this study provides insight into amendment-assisted soilless revegetation and its effects on microecology to expand ecological restoration of gold mine tailings.

Variation in Sphingomonas traits across habitats and phylogenetic clades

Whether microbes show habitat preferences is a fundamental question in microbial ecology. If different microbial lineages have distinct traits, those lineages may occur more frequently in habitats where their traits are advantageous. Sphingomonas is an ideal bacterial clade in which to investigate how habitat preference relates to traits because these bacteria inhabit diverse environments and hosts. Here we downloaded 440 publicly available Sphingomonas genomes, assigned them to habitats based on isolation source, and examined their phylogenetic relationships. We sought to address whether: (1) there is a relationship between Sphingomonas habitat and phylogeny, and (2) whether there is a phylogenetic correlation between key, genome-based traits and habitat preference. We hypothesized that Sphingomonas strains from similar habitats would cluster together in phylogenetic clades, and key traits that improve fitness in specific environments should correlate with habitat. Genome-based traits were categorized into the Y-A-S trait-based framework for high growth yield, resource acquisition, and stress tolerance. We selected 252 high quality genomes and constructed a phylogenetic tree with 12 well-defined clades based on an alignment of 404 core genes. Sphingomonas strains from the same habitat clustered together within the same clades, and strains within clades shared similar clusters of accessory genes. Additionally, key genome-based trait frequencies varied across habitats. We conclude that Sphingomonas gene content reflects habitat preference. This knowledge of how environment and host relate to phylogeny may also help with future functional predictions about Sphingomonas and facilitate applications in bioremediation.

Removal of sulfamethoxazole and antibiotic resistance genes in paddy soil by earthworms (Pheretima guillelmi): Intestinal detoxification and stimulation of indigenous soil bacteria

Vermiremediation, which use earthworms to remove contaminants from soil, has been proven to be an alternative, low-cost technology. However, the effects of earthworm activity, especially the degraders in earthworm intestines, on the fate of sulfamethoxazole (SMX), and the effects of intestinal bacteria on degrading bacteria in soil are unclear. In this study, the effects of earthworms on the fate of SMX and related antibiotic resistance genes (ARGs) were investigated. Special attention was paid to the impact of earthworms on SMX degradation efficiency, degradation products, related ARGs, and degraders in both soil and earthworm intestines; the effect of intestinal bacteria on soil bacteria associated with SMX was also studied. Earthworms significantly accelerated SMX degradation by both intestinal detoxification and the stimulation of indigenous soil bacteria. Compared with the treatment without earthworms, the treatment with earthworms reduced SMX residues by 25.1 %, 49.2 %, 35.7 %, 34.2 %, and 35.7 % on the 10th, 20th, 30th, 60th, and 90th days, respectively. Compared with those in soil (treated with earthworms), the SMX residues in wormcasts were further reduced by 12.2-29.0 % from the 2nd to the 20th day, producing some unique anaerobic degradation products that were distinct from those in the soil. In earthworm intestines, SMX degradation was enhanced by bacteria of the genera Microvirga, Sphingomonas, Methylobacterium, Bacillus, and Tumebacillus. All of these bacteria (except Bacillus spp.) entered and colonised the soil with wormcasts, further promoting SMX degradation. Additionally, earthworms removed a significant number of ARGs by increasing the fraction of potential SMX degraders and inhibiting the potential hosts of ARGs and int1. This study demonstrated that earthworms could remediate SMX-contaminated soil by enhancing the removal of SMX and ARGs.

Low fish meal diet supplemented with probiotics ameliorates intestinal barrier and immunological function of Macrobrachium rosenbergii via the targeted modulation of gut microbes and derived secondary metabolites

The unsuitable substitution ratio of fish meal by plant protein will reshape the intestinal microbial composition and intestine immunity. However, previous studies were mostly limited to investigating how different feed or probiotics characterized the microbial composition but ignored the biological interactions between bacteria and host physiology through secondary metabolites. Therefore, this study integrates the apparent indicators monitoring, 16S rDNA sequencing, and metabonomics to systematically investigate the effects of cottonseed protein concentrate (CPC) substitution of fish meal and Bacillus coagulans intervention on gut microbes, secondary metabolites, and intestinal immunity of Macrobrachium rosenbergii. Prawns were fed with three diets for 70 days: HF diets contained 25% fish meal, CPC in LF diets were replaced with 10% fish meal, and LF diets supplemented with 2 × 108 CFU/g diet B. coagulans were designated as BC diets. Results showed that CPC substitution induced a significant decrease in digestive enzyme activities (trypsin and lipase) and gut barrier protein PT-1 expression and a significant increase in γ-GT enzyme activity and inflammatory-related factors (Relish and Toll) expression. B. coagulans treatment mitigated the negative changes of the above indicators. Meanwhile, it significantly improved the expression levels of the barrier factor PT-1, the reparative cytokine IL-22, and Cu/Zn-SOD. CPC substitution resulted in a remarkable downregulated abundance of Firmicutes phyla, Flavobacterium spp., and Bacillus spp. B. coagulans treatment induced the callback of Firmicutes abundance and improved the relative abundance of Sphingomonas, Bacillus, and Ralstonia. Functional prediction indicated that CPC substitution resulted in elevated potential pathogenicity of microbial flora, and B. coagulans reduces the pathogenesis risk. Pearson's correlation analysis established a significant positive correlation between differential genera (Sphingomonas, Bacillus, and Ralstonia) and secondary metabolites (including sphingosine, dehydrophytosphingosine, amino acid metabolites, etc.). Meanwhile, the latter were significantly associated with intestinal immunoregulation-related genes (Cu/Zn-SOD, IL-22, PT-1, Toll, and Relish). This study indicated that B. coagulans could mediate specific gut microbes and the combined action of multiple functional secondary metabolites to affect intestinal barrier function, digestion, and inflammation. Our study revealed the decisive role of gut microbes and derived secondary metabolites in the model of dietary composition-induced intestinal injury and probiotic treatment from a new perspective.

EFSA Panel on Genetically Modified Organisms (GMO), Mullins E, Bresson J, Dalmay T, Dewhurst IC, Epstein MM, Firbank LG, Guerche P, Hejatko J, Moreno FJ, Naegeli H, Nogué F, Rostoks N, Serrano JJS, Savoini G, Veromann E, Veronesi F, Ardizzone M, Camargo AM, de Sanctis G, Federici S, Dumont AF, Gennaro A, Ruiz JAG, Goumperis T, Kagkli DM, Lanzoni A, Lewandowska A, Lenzi P, Neri FM, Papadopoulou N, Paraskevopoulos K, Piffanelli P, Raffaello T, Streissl F. Assessment of genetically modified Maize MON 87429 for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA-GMO-NL-2019-161)

Maize MON 87429 was developed to confer tolerance to dicamba, glufosinate, quizalofop and 2,4-D herbicides. The molecular characterisation data and bioinformatic analyses do not identify issues requiring food/feed safety assessment. None of the identified differences in the agronomic/phenotypic and compositional characteristics tested between maize MON 87429 and its conventional counterpart needs further assessment, except for the levels of phytic acid in grains, which do not raise nutritional and safety concerns. The GMO Panel does not identify safety concerns regarding the toxicity and allergenicity of the DMO, PAT, FT_T and CP4 EPSPS proteins as expressed in maize MON 87429. The GMO Panel finds no evidence that the genetic modification impacts the overall safety of maize MON 87429. In the context of this application, the consumption of food and feed from maize MON 87429 does not represent a nutritional concern in humans and animals. The GMO Panel concludes that maize MON 87429 is as safe as the conventional counterpart and non-GM maize reference varieties tested, and no post-market monitoring of food/feed is considered necessary. In the case of accidental release of viable maize MON 87429 grains into the environment, this would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of maize MON 87429. The GMO Panel concludes that maize MON 87429, as described in this application, is as safe as its conventional counterpart and the tested non-GM maize reference varieties with respect to potential effects on human and animal health and the environment.

Peroxidases-based enticing biotechnological platforms for biodegradation and biotransformation of emerging contaminants

Rampant industrial boom, urbanization, and exponential population growth resulted in widespread environmental pollution, with water being one of the leading affected resources. All kinds of pollutants, including phenols, industrial dyes, antibiotics, pharmaceutically active residues, and persistent/volatile organic compounds, have a paramount effect, either directly or indirectly, on human health and aquatic entities. Strategies for affordable and efficient decontamination of these emerging pollutants have become the prime focus of academic researchers, industry, and government to constitute a sustainable human society. Classical treatment techniques for environmental contaminants are associated with several limitations, such as inefficiency, complex pretreatments, overall high process cost, high sludge generation, and highly toxic side-products formation. Enzymatic remediation is considered a green and ecologically friendlier method that holds considerable potential to mitigate any kinds of contaminating agents. Exploiting the potential of various peroxidases for pollution abatement is an emerging research area and has considerable advantages, such as efficiency and ease of handling, over other methods. This work is designed to provide recent progress in deploying peroxidases as green and versatile biocatalytic tools for the degradation and transformation of a spectrum of potentially hazardous environmental pollutants to broaden their scope for biotechnological and environmental purposes. More studies are required to explicate the degradation mechanisms, assess the toxicology levels of bio-transformed metabolites, and standardize the treatment strategies for economic viability.

Microbially mediated arsenic mobilization in the clay layer and underlying aquifer in the Hetao Basin, Inner Mongolia, China

The clay layer is a source to facilitate arsenic (As) enrichment in the aquifer. However, little is known about microbial processes in the clay layer and their roles in As mobilization in the underlying aquifer. In this study, high-throughput sequencing of full-length 16S rRNA gene and metagenomics were used to characterize the microbial composition and functional potential in a sediment borehole across the clay and sand layers in Hetao Basin, Inner Mongolia, China. Results showed the significant differences between the clay layer and underlying sand layer in the geochemistry, microbial composition and functional potential. Fermentation, Fe(III) reduction, As(V) reduction, sulfate reduction, thiosulfate disproportionation, reductive tricarboxylic acid and Wood-Ljungdahl pathway identified in sediments from the clay layer were positively correlated to the observed high levels of TOC, soluble ammonium, H₃PO₄-extractable As(III) and As(V) and HCl-extractable Fe(II). Although the microbial compositions of the clay and sand layers were different, the microbial functional potential at the interface between the clay and sand layers was similar with the characteristics of fermentation, ammonification and As(V) reduction. The similarity of microbial functional potential at the interface may be attributable to the interaction between the sand and adjacent clay layer with the fluctuation of groundwater level. These metabolic products from the microbial processes in the clay layers and interface would migrate into the underlying groundwater during groundwater overpumping, which facilitates As enrichment in groundwater.

A critical review on microbes-based treatment strategies for mitigation of toxic pollutants

Contamination of the environment through toxic pollutants poses a key risk to the environment due to irreversible environmental damage(s). Industrialization and urbanization produced harmful elements such as petrochemicals, agrochemicals, pharmaceuticals, nanomaterials, and herbicides that are intentionally or unintentionally released into the water system, threatening biodiversity, the health of animals, and humans. Heavy metals (HMs) in water, for example, can exist in a variety of forms that are inclined by climate features like the presence of various types of organic matter, pH, water system hardness, transformation, and bioavailability. Biological treatment is an important tool for removing toxic contaminants from the ecosystem, and it has piqued the concern of investigators over the centuries. In situ bioremediation such as biosparging, bioventing, biostimulation, bioaugmentation, and phytoremediation and ex-situ bioremediation includes composting, land farming, biopiles, and bioreactors. In the last few years, scientific understanding of microbial relations with particular chemicals has aided in the protection of the environment. Despite intensive studies being carried out on the mitigation of toxic pollutants, there have been limited efforts performed to discuss the solutions to tackle the limitations and approaches for the remediation of heavy metals holistically. This paper summarizes the risk assessment of HMs on aquatic creatures, the environment, humans, and animals. The content of this paper highlights the principles and limitations of microbial remediation to address the technological challenges. The coming prospect and tasks of evaluating the impact of different treatment skills for pollutant remediation have been reviewed in detail. Moreover, genetically engineered microbes have emerged as powerful bioremediation capabilities with significant potential for expelling toxic elements. With appropriate examples, current challenging issues and boundaries related to the deployment of genetically engineered microbes as bioremediation on polluted soils are emphasized.

Micro-synteny conservation analysis revealed the evolutionary history of bacterial biphenyl degradation pathway

Phenolic compounds have been enlisted by the United States Environmental Protection Agency (USEPA) and the European Union (EU) as pollutants of priority concern. The biphenyl degradation pathway plays an essential role in prokaryote polychlorinated biphenyls degradation. Our understanding of prokaryotic pathways and their evolution has dramatically increased in recent years with the advancements in prokaryotic genome sequencing and analysis tools. In this work, we applied bioinformatics tools to study the evolution of the biphenyl degradation pathway focusing on the phylogeny and initiation of four representative species (Burkholderia xenovorans LB400, Polaromonas naphthalenivorans CJ2, Pseudomonas putida F1 and Rhodococcus jostii RHA1). These species contained partial or full concatenated genes from bph gene cluster (i.e. bphRbphA1A2A3A4BCKHJID). The aim was to establish this pathway's origin and development mode in the prokaryotic world. Genomic screening revealed that many bacterial species possess genes for the biphenyl degradation pathway. However, the micro-synteny conservation analysis indicated that massive gene recruitment events might have occurred during the evolution of the biphenyl degradation pathway. Combining with the phylogenetic positions, this work points to the evolutionary process of acquiring the biphenyl degradation pathway by different fragments through horizontal gene transfer in these bacterial groups. This study reports the first-ever evidence of the birth of this pathway in the represented species.

Genome Functional Analysis of the Psychrotrophic Lignin-Degrading Bacterium Arthrobacter sp. C2 and the Role of DyP in Catalyzing Lignin Degradation

In the cold regions of China, lignin-rich corn straw accumulates at high levels due to low temperatures. The application of psychrotrophic lignin-degrading bacteria should be an effective means of overcoming the low-temperature limit for lignin degradation and promoting the utilization of corn straw. However, this application is limited by the lack of suitable strains for decomposition of lignin; furthermore, the metabolic mechanism of psychrotrophic lignin-degrading bacteria is unclear. Here, the whole genome of the psychrotrophic lignin-degrading bacterium Arthrobacter sp. C2, isolated in our previous work, was sequenced. Comparative genomics revealed that C2 contained unique genes related to lignin degradation and low-temperature adaptability. DyP may participate in lignin degradation and may be a cold-adapted enzyme. Moreover, DyP was proven to catalyze lignin Cα-Cβ bond cleavage. Deletion and complementation of the DyP gene verified its ability to catalyze the first-step reaction of lignin degradation. Comparative transcriptomic analysis revealed that the transcriptional expression of the DyP gene was upregulated, and the genetic compensation mechanism allowed C2ΔDyP to degrade lignin, which provided novel insights into the survival strategy of the psychrotrophic mutant strain C2ΔdyP. This study improved our understanding of the metabolic mechanism of psychrotrophic lignin-degrading bacteria and provided potential application options for energy-saving production using cold-adapted lignin-degrading enzymes.

Characterizing the Microbial Consortium L1 Capable of Efficiently Degrading Chlorimuron-Ethyl via Metagenome Combining 16S rDNA Sequencing

Excessive application of the herbicide chlorimuron-ethyl (CE) severely harms subsequent crops and poses severe risks to environmental health. Therefore, methods for efficiently decreasing and eliminating CE residues are urgently needed. Microbial consortia show potential for bioremediation due to their strong metabolic complementarity and synthesis. In this study, a microbial consortium entitled L1 was enriched from soil contaminated with CE by a “top-down” synthetic biology strategy. The consortium could degrade 98.04% of 100 mg L−1 CE within 6 days. We characterized it from the samples at four time points during the degradation process and a sample without degradation activity via metagenome and 16S rDNA sequencing. The results revealed 39 genera in consortium L1, among which Methyloversatilis (34.31%), Starkeya (28.60%), and Pseudoxanthomonas (7.01%) showed relatively high abundances. Temporal succession and the loss of degradability did not alter the diversity and community composition of L1 but changed the community structure. Taxon-functional contribution analysis predicted that glutathione transferase [EC 2.5.1.18], urease [EC 3.5.1.5], and allophanate hydrolase [EC 3.5.1.54] are relevant for the degradation of CE and that Methyloversatilis, Pseudoxanthomonas, Methylopila, Hyphomicrobium, Stenotrophomonas, and Sphingomonas were the main degrading genera. The degradation pathway of CE by L1 may involve cleavage of the CE carbamide bridge to produce 2-amino-4-chloro-6-methoxypyrimidine and ethyl o-sulfonamide benzoate. The results of network analysis indicated close interactions, cross-feeding, and co-metabolic relationships between strains in the consortium, and most of the above six degrading genera were keystone taxa in the network. Additionally, the degradation of CE by L1 required not only “functional bacteria” with degradation capacity but also “auxiliary bacteria” without degradation capacity but that indirectly facilitate/inhibit the degradation process; however, the abundance of “auxiliary bacteria” should be controlled in an appropriate range. These findings improve the understanding of the synergistic effects of degrading bacterial consortia, which will provide insight for isolating degrading bacterial resources and constructing artificial efficient bacterial consortia. Furthermore, our results provide a new route for pollution control and biodegradation of sulfonylurea herbicides.

Recent advancements in hydrocarbon bioremediation and future challenges: a review

Petrochemicals are important hydrocarbons, which are one of the major concerns when accidently escaped into the environment. On one hand, these cause soil and fresh water pollution on land due to their seepage and leakage from automobile and petrochemical industries. On the other hand, oil spills occur during the transport of crude oil or refined petroleum products in the oceans around the world. These hydrocarbon and petrochemical spills have not only posed a hazard to the environment and marine life, but also linked to numerous ailments like cancers and neural disorders. Therefore, it is very important to remove or degrade these pollutants before their hazardous effects deteriorate the environment. There are varieties of mechanical and chemical methods for removing hydrocarbons from polluted areas, but they are all ineffective and expensive. Bioremediation techniques provide an economical and eco-friendly mechanism for removing petrochemical and hydrocarbon residues from the affected sites. Bioremediation refers to the complete mineralization or transformation of complex organic pollutants into the simplest compounds by biological agents such as bacteria, fungi, etc. Many indigenous microbes present in nature are capable of detoxification of various hydrocarbons and their contaminants. This review presents an updated overview of recent advancements in various technologies used in the degradation and bioremediation of petroleum hydrocarbons, providing useful insights to manage such problems in an eco-friendly manner.

Microbial bioremediation strategies with wastewater treatment potentialities - A review

The demand for innovative waste treatment techniques has arisen because of the establishment and operation of rigorous waste discharge guidelines into the environment. Due to the rapid increase in the human population, wastewater treatment is a procedure of increasing significance. As a result, wastewater treatment systems are intended to sustain high activities and densities of such microorganisms which meet the different purification requirements. The waste produced by the pharmaceutical industry, if not adequately treated, has harmful repercussions for the environment as well as public health. Bioremediation is an innovative and optimistic technology that can be used to remove and reduce heavy metals from polluted water and contaminated soil. Because of cost-effectiveness and environmental compatibility, bioremediation using microorganisms has an excellent potential for future development. A diverse range of microorganisms, including algae, fungi, yeasts, and bacteria, can function as biologically active methylators, capable of modifying toxic species. Microorganisms play a crucial role in heavy metal bioremediation. Nanotechnology may minimize industry expenses by producing environmentally friendly nanomaterials to alleviate these contaminants. The use of microorganisms in nanoparticle synthesis gives green biotechnology a positive impetus to cost reduction and sustainable production as a developing nanotechnology sector.

Laccases—Versatile Enzymes Used to Reduce Environmental Pollution

The accumulation of waste and toxic compounds has become increasingly harmful to the environment and human health. In this context, the use of laccases has become a focus of interest, due to the properties of these versatile enzymes: low substrate specificity, and water formation as a non-toxic end product. Thus, we begin our study with a general overview of the importance of laccase for the environment and industry, starting with the sources of laccases (plant, bacterial and fungal laccases), the structure and mechanism of laccases, microbial biosynthesis, and the immobilization of laccases. Then, we continue with an overview of agro-waste treatment by laccases wherein we observe the importance of laccases for the biodisponibilization of substrates and the biodegradation of agro-industrial byproducts; we then show some aspects regarding the degradation of xenobiotic compounds, dyes, and pharmaceutical products. The objective of this research is to emphasize and fully investigate the effects of laccase action on the decomposition of lignocellulosic materials and on the removal of harmful compounds from soil and water, in order to provide a sustainable solution to reducing environmental pollution.

Seasonal shift of water quality in China Yangtze River and its impacts on membrane fouling development during the drinking water supply by membrane distillation system

Membrane distillation (MD) technique is increasingly regarded as a promising process for drinking water supply and wastewater treatment owing to its great water purification and usage of renewable energy. Like other membrane separation processes, the membrane fouling issue is widely considered as the main obstacle for real applications of large-scale MD systems. Feedwater characteristics, as the predominant factors for membrane fouling layer formation, mostly determined the membrane fouling trend of MD. Thus the impacts of seasonal shifts of initial feedwater quality on the MD membrane fouling were detailedly researched in this study, and the biofilm development mechanism was especially explored. The bacterial community structure of membrane biofilms was clearly clarified in MD runs of Yangtze River waters that collected in four seasons. The results revealed that the winter run posed a quite sharp flux drop, while a relatively milder flux decline behaviour was seen for other groups despite of the higher bacteria concentration of initial feedwaters. The poorer water quality in winter induced the establishment of a rather thick biofilm on the MD membrane, in which the biofilm-forming bacteria (Gammaproteobacteria and Alphaproteobacteria) and organic matters (EPS) were remarkably observed. Comparatively, a relatively thin biofilm containing abundant live cells and fewer organics finally formed in summer and autumn runs, causing a mitigated flux decline trend. Hence, it can be inferred that the membrane flux decline of MD was likely to be more sensitive to the organic attachment on the membrane in comparison with the bacteria adhesion. Finally, a three-phase pretreatment method was suggested for MD fouling control, including heating course, sterilization course, and filtration course.

Cadmium Exposure Alters Rhizospheric Microbial Community and Transcriptional Expression of Vetiver Grass

Vetiver grass (Chrysopogon zizanioides L.) has been used to remediate cadmium (Cd)-contaminated soil, while there have been few studies on the influence of Cd exposure on the rhizospheric microbial community and transcriptional expression of C. zizanioides. In this study, we investigated the response of the rhizospheric microbial community and transcriptional expression of C. zizanioides in 20 mg/kg Cd-contaminated soil. The results showed that Cd levels in the roots and shoots of C. zizanioides reached 250.80 and 73.40 mg/kg, respectively. The Cd exposure changed the rhizospheric bacterial community, resulting in the significant enrichment of Sphingomonas, Lysobacter, and Gemmatimonadetes in Cd-contaminated soil. In addition, 880 and 3,419 differentially expressed genes were identified in the plant roots and shoots, respectively, in response to Cd stress. Among these, the overexpressed genes associated with redox homeostasis, glutathione (GSH) metabolism, cell wall biosynthesis, and transmembrane transport pathways were found to participate in Cd detoxification in C. zizanioides. These findings could be useful for understanding the selective variation of the rhizospheric microbial community and the detoxification mechanisms of C. zizanioides in Cd phytoremediation.

Fluoroquinolone antibiotics disturb the defense system, gut microbiome, and antibiotic resistance genes of Enchytraeus crypticus

Antibiotic residues from animal manure cause soil pollution and can pose a threat to soil animals. In this study, the toxicological effects of fluoroquinolone antibiotics on Enchytraeus crypticus, including defence response, gut microbiome, and antibiotic resistance genes (ARGs), were studied. The cytochrome P450 enzyme activity and reactive oxygen species levels increased, activating the defense response. The superoxide dismutase and glutathione S-transferase activity, and the expression of immune defense molecules such as coelomic cytolytic factor, lysozyme, bactericidal protein fetidins and lysenin changed. Furthermore, the diversity of the gut microbiome decreased, and the relative abundance of Bacteroidetes decreased significantly at the phylum level but increased in pathogenic and antibiotic-secreting bacteria (Rhodococcus and Streptomyces) at the genus level. However, the soil microbiome was not significantly different from that of the control group. The relative abundance of ARGs in the gut and soil microbiome significantly increased with enrofloxacin concentration, and the fluoroquinolone ARGs were significantly increased in both the soil (20.85-fold, p < 0.001) and gut (11.72-fold, p < 0.001) microbiomes. Subtypes of ARGs showed a positive correlation with Rhodococcus, which might increase the risk of disease transmission and the probability of drug-resistant pathogens. Furthermore, mobile genetic elements significantly promote the spread of ARGs.

Bioaugmentation as a green technology for hydrocarbon pollution remediation. Problems and prospects

Environmental pollution mitigation measure involving bioremediation technology is a sustainable intervention for a greener ecosystem biorecovery, especially the obnoxious hydrocarbons, xenobiotics, and other environmental pollutants induced by anthropogenic stressors. Several successful case studies have provided evidence to this paradigm including the putative adoption that the technology is eco-friendly, cost-effective, and shows a high tendency for total contaminants mineralization into innocuous bye-products. The present review reports advances in bioremediation, types, and strategies conventionally adopted in contaminant clean-up. It identified that natural attenuation and biostimulation are faced with notable limitations including the poor remedial outcome under the natural attenuation system and the residual contamination occasion following a biostimulation operation. It remarks that the use of genetically engineered microorganisms shows a potentially promising insight as a prudent remedial approach but is currently challenged by few ethical restrictions and the rural unavailability of the technology. It underscores that bioaugmentation, particularly the use of high cell density assemblages referred to as microbial consortia possess promising remedial prospects thus offers a more sustainable environmental security. The authors, therefore, recommend bioaugmentation for large scale contaminated sites in regions where environmental degradation is commonplace.

Role of Plasmid in Pesticide Degradation and Metal Tolerance in Two Plant Growth-Promoting Rhizobacteria Bacillus cereus (NCIM 5557) and Bacillus safensis (NCIM 5558)

Disha A (Bacillus cereus) and Disha B (Bacillus safensis) were isolated from pesticide-infested agricultural field and showed tolerance against pesticides, heavy metals, and antibiotics. The isolates exhibited PGPR activities in vitro as well as in field conditions in lentil (Lens culinaris) and cow pea (Vigna unguiculata). Both the Bacillus species could not be grown in mineral salt medium but efficiently grown in the media supplemented with pesticide (imidacloprid/carbendazim) demonstrating the utilization of pesticide as carbon/nitrogen source. The HPLC studies exhibited the pesticide (imidacloprid/carbendazim) degradation by both the bacteria. B. safensis showed better degradation of carbendazim (88.93%) and imidacloprid (82.48%) than that of B. cereus 78.07% and 49.12%, respectively. The bacterial isolates showed high concentration of heavy metal tolerance viz. lead, molybdenum, cadmium, copper, cobalt, and zinc, except mercury. Both the bacteria possessed single plasmid. The plasmid-cured isolates of B. cereus did not tolerate any pesticide, whereas that of B. safensis tolerated all the pesticides, like wild strains. The plasmid curing experiments did not affect the heavy metal tolerance ability of both the bacteria indicating the genomic nature of heavy metal tolerance genes, whereas pesticide resistance genes are plasmid-dependent in B. cereus but genomic in B. safensis.

Ecological selection of bacterial taxa with larger genome sizes in response to polycyclic aromatic hydrocarbons stress

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous priority pollutants that cause great damage to the natural environment and health. Average genome size in a community is critical for shedding light on microbiome's functional response to pollution stress within an environment. Here, microcosms under different concentrations were performed to evaluate the selection of PAHs stress on the average genome size in a community. We found the distinct communities of significantly larger genome size with the increase of PAHs concentration gradients in soils, and consistent trends were discovered in soils at different latitudes. The abundance of Proteobacteria and Deinococcus-Thermus with relatively larger genomes increased along with PAHs stress and well adapted to polluted environments. In contrast, the abundance of Patescibacteria with a highly streamlined and smaller genome decreased, implying complex interactions between environmental selection and functional fitness resulted in bacteria with larger genomes becoming more abundant. Moreover, we confirmed the increased capacity for horizontal transfer of degrading genes between communities by showing an increased connection number per node positively related to the nidA gene along the concentration gradients in the co-occurrence network. Our findings suggest PAHs tend to select bacterial taxa with larger genome sizes, with significant consequences for community stability and potential biodegradation strategies.

Isolation, Identification, and Analysis of Potential Functions of Culturable Bacteria Associated with an Invasive Gall Wasp, Leptocybe invasa

Symbioses between invasive insects and bacteria are one of the key drivers of insect invasion success. Gall-inducing insects stimulate host plants to produce galls, which affects the normal growth of plants. Leptocybe invasa Fisher et La Salle, an invasive gall-inducing wasp, mainly damages Eucalyptus plantations in Southern China, but little is known about its associated bacteria. The aim of this study was to assess the diversity of bacterial communities at different developmental stages of L. invasa and to identify possible ecological functions of the associated bacteria. Bacteria associated with L. invasa were isolated using culture-dependent methods and their taxonomic statuses were determined by sequencing the 16S rRNA gene. A total of 88 species belonging to four phyla, 27 families, and 44 genera were identified by phylogenetic analysis. The four phyla were Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes, mainly from the genera Pantoea, Enterobacter, Pseudomonas, Bacillus, Acinetobacter, Curtobacterium, Sphingobium, Klebsiella, and Rhizobium. Among them, 72 species were isolated in the insect gall stage and 46 species were isolated from the adult stage. The most abundant bacterial species were γ-Proteobacteria. We found significant differences in total bacterial counts and community compositions at different developmental stages, and identified possible ecological roles of L. invasa-associated bacteria. This study is the first to systematically investigate the associated bacteria of L. invasa using culture-dependent methods, and provides a reference for other gall-inducing insects and associated bacteria.

Responses of bacterial taxonomic attributes to mercury species in rhizosphere paddy soil under natural sulphur-rich biochar amendment

Biochar and sulphur (S) are important factors regulating the level, speciation and transformation of mercury (Hg), leading to alterations in the assemblage of the soil microbial community. However, variations in the taxonomic attributes of the rhizosphere soil bacterial community arising from the Hg speciation in paddy soil, amended with natural S-rich biochar (NSBC) derived from the pyrolysis of S-rich oilseed rape straw, remain unclear. Herein, a rice pot experiment was conducted. Hg-polluted paddy soils were amended with NSBC and low-S biochar (LSBC) to evaluate the role of Hg chemical form affected by NSBC in regulating the taxonomic attributes of rhizosphere soil, including microbial abundance, composition, and ecological clusters within the co-occurrence network of microbial communities. Results showed that microbial abundance was higher in soils with lower Hg levels, and mean increases of 149 observed operational taxonomic units (OTUs) and 238 predicted OTUs (Chao 1) were observed, with a 1 mg kg^-1 decrease in the total Hg (T-Hg) content. Among the 13 predictor variables, the T-Hg content was the strongest and most consistent predictor of the bacterial taxonomic attributes. This finding may be attributed to the fact that the drastic reduction in T-Hg and Hg bioavailability induced by NSBC results in the decrease of Hg stress on the soil microbiome. Moreover, NSBC amendment shifted the ecological clusters toward the amelioration of Hg pollution.

Biodegradation of poly (vinyl alcohol) by an orychophragmus rhizosphere-associated fungus Penicillium brevicompactum OVR-5, and its proposed PVA biodegradation pathway

In recent years, the utilisation of endophytes has emerged as a promising biological treatment technology for the degradation of plastic wastes such as biodegradation of synthetic plastics. This study, therefore, aimed to explore and extensively screen endophytic fungi (from selected plants) for efficient in vitro polyvinyl alcohol (PVA) biodegradation. In total, 76 endophytic fungi were isolated and cultivated on a PVA screening agar medium. Among these fungi, 10 isolates showed potential and were subsequently identified based on phenotypical characteristics, ITS ribosomal gene sequences, and phylogenetic analyses. Four strains exhibited a maximum level of PVA-degradation in the liquid medium when cultivated for 10 days at 28 °C and 150 rpm. These strains showed varied PVA removal rates of 81% (Penicillium brevicompactum OVR-5), 67% (Talaromyces verruculosus PRL-2), 52% (P. polonicum BJL-9), and 41% (Aspergillus tubingensis BJR-6) respectively. The most promising PVA biodegradation isolate 'OVR-5', with an optimal pH at 7.0 and optimal temperature at 30 °C, produced lipase, manganese peroxidase, and laccase enzymes. Based on analyses of its metabolic intermediates, as identified with GC-MS, we proposed the potential PVA degradation pathway of OVR-5. Biodegradation results were confirmed through scanning electron microscopy and Fourier transform infrared spectroscopy. This study provides the first report on an endophytic P. brevicompactum strain (associated with Orychophragmus violaceus) that has a great ability for PVA degradation providing more insight on potential fungus-based applications in plastic waste degradation.

Bioengineered Microbes for Soil Health Restoration - Present Status and Future

According to the United Nations Environment Programme (UNEP), soil health is declining over the decades and it has an adverse impact on human health and food security. Hence, soil health restoration is a need of the hour. It is known that microorganisms play a vital role in remediation of soil pollutants like heavy metals, pesticides, hydrocarbons, etc. However, the indigenous microbes have a limited capacity to degrade these pollutants and it will be a slow process. Genetically modified organisms (GMOs) can catalyze the degradation process as their altered metabolic pathways lead to hypersecretions of various biomolecules that favor the bioremediation process. This review provides an overview on the application of bioengineered microorganisms for the restoration of soil health by degradation of various pollutants. It also sheds light on the challenges of using GMOs in environmental application as their introduction may affect the normal microbial community in soil. Since soil health also refers to the potential of native organisms to survive, the possible changes in the native microbial community with the introduction of GMOs are also discussed. Finally, the future prospects of using bioengineered microorganisms in environmental engineering applications to make the soil fertile and healthy have been deciphered. With the alarming rates of soil health loss, the treatment of soil and soil health restoration need to be fastened to a greater pace and the combinatorial efforts unifying GMOs, plant growth-promoting rhizobacteria, and other soil amendments will provide an effective solution to soil heath restoration ten years ahead.

A Synergistic Consortium Involved in rac-Dichlorprop Degradation as Revealed by DNA Stable Isotope Probing and Metagenomic Analysis

rac-Dichlorprop, a commonly used phenoxyalkanoic acid herbicide, is frequently detected in environments and poses threats to environmental safety and human health. Microbial consortia are thought to play key roles in rac-dichlorprop degradation. However, the compositions of the microbial consortia involved in rac-dichlorprop degradation remain largely unknown. In this study, DNA stable isotope probing (SIP) and metagenomic analysis were integrated to reveal the key microbial consortium responsible for rac-dichlorprop degradation in a rac-dichlorprop-degrading enrichment. OTU340 (Sphingobium sp.) and OTU348 (Sphingopyxis sp.) were significantly enriched in the rac-[¹³C]dichlorprop-labeled heavy DNA fractions. A rac-dichlorprop degrader, Sphingobium sp. strain L3, was isolated from the enrichment by a traditional enrichment method but with additional supplementation of the antibiotic ciprofloxacin, which was instructed by metagenomic analysis of the associations between rac-dichlorprop degraders and antibiotic resistance genes. As revealed by functional profiling of the metagenomes of the heavy DNA, the genes rdpA and sdpA, involved in the initial degradation of the (R)- and (S)-enantiomers of dichlorprop, respectively, were mostly taxonomically assigned to Sphingobium species, indicating that Sphingopyxis species might harbor novel dichlorprop-degrading genes. In addition, taxonomically diverse bacterial genera such as Dyella, Sphingomonas, Pseudomonas, and Achromobacter were presumed to synergistically cooperate with the key degraders Sphingobium/Sphingopyxis for enhanced degradation of rac-dichlorprop. IMPORTANCE Understanding of the key microbial consortium involved in the degradation of the phenoxyalkanoic acid herbicide rac-dichlorprop is pivotal for design of synergistic consortia used for enhanced bioremediation of herbicide-contaminated sites. However, the composition of the microbial consortium and the interactions between community members during the biodegradation of rac-dichlorprop are unclear. In this study, DNA-SIP and metagenomic analysis were integrated to reveal that the metabolite 2,4-dichlorophenol degraders Dyella, Sphingomonas, Pseudomonas, and Achromobacter synergistically cooperated with the key degraders Sphingobium/Sphingopyxis for enhanced degradation of rac-dichlorprop. Our study provides new insights into the synergistic degradation of rac-dichlorprop at the community level and implies the existence of novel degrading genes for rac-dichlorprop in nature.