Recalcitrant plastics in the environment are gradually fragmented into weathered debris distinguished from their original state by the integrative action of influencing factors, such as UV light, heating and physical abrasion. As new artificial carbon-source substrates in aquatic ecosystems, plastic products can be colonized by biofilms and even utilized by microorganisms. To investigate the influences of weathering of plastics on the colonized biofilms, freshwater samples from the Yangtze River (Nanjing, China) were collected for biofilm incubation. Based on the characterization of plastics and biofilms, the effects of plastic surface properties on biofilm characteristics were revealed by the analysis of partial least squares regression (PLSR). Roughness was the principal influencing factor, while rigidity had the opposite effect to it. 16S rRNA gene high-throughput sequencing results indicated the high relative abundance of Cyanobacteria and rising proportion of harmful components (e.g., Flavobacterium) on photoaged polyethylene plastics. The microbial functional profiles (KEGG) predicted by Tax4Fun showed that the functions (e.g., membrane transport, energy metabolism, etc.) of biofilm on photoaged plastics were dissimilar with those on original ones. These findings suggested that the distinct microbial community and the adverse functional changes in biofilms on photoaged plastics potentially enhanced their environmental risks. On the other hand, 28-day cultured biofilms on original low-density polyethylene (LDPE) films were dominated by Exiguobacterium. The previously ignored potentials of this microorganism in rapidly accommodating to a hydrophobic substrate and its plastic degrading ability were both worthy of attention. Therefore, it is necessary to consider the weathering process of plastics in exploring the “plastisphere”, and to give further insights into the double-edged nature of the “plastisphere".

This study investigated the control of dissolved organic matter (DOM) molecular compositions by microbial community shifts under temperature regulation (range from 5 to 35 °C), using riverine DOM and in situ microorganisms as examples. The functioning of different microbial metabolisms, including the utilization and generation processes, was comprehensively analyzed. Though the overall quantity of DOM was less temperature-affected, more molecules were identified at moderate temperatures (e.g., 15 and 25 °C) and their accumulated mass peak intensities increased with the temperature. The results were ascribed to 1) the microbial production of macromolecular (m/z > 600) CHO, CHON, and CHONS species was stimulated at higher temperatures; 2) the microorganisms consumed more DOM molecules at both higher and lower temperatures; and 3) the simultaneously decreased utilization and increased generation of recalcitrant CHO and CHON molecules with m/z < 600 at higher temperatures. The strong correlations among the temperature, community structures, and DOM chemodiversity suggested that temperature promoted the community evenness to increase the DOM generation. In addition, the higher temperature decreased the abundance of microorganisms that utilized more recalcitrant molecules and produced fewer new molecules (e.g., Proteobacteria, Acinetobacter, and Erythrobacter) while increased others that functioned the opposite (e.g., Verrucomicrobia, Bacteroidetes, and Flavobacterium) to increase the DOM production. The constructed temperature-community-DOM chemistry relationship deepened the molecular-level understanding of DOM variations and provided implications for the warming future.

Selenium engineered nanomaterials (Se ENMs)-enabled agriculture has developed rapidly, however, the roles of surface charge in the bioavailability and enrichment efficiency of Se ENMs are still unknown. Herein, various Se ENMs of homogenous size (40–60 nm) and different surface charges (3.2 ± 0.7, −29.0 ± 0.4, and 45.5 ± 1.3 mV) were prepared to explore the Se content and nutritional quality in Brassica chinensis L. The results demonstrated that soil application of various Se ENMs (0.05 mg kg⁻¹) displayed different bio-availabilities via modulating the secretion of root exudates (e.g., tartaric, malic, and citric acids), microbial community composition (e.g., Flavobacterium, Pseudomonas, Paracoccus, Bacillus and Rhizobium) and root cell wall. Negatively charged Se ENMs (Se (−)) showed the highest Se content in the shoot of B. chinensis (3.7-folds). Se (−) also significantly increased yield (156.9%) and improved nutritional quality (e.g., ascorbic acid, amino acids, flavonoids, fatty acids, and tricarboxylic acid) of B. chinensis. Moreover, after harvest, the Se (−) did not lead to significant change in Se residue in soil, but the amount of Se residue in soil was increased by 5.5% after applying the traditional Se fertilizer (selenite). Therefore, this study provides useful information for producing Se-fortified agricultural products, while minimizing environmental risk.

The presence of large amounts of antibiotic resistance genes (ARGs) in livestock manures poses an impending, tough safety risk to ecosystems. To investigate more comprehensively the mechanisms of ARGs removal from industrial-scale composting of livestock manure based on biochar addition, we tracked the dynamics of bacterial community and ARGs at various stages of aerobic composting of livestock manures with 10% biochar. There were no significant effects of biochar on the bacterial community and the profiles of ARGs. During aerobic composting, the relative abundance of ARGs and mobile genetic elements (MGEs) showed overall trends of decreasing and then increasing. The key factor driving the dynamics of ARGs was bacterial community composition, and the potential hosts of ARGs were Caldicoprobacter, Tepidimicrobium, Ignatzschineria, Pseudogracilibacillus, Actinomadura, Flavobacterium and Planifilum. The retention of the thermophilic bacteria and the repopulation of the initial bacteria were the dominant reasons for the increase in ARGs at maturation stage. Additionally, among the MGEs, the relative abundance of transposon gene was substantially removed, while the integron genes remained at high relative abundance. Our results highlighted that the suitability of biochar addition to industrial-scale aerobic composting needs to be further explored and that effective measures are needed to prevent the increase of ARGs content on maturation stage.

Bio-stimulation of the indigenous microbial community is considered as an effective strategy for the bioremediation of polluted environments. This examination explored the near effects of various bio-stimulants on pyrene degradation, prokaryotic community compositions, and functions using 16S rRNA amplicon sequencing and qPCR. At first, the results displayed significant differences (p < 0.05) between the prokaryotic community structures of the control group, PYR (contains pyrene only), and bio-stimulants amended groups. Among the bio-stimulants, biochar, oxalic acid, salicylate, NPK, and ammonium sulfate augmented the pyrene degradation potential of microbial communities. Moreover, the higher abundance of genera, such as Flavobacterium, Hydrogenophaga, Mycobacterium, Rhodococcus, Flavihumibacter, Pseudomonas, Novosphingobium, etc., across the treatments indicated that these genera play a vital role in pyrene metabolism. Based on the higher abundance of GP-RHD and nidA genes, we speculated that Gram-positive prokaryotic communities are more competent in pyrene dissipation than Gram-negative. Furthermore, the marked abundance of nifH, and pqqC genes in the NPK and SA treatments, respectively, suggested that different bio-stimulants might enrich certain bacterial assemblages. Besides, the significant distinctions (p < 0.05) between the bacterial consortia of HA (humic acid) and SA (sodium acetate) groups from NPK, OX (oxalic acid), UR (urea), NH4, and SC (salicylate) groups also suggested that different bio-stimulants might induce distinct ecological impacts influencing the succession of prokaryotic communities in distinct directions. This work provides new insight into the bacterial degradation of pyrene using the bio-stimulation technique. It suggests that it is equally important to investigate the community structure and functions along with studying their impacts on degradation when devising a bio-stimulation technology.

Chlordane is an organochlorine pesticide that is applied extensively. Residual concentrations that remain in soils after application are highly toxic to soil organisms, particularly affecting the earthworm gut and indigenous soil microorganisms. However, response mechanisms of the earthworm gut and indigenous soil microorganism communities to chlordane exposure are not well known. In this study, earthworms (Metaphire guillelmi) were exposed to chlordane-contaminated soils to investigate their response mechanisms over a gradient of chlordane toxicity. Results from high-throughput sequencing and network analysis showed that the bacterial composition in the earthworm gut varied more significantly than that in indigenous soil microbial communities under different concentrations of chlordane stress (2.3–60.8 mg kg⁻¹; p < 0.05). However, keystone species of Flavobacterium, Candidatus Nitrososphaera, and Acinetobacter remained stable in both the earthworm gut and bacterial communities despite varying degrees of chlordane exposure, and their relative abundance was slightly higher in the low-concentration treatment group (T1, T2) than in the high-concentration treatment group (T3, T4). Additionally, network analysis demonstrated that the average value of the mean degree of centrality, closeness centrality, and eigenvector centrality of all keystone species screened by four methods (MetagenomeSeq, LEfSe, OPLS-DA, Random Forest) were 161.3, 0.5, and 0.63, respectively, and that these were significantly higher (p < 0.05) than values for non-keystone species (84.9, 0.4, and 0.2, respectively). Keystone species had greater network connectivity and a stronger capacity to degrade pesticides and transform carbon and nitrogen than non-keystone species. The keystone species, which were closely related to the microbial community in soil indigenous flora and earthworm intestinal flora, could resist chlordane stress and undertake pesticide degradation. These results have increased understanding of the role of the earthworm gut and indigenous soil bacteria in resisting chlordane stress and sustaining microbial equilibrium in soil.

DNA-based analyses of bacterial communities were performed to identify the bacteria co-occurring with cyanobacterial blooms in samples collected at a single site over 2 years. Microcystis aeruginosa was the most predominant species (81% in 2018, and 94% in 2019) within the phylum Cyanobacteria, and microcystins were detected during all cyanobacterial blooms. The stereo microscope and scanning electron microscope observations showed bacterial associations on and around the aggregated M. aeruginosa cells. Culture-independent analyses of filtered bacterial communities showed that the Flavobacterium species in phylum Bacteroidetes (19%) was dominant in the cyanobacterial phycosphere, followed by the Limnohabitans species in Betaproteobacteria (11%). Using principal component analysis, major bacterial genus, including Microcystis and Flavobacterium species, were clustered during cyanobacterial blooms in both years. To identify key bacterial species that develop long-term symbiosis with M. aeruginosa, another culture-independent analysis was performed after the environmental sample had been serially subcultured for 1 year. Interestingly, Brevundimonas (14%) was the most dominant species, followed by Porphyrobacter (7%) and Rhodobacter (3.5%) within the Alphaproteobacteria. Screening of 100 colonies from cyanobacterial bloom samples revealed that the majority of culturable bacteria belonged to Gammaproteobacteria (28%) and Betaproteobacteria (57%), including Pseudomonas, Curvibacter, and Paucibacter species. Several isolates of Brevundimonas, Curvibacter, and Pseudomonas species could promote the growth of axenic M. aeruginosa PCC7806. The sensitivity of M. aeruginosa PCC7806 cells to different environmental conditions was monitored in bacteria-free pristine freshwater, indicating that nitrogen addition promotes the growth of M. aeruginosa.

Poultry manure is a reservoir for antibiotics and antibiotic resistance genes and composting is an effective biological treatment for manure. This study explored the effect of using two methods of adding a complex microbial agent to the composting of laying-hen manure on doxycycline degradation and tetracycline resistance genes elimination. The results showed that incorporating a complex microbial agent at 0.8% (w/w) on the 0ᵗʰ and 11th day (group MT2) effectively degraded doxycycline with a final degradation rate of 46.83 ± 0.55%. The half-life of doxycycline in this group was 21.90 ± 0.00 days and was significantly lower than that of group MT1 (1.6% (w/w) complex microbial agent added on the 0ᵗʰ day) and group DT (compost without complex microbial agent). But there was no significant difference in the final degradation rate of doxycycline between group DT and group MT1. The addictive with the complex microbial agent changed the microbial community structure. Bacteroidetes, Firmicutes and Proteobacteria were the dominant phyla during composting. Aerococcus, Desemzia, Facklamia, Lactobacillus, Streptococcus, and Trichococcus were the bacteria related to the degradation of doxycycline. Moreover, the incorporation of a complex microbial agent could decrease the risk on spreading tetracycline resistance genes. The single addition promoted the elimination of tetM, whose possible hosts were Enterococcus, Lactobacillus, Staphylococcus, and Trichococcus. Adding the complex microbial agent twice promoted the elimination of tetX, which was related to the low abundance of Chryseobacterium, Flavobacterium and Neptunomonas in group MT2. Redundancy analysis showed that the bacterial community, residual doxycycline and physiochemical properties have a potential effect on the variation in tetracycline resistance genes levels. Overall, adding the complex microbial agent twice is an effective measure to degrade doxycycline.

The Deception Island, located in Maritime Antarctica, is a volcanic island with geothermal activity and one of the most visited by tourists. However, the extent of the anthropogenic impact remains largely unknown and the factors shaping the resistance/tolerance mechanisms in the microbiomes from Whalers Bay ecosystems have never been investigated. In this context, this study aimed to reveal the resistome profiles of Whalers Bay sediments and correlate them with environmental factors. Samples were collected at four sites during the summer 2014/2015 along a transect of 27.5 m in the Whalers Bay sediments. DNA isolated from sediment samples was sequenced using the Illumina HiSeq platform. Bioinformatic analyses allowed the assembly of contigs and scaffolds, prediction of ORFs, and taxonomic and functional annotation using NCBI RefSeq database and KEGG orthology, respectively. Microorganisms belonging to the genera Psychrobacter, Flavobacterium and Polaromonas were shown to dominate all sites, representing 60% of taxonomic annotation. Arsenic (As), copper (Cu) and iron (Fe) were the most abundant metal resistance/tolerance types found in the microbiomes. Beta-lactam was the most common class related to antibiotics resistance/tolerance, corroborating with previous environmental resistome studies. The acridine class was the most abundant amongst the biocide resistance/tolerances, related to antiseptic compounds. Results gathered in this study reveal a repertoire of resistance/tolerance classes to antibiotics and biocides unusually found in Antarctica. However, given the volcanic nature (heavy metals-rich region) of Deception Island soils, this putative impact must be viewed with caution.

Microbial diversity in machine oil contaminated soil was determined by high-throughput amplicon sequencing technology. The diversity of culturable microbes in the contaminated soil was further characterized using polymerase chain reaction method. Proteobacteria and Bacteroidetes were the most dominant phyla and occupied 52.73 and 16.77%, respectively, while the most abundant genera were Methylotenera (21.62%) and Flavobacterium (3.06%) in the soil. In the culturable microbes, the major phyla were Firmicutes (46.15%) and Proteobacteria (37.36%) and the most abundant genera were Bacillus (42.86%) and Aeromonas (34.07%). Four isolated microbes with high machine oil degradation efficiency were selected to evaluate their characteristics on the oil degradation. All of them reached their highest oil degradation rate after 7 days of incubation. Most of them significantly increased their oil degradation rate by additional carbon or organic nitrogen source in the incubation medium. The oil degradation rate by combination of the four microbes at the same level was also higher than the rate from each individual microbe. The protocol and findings of this study are very useful for developing micro-bioremediation method to eliminate machine oil contaminants from soil.