Isolation of lindane- and endosulfan-degrading bacteria and dominance analysis in the microbial communities by culture-dependent and independent methods

Potential bacterial resources for bioremediation of organochlorine pesticides and flame retardants recognized from forest soil across China

Microbe-mediated remediation becomes a desire method for removal of persistent organic pollutants (POPs) due to its eco-friendly and sustainable nature. The improvement of practical feasibility requires constructing comprehensive species pool, while it is still limited by the rapid recognition of potential bacterial resources from environment. Here, based on the relative abundances of bacterial OTUs and pollutant concentrations, we established indexes to assess their tolerance to organochlorine pesticides (OCPs) and flame retardants (FRs) that are atmospheric transported and naturally accumulated in forest soil via forest filter effect. By exploring the tolerance pattern from tropical to temperate forests across China, we demonstrated that diversity, community composition, and relative abundances of POP-tolerant bacteria were significantly related to POPs' distribution and concentration. By recognizing over a hundred of genera composed of POP-tolerant species, we found that OCP-tolerant taxa were wide-distributed, while bacterial communities were more responsive to the contamination level of FRs and FR-tolerant taxa were accumulated along the increase of FRs pollution. Our indexes successfully recognized well-known POPs-degrading genera, including Rhodococcus, Bacillus, Arthrobacter, Stenotrophomonas, and Pseudomonas, as well as a series of versatile taxa affiliated with families Ktedonobacteraceae, Acetobacteraceae, Solirubrobacteraceae, and Nocardiaceae, which were extremely rare and likely ignored in laboratory-scale experiments. Together, our findings provide valuable clues to expand the library of POPs-degrading candidates that is helpful in screening bacterial resources for bioremediation.

Metagenomic approaches in bioremediation of environmental pollutants

Metagenomics has emerged as a pivotal tool in bioremediation, providing a deeper understanding of the structure and function of the microbial communities involved in pollutant degradation. By circumventing the limitations of traditional culture-based methods, metagenomics enables comprehensive analysis of microbial ecosystems and facilitates the identification of new genes and metabolic pathways that are critical for bioremediation. Advanced sequencing technologies combined with computational and bioinformatics approaches have greatly enhanced our ability to detect sources of pollution and monitor dynamic changes in microbial communities during the bioremediation process. These tools enable the precise identification of key microbial players and their functional roles, and provide a deeper understanding of complex biodegradation networks. The integration of artificial intelligence (AI) with machine learning algorithms has accelerated the process of discovery of novel genes associated with bioremediation and has optimized metabolic pathway prediction. Novel strategies, including sequencing techniques and AI-assisted analysis, have the potential to revolutionize bioremediation by enabling the development of highly efficient, targeted, and sustainable remediation strategies for various contaminated environments. However, the complexity of microbial interactions, data interpretation, and high cost of these advanced technologies remain challenging. Future research should focus on improving computational tools, reducing costs, and integrating multidisciplinary approaches to overcome these limitations.

Co-metabolic growth and microbial diversity: Keys for the depletion of the α, δ, β and γ-HCH isomers

The objective of this study was the isolation and enrichment of microbiomes capable of degrading the main hexachlorocyclohexane isomers quantified in environmental matrices, e.g.: the α, δ, β and γ-HCH isomers. Four microbiomes were isolated and enriched from an HCH-contaminated dumpsite in Italy, both in the presence of HCH isomers (1:1:1:1) as the sole carbon sources and under co-metabolic growth conditions in presence of glucose (0.1 % v/v). The microbiomes were assessed for their relevant metabolic capabilities. A quantitative metabarcoding approach was employed to analyze the compositional evolution of the four microbiomes during the enrichment phase and the phase of testing of the HCH isomers degradation kinetics. The use of a co-metabolic substrate during enrichment process was essential for selecting microbiomes with higher biodiversity. All microbiomes efficiently degraded the α, δ, and γ-HCH isomers. The highest efficiency in the β-HCH degradation capacity was positively correlated to the highest biodiversity of the microbiome, and the involvement of Chryseobacterium and Asinibacterium sps. have been proposed for a recorded increment in bacterial load during the HCH degradation process.

Metabolic and physiological effects of antibiotic-induced dysbiosis in citrus

Streptomycin (Str) and oxytetracycline (Otc) are widely used antibiotics to manage bacterial diseases in citrus and other crops. However, their impacts on the rhizosphere bacterial assembly and plant physiology are poorly understood. The aim of this study was to examine the effects of Str and Otc on the physiology (assimilation, transpiration rate, intracellular CO2, and stomatal conductance to water vapor), rhizosphere bacterial assemblages (16S rRNA gene high-throughput amplicon sequencing), and rhizosphere metabolite profiles in healthy Citrus reticulata trees. The results indicated a reduction in photosynthesis after Str and Otc treatments, whereas CO2 outflow stayed constant. Both antibiotics decreased the culturable numbers of bacteria. Analysis of the microbiome showed changes in relative abundance of bacterial groups, specifically Pseudomonas, Agrobacterium, and Streptomyces, in response to the antibiotics. Metabolite profiles changed in streptomycin- and oxytetracycline-treated citrus plants suggesting response to microbe targets or induction of stress responses. This study advances knowledge of antibiotic-driven effects on the rhizosphere microbiome, rhizosphere metabolome, and plant physiology, which is essential for managing plant diseases while safeguarding rhizosphere ecology and long-term plant health.

Effect of Multiple Rounds of Enrichment on Metabolite Accumulation and Microbiota Composition of Pit Mud for Baijiu Fermentation

Pit mud (PM) is the main component of Baijiu (traditional Chinese liquor), and its microorganisms are the primary sources of the aroma of Chinese strong-flavor Baijiu (SFB). Enrichment plays an important role in the selection of functional microorganisms in PM. Herein, the PM of SFB was submitted to six rounds of enrichment using clostridial growth medium (CGM), and changes in the metabolite accumulation and microbiota composition were evaluated. Based on the metabolite production and microbiota composition, the enrichment rounds were classified as the acclimation stage (round 2), main fermentation stage (rounds 3 and 4), and late fermentation stage (rounds 5 and 6). Species within the genus Clostridium dominated in the acclimation stage (65.84-74.51%). In the main fermentation stage, the dominant microbial groups were producers of butyric acid, acetic acid, and caproic acid, which included Clostridium (45.99-74.80%), Caproicibacter (1.45-17.02%), and potential new species within the order of Oscillataceae (14.26-29.10%). In the late stage of enrichment, Pediococcus dominated (45.96-79.44%). Thus, the main fermentation stage can be considered optimal for the isolation of acid-producing bacteria from PM. The findings discussed herein support the development and application of functional bacteria by bioaugmentation, and contribute to improving the quality of PM and SFB production.

Occurrence of OCPs & PCBs and their effects on multitrophic biological communities in riparian groundwater of the Beiluo River, China

Persistent Organic Pollutants (POPs) may exert adverse effects on human and ecosystem health. However, as an ecologically fragile zone with strong interaction between river and groundwater, the POPs pollution in the riparian zone has received little attention. The goal of this research is to examine the concentrations, spatial distribution, potential ecological risks, and biological effects of organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) in the riparian groundwater of the Beiluo River, China. The results showed that the pollution level and ecological risk of OCPs in riparian groundwater of the Beiluo River were higher than PCBs. The presence of PCBs (Penta-CBs, Hexa-CBs) and CHLs, respectively, may have reduced the richness of bacteria (Firmicutes) and fungi (Ascomycota). Furthermore, the richness and Shannon's diversity index of algae (Chrysophyceae and Bacillariophyta) decreased, which could be linked to the presence of OCPs (DDTs, CHLs, DRINs), and PCBs (Penta-CBs, Hepta-CBs), while for metazoans (Arthropoda) the tendency was reversed, presumably as a result of SULPHs pollution. In the network analysis, core species belonging to bacteria (Proteobacteria), fungi (Ascomycota), and algae (Bacillariophyta) played essential roles in maintaining community function. Burkholderiaceae and Bradyrhizobium can be considered biological indicators of PCBs pollution in the Beiluo River. Note that the core species of interaction network, playing a fundamental role in community interactions, are strongly affected by POPs pollutants. This work provides insights into the functions of multitrophic biological communities in maintaining the stability of riparian ecosystems through the response of core species to riparian groundwater POPs contamination.

Ecological risk assessment of glyphosate and its possible effect on bacterial community in surface sediments of a typical shallow Lake, northern China

Glyphosate is a widely used herbicide worldwide and its prevalent presence in aquatic ecosystems poses a threat to living organisms. This study evaluated potential ecological risk of glyphosate to sediment-dwelling organisms and assessed the probable effect of glyphosate on structure and predicated function of sediment-attached bacterial communities from a large shallow lake in northern China based on 16S rRNA high-throughput sequencing. Results suggested that glyphosate showed a medium to high concentration (up to 8.63 mg/kg) and chronic risk to sediment-dwelling organisms (10% samples exhibiting medium to high risk quotient), especially in sites nearby farmland and residential areas in August. Bacterial community identification based on 16S rRNA sequence indicated some species of dominant phylum Proteobacteria and Campilobacterota (e.g., Steroidobacteraceae, Thiobacillus, Gallionellaceae, Sulfurimonadaceae) were stimulated while some species of dominant phylum Actinobacteriota, Acidobacteriota and Firmicutes (e.g., Nocardioidaceae, Microtrichales, Vicinamibacteraceae, Paenisporosarcina) were inhibited by glyphosate accumulation. The stimulating species were related to sulfur-oxidizing, sulfate-, iron-, or nitrate-reducing bacteria; The inhibiting species were related to plant bacterial endophytes, polyphosphate-accumulating organisms (PAOs) and denitrifers. Correspondingly, promoted bacterial metabolic functions of "sulfite respiration", "nitrogen respiration", "aromatic compound degradation" and "nitrification" but suppressed "cellulolysis", "manganese oxidation", "anoxygenic photoautotrophy S oxidizing" and "nitrate denitrification" were predicated on functional annotation of prokaryotic taxa. Although these results could only partly suggest the impacts of glyphosate on the bacterial communities due to the lack of actual results from control experiments, the identified Steroidobacteraceae could be thought as a bioindicator in the future mechanism study for the ecological effect and bioremediation of glyphosate. This work intends to arise the concern about the depletion of biodiversity and bacterial metabolic functions with contribution of glyphosate in part in eutrophic lakes.

Enhanced removal of sulfur-containing organic pollutants from actual wastewater by biofilm reactor: Insights of sulfur transformation and bacterial metabolic traits

Sulfur-containing organic pollutants in wastewater could threaten human health due to their high malodor and toxicity, and their conversion processes are more complex than inorganic sulfur compounds. Membrane aerated biofilm reactor (MABR), as a novel and environmentally-friendly biofilm-based technology, is able to remove inorganic sulfur in synthetic wastewater. However, it is unknown how sulfur-containing organic pollutants in actual wastewater are transformed in MABR system. This work demonstrated the feasibility of MABR to eliminate sulfur-containing organic pollutants in actual wastewater, and the removal efficiency could be reached at approximately 100%. Meanwhile, over 70% of sulfur-containing organic contaminants were transformed to SO₄^2- during the long-term operation. Further analysis indicated that the functional bacteria that participated in sulfur transformation and carbohydrates degradation (e.g., Chujaibacter, Microscillaceaesp., and Thiobacillus) were evidently enriched when treating actual wastewater. Moreover, the critical metabolic pathways (e.g., sulfur metabolism, glycolysis metabolism, and pyruvate metabolism), and the corresponding genetic expressions (e.g., nrrA, tauA, tauC, sorA, and SUOX) were evidently up-regulated during long-term operation, which was beneficial for the transformation of sulfur-containing organic pollutants in actual wastewater by MABR. This work would expand the application of MABR for treating the actual sulfur-containing organic wastewater and provide an in-depth understanding of the organic sulfur transformation in MABR.

Biodegradation of Endosulfan-a Chlorinated Cyclodiene Pesticide by Indigenous Pseudomonas sp. MSCAS BT01

Endosulfan remains as a lipophilic insecticide that causes serious medical problems because of biological stability and toxicity also found in air, water, soil sediments, and foodstuffs. Henceforward, the present study reveals a novel bacterial species isolated from pesticide-contaminated soil for enhanced endosulfan degradation. Next, isolated bacterial species was characterized with biochemical assays and 16S rRNA sequencing technique. Subsequently, the optimal conditions for endosulfan biodegradation such as pH, concentration of endosulfan, and bacterial growth were estimated with non-sulfur medium (NSM). Sequentially, the amount of endosulfan and compound degradation were analyzed through thin-layer chromatography and gas chromatography/mass spectrometry. Overall, the obtained results revealed the endosulfan acting as primary carbon source for bacterial growth. From the GC-MS analysis, the metabolic products released during endosulfan degradation by Pseudomonas sp. MSCAS BT01 were compared with standard GC-MS spectra. The highest (98%) endosulfan degradation was obtained at pH 7.0. The complete endosulfan degradation was achieved at 14th day of incubation and the less toxic endosulfan diol produced was observed via GC-MS. To conclude, the pesticide-contaminated isolate Pseudomonas sp. MSCAS BT01 emerged as a promising bioremediation tool and effectively employed to degrade endosulfan from contaminated soils, sediments, and wastewaters in the days yet to come.