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Low-density polyethylene (LDPE) is a widely used plastic that significantly contributes to environmental pollution, and its biodegradation remains challenging. This study investigates the dynamics of bacterial communities in consortia enriched with LDPE as the sole carbon source. The potential for microbial diversity to adapt to polluted environments underscores its role in bioremediation. Community analysis identified Actinobacteria and Proteobacteria as key contributors to LDPE degradation, with dominant genera including Mycobacterium , Cupriavidus , Gordonia , Ochrobactrum , Nocardia , Agromyces , Amycolatopsis , and Cellulosimicrobium . The biodegradation of untreated and pretreated LDPE films was also examined, revealing that UV pretreatment significantly enhances degradation, with weight losses of 2.22–5.17% after 120 days. In contrast, sunlight and thermal treatments resulted in lower weight losses of 1.67–4.56% and 1.42–3.22%, respectively, while untreated LDPE showed only 1.32–2.80% weight loss. These findings underscore the importance of UV pretreatment in facilitating plastic biodegradation. Furthermore, potential LDPE-degrading Actinobacteria and Proteobacteria were isolated, identified as key players in the communities and co-occurrence networks, suggesting promising candidates for developing sustainable plastic waste management solutions. Moreover, this study is the first to reveal the potential LDPE degradation abilities of several genera, including Mesorhizobium , Agromyce s, Amycolatopsis , Olivibacter , Aquamicrobium , Pseudaminobacter , and others.

Recently, there has been significant interest in bio-based degradable plastics owing to their potential as a green and sustainable alternative to synthetic plastics due to their biodegradable properties. Polyhydroxybutyrate (PHB) is a biodegradable polymer that is produced by bacteria and archaea as carbon and energy reserves. Due to its rapid degradation in natural environments, it can be considered a biodegradable plastic alternative. In the present study, a dye-based procedure was used to screen PHB-producing bacteria isolated from mangrove soil samples. Among the seven isolates, Agromyces indicus (A. indicus), identified by means of 16S rRNA analysis, accumulated the highest amount of PHB. The extracted polymer was characterized by a UV–Vis spectrophotometer, Fourier-transform infrared (FTIR) spectroscopy, and for the presence of the phbB gene, which confirmed the structure of the polymer as PHB. The maximum PHB production by A. indicus was achieved after 96 h of incubation at a pH of 8.0 and 35 °C in the presence of 2% NaCl, with glucose and peptone as the carbon and nitrogen sources, respectively. The strain was found to be capable of accumulating PHB when various cheap agricultural wastes, such as rice, barley, corn, and wheat bran, were used as the carbon sources. The response surface methodology (RSM) through the central composite design (CCD) for optimizing the PHB synthesis was found to be highly efficient at augmenting the polymer yields. As a result of the optimum conditions obtained from the RSM, this strain can increase the PHB content by approximately 1.4-fold when compared with an unoptimized medium, which would substantially lower the production cost. Therefore, the isolate A. indicus strain B2 may be regarded as one of the best candidates for the industrial production of PHB from agricultural wastes, and it can remove the environmental concerns associated with synthetic plastic.

With rapid urbanization and industrialization, rural rivers in China are facing deterioration in water quality and ecosystem health. Microorganisms living in river sediments are involved in biogeochemical processes, mineralization, and degradation of pollutants. Understanding bacterial community distribution in rural rivers could help evaluate the response of river ecosystems to environmental pollution and understand the river self-purification mechanism. In this study, the relationship between characteristics of sediment microbial communities and the surrounding environmental factors in a typical rural river was analyzed using 16S rRNA gene sequencing technology. The results showed that the dominant bacterial groups in the river sediment were Proteobacteria , Actinobacteria , Chloroflexi , Acidobacteria , Bacteroidetes , and Firmicutes , accounting for 83.61% of the total microbial load. Different areas have different sources of pollution which give rise to specific dominant bacteria. The upstream part of the river flows through an agricultural cultivation area where the dominant bacteria were norank_f_Gemmatimonadaceae , Haliangium , and Pseudolabrys , possessing obvious nitrogen- and phosphorus-metabolizing activities. The midstream section flows through an urban area where the dominant bacteria were Marmoricola , Nocardioides , Gaiella , Sphingomonas , norank_f_67-14 , Subgroup_10 , Agromyces , and Lysobacter , with strong metabolizing activity for toxic pollutants. The dominant bacteria in the downstream part were Clostridium_sensu_stricto_1 , norank_f__Bacteroidetes_vadinHA17 , Candidatus_Competibacter , and Methylocystis . Redundancy analysis and correlation heatmap analysis showed that environmental factors: ammonia nitrogen (NH 4 + –N) and total nitrogen (TN) in the sediment, and pH, temperature, TN, electrical conductivity (EC), and total dissolved solids (TDS) in the water, significantly affected the bacterial community in the sediment. The PICRUSt2 functional prediction analysis identified that the main function of bacteria in the sediment was metabolism (77.3%), specifically carbohydrate, amino acid, and energy metabolism. These activities are important for degrading organic matter and removing pollutants from the sediments. The study revealed the influence of organic pollutants derived from human activities on the bacterial community composition in the river sediments. It gave a new insight into the relationship between environmental factors and bacterial community distribution in rural watershed ecosystems, providing a theoretical basis for self-purification and bioremediation of rural rivers.

Considerable efforts that isolate and characterize degrading bacteria for polycyclic aromatic hydrocarbons (PAHs) have focused on contaminated environments so far. Here we isolated three distinctive pyrene (PYR)-degrading bacteria from a paddy soil that was not contaminated with PAHs. These included a novel Bacillus sp. PyB-9 and efficient degraders, Shigella sp. PyB-6 and Agromyces sp. PyB-10. All three strains could utilize naphthalene, phenanthrene, anthracene, fluoranthene and PYR as sole carbon sources, and degraded PYR in a range of temperatures (27–37 °C) and pH (5–8). Strains PyB-6 and PyB-10 almost completely degraded 50 mg L−1 PYR within 15 days, and 75.5% and 98.9% of 100 mg L−1 PYR in 27 days, respectively. The kinetics of PYR biodegradation was well represented by the Gompertz model. Ten and twelve PYR metabolites were identified in PYR degradation process by strains PyB-6 and PyB-10, respectively. Chemical analyses demonstrated that the degradation mechanisms of PYR were the same for strains PyB-6 and PyB-10 with initial dioxygenation mainly on C-4,5 positions of PYR. The degradation of 4,5-phenanthrenedicarboxylic acid was branched to 4-phenanthrenecarboxylic acid pathway and 5-hydroxy-4-phenanthrenecarboxylic acid pathway, both of which played important roles in PYR degradation by strains PyB-6 and PyB-10. To our knowledge, Shigella sp. and Agromyces sp. were found for the first time to possess the capability for PAHs degradation. These findings contributed to upgrading the bank of microbial resource and knowledge on PAH biodegradation.

Bacterial community and diversity in a long-term petroleum-contaminated soil of an oilfield were characterized using 16S rRNA gene-based Illumina MiSeq high-throughput sequencing. Results indicated that Proteobacteria (49.11%) and Actinobacteria (24.24%) were the most dominant phyla, and the most abundant genera were Pseudoxanthomonas (8.47%), Luteimonas (3.64%), Alkanindiges (9.76%), Acinetobacter (5.26%) and Agromyces (8.56%) in the soil. Meanwhile a series of cultivations were carried out for isolation of alkane degraders from petroleum-contaminated soil with gellan gum and agar as gelling agents. And the isolates were classified by their 16S rRNA genes. Nine of the isolates including Enterobacter, Pseudomonas,Acinetobacter, Rhizobium, Bacillus, Sphingomonas, Paenibacillus, Variovorax and Rhodococcus showed strong biodegradability of alkane mixture (C9–C30) in a wide range of chain-length, which could be potentially applied in enhancement of bioremediation.

A variety of plants growing on metalliferous soils accumulate metals in their harvestable parts and have the potential to be used for phytoremediation of heavy metal polluted land. There is increasing evidence that rhizosphere bacteria contribute to the metal extraction process, but the mechanisms of this plant-microbe interaction are not yet understood. In this study ten rhizosphere isolates obtained from heavy metal accumulating willows affiliating with Pseudomonas, Janthinobacterium, Serratia, Flavobacterium, Streptomyces and Agromyces were analysed for their effect on plant growth, Zn and Cd uptake. In plate assays Zn, Cd and Pb resistances and the ability of the bacteria to produce indole-3-acetic acid (IAA), 1-amino-cyclopropane-1-carboxylic acid deaminase (ACC deaminase) and siderophores were determined. The isolates showed resistance to high Zn concentrations, indicating an adaptation to high concentrations of mobile Zn in the rhizosphere of Salix caprea. Four siderophore producers, two IAA producers and one strain producing both siderophores and IAA were identified. None of the analysed strains produced ACC deaminase. Metal mobilization by bacterial metabolites was assessed by extracting Zn and Cd from soil with supernatants of liquid cultures. Strain Agromyces AR33 almost doubled Zn and Cd extractability, probably by the relase of Zn and Cd specific ligands. The remaining strains, immobilized both metals. When Salix caprea plantlets were grown in γ-sterilized, Zn/Cd/Pb contaminated soil and inoculated with the Zn resistant isolates, Streptomyces AR17 enhanced Zn and Cd uptake. Agromyces AR33 tendentiously promoted plant growth and thereby increased the total amount of Zn and Cd extracted from soil. The IAA producing strains did not affect plant growth, and the siderophore producers did not enhance Zn and Cd accumulation. Apparently other mechanisms than the production of IAA, ACC deaminase and siderophores were involved in the observed plant-microbe interactions.

Background The midgut microbiota of mosquitoes maintain basal immune activity and immune priming. In recent years, scientists have focused on the use of microbial communities for vector control interventions. In the present study, the midgut bacteria of larvae and adults of Aedes aegypti and Ae. albopictus were assessed using both field-collected and laboratory-reared mosquitoes from Sri Lanka. Methods Adults and larvae of Ae. aegypti and Ae. albopictus were collected from three selected areas in Gampaha Medical Officer of Health area, Gampaha District, Western Province, Sri Lanka. Bacterial colonies isolated from mosquito midgut dissections were identified by PCR amplification and sequencing of partial 16S rRNA gene fragments. Results Adults and larvae of Ae. aegypti and Ae. albopictus harbored 25 bacterial species. Bacillus endophyticus and Pantoea dispersa were found more frequently in field-collected Ae. aegypti and Ae. albopictus adults, respectively. The midgut bacteria of Ae. aegypti and Ae. albopictus adults ( X 2  = 556.167, df  = 72, P  < 0.001) and larvae ( X 2  = 633.11, df  = 66, P  < 0.001) were significantly different. There was a significant difference among the bacterial communities between field-collected adults ( X 2  = 48.974, df  = 10, P  < 0.001) and larvae ( X 2  = 84.981, df  = 10, P  < 0.001). Lysinibacillus sphaericus was a common species in adults and larvae of laboratory-reared Ae. aegypti. Only P. dispersa occurred in the field-collected adults of Ae. aegypti and Ae. albopictus . Species belonging to genera Terribacillus , Lysinibacillus , Agromyces and Kocuria were recorded from Aedes mosquitoes, in accordance with previously reported results. Conclusions This study generated a comprehensive database on the culturable bacterial community found in the midgut of field-collected ( Ae. aegypti and Ae. albopictus ) and laboratory-reared ( Ae. aegypti ) mosquito larvae and adults from Sri Lanka. Data confirm that the midgut bacterial diversity in the studied mosquitoes varies according to species, developmental stage and strain (field vs laboratory). Graphical abstract

Background Soil contamination with metal(loid)s and organic pollutants creates environmental and health concerns, driving the need for sustainable remediation strategies. Organic amendments can mitigate contamination effects, enhancing soil quality, and potentially increasing biomass production; however, their long-term influence remains an open question. In a five-year field experiment at a former wood-preservation site, this study evaluates the effects of five organic amendments—fresh pig manure (PM), biodigested pig manure (PD), compost (C), compost pellets (Pt), and green waste compost (G)—on Cu-contaminated soils. Here, we evaluated their impacts on physico-chemical soil properties, metal bioavailability, microbial community structure, plant growth and soil fertility. Results All amendments led to an overall soil improvement, including enhanced physico-chemical properties, increased enzyme activities. The amendments promoted the concentration of soil 16S bacterial genes and improved the yield of winter barley cultivated in the plots. The most abundant phyla detected across soil samples were Actinobacteriota , Proteobacteria , and Firmicutes , with Bacillus , Streptomyces , and Bradyrhizobium among the dominant genera. Compost-based amendments at 5% w/w addition rate (C5 and Pt5) showed the most promising results, significantly increasing soil carbon, nitrogen, and phosphorus contents, while reducing bioavailability of Cd, Ni, Pb, and Zn compared with untreated control plots ( p  < 0.01). A decrease in Cu availability was observed but it was not significant. The Pt5 soils exhibited the highest 16S rRNA gene copy number ( p  < 0.01). Both compost and compost pellets amendments enriched microbial communities associated with soil quality and plant yield, leading to significant improvements in soil fertility and barley yield (+ 200% on average). Conclusion This integrative approach identified organic amendments, notably compost and pelleted compost, that effectively contribute to soil remediation from multiple perspectives: chemical properties (pH, organic content, nutrients), reduction of bioavailable soil Cd and Zn, enzyme activities, microbial abundance and diversity (16S rRNA), and winter barley yield. The study evidenced signature biomarkers characteristic of healthy soils ( Paenibacillus , Lysinibacillus , and Agromyces ) and polluted soils ( Candidatus Solibacter and Mycobacterium ). Our findings support the use of compost (raw and pelleted) as a balanced approach for phyto-managing metal-contaminated soils, reducing 1 M NH 4 NO 3 -extractable soil Cd and Zn while enhancing microbial activity and soil fertility. Graphical Abstract

Transgenic Bacillus thuringiensis (Bt) rice extends significant protection against insect pests and meets the increasing demands for food and energy. Many studies have been conducted investigating the impacts of Bt rice to the agricultural ecosystem, but much less attention has been given to efforts attempting to determine how the presence of Bt rice influences and shapes the microbial community, especially the active microbes. Stable isotope probing and high-throughput sequencing were employed to explore the active microbes involved in Bt-containing straw decomposition. Compared to its near isoline, the Bt straw contained higher contents of total N, total P, total K, lignin, cellulose, and Cry1Ab toxin protein. These chemical differences did not affect the decomposition rate but significantly changed the active microbial decomposer communities. During the decomposition of Bt-containing straw, fungi were more affected than bacteria. Agromyces, Terrabacter, Microbacterium, Glycomyces, and Kribbella were the most representative unique (existed only in the Bt treatments and appeared at the early stage) bacterial genera, and Trichoderma was the most representative unique fungal genus in the Bt straw decomposition. By using similarity index calculation and function prediction, the significant differences between Bt straw and non-Bt straw treatments were found to be transient for both microbial taxa and functional traits. These results suggested that Bt rice has a significant but transient impact on soil microbes in terms of microbial straw decomposition.

At deep-sea hydrothermal vents, sulfur oxidation and iron oxidation are of the highest importance to microbial metabolisms, which are thought to contribute mainly in chemolithoautotrophic groups. In this study, 17 mixotrophic neutrophilic thiosulfate- and iron-oxidizing bacteria were isolated from hydrothermal fields on the Carlsberg Ridge in the Indian Ocean, nine to the γ-proteobacteria (Halomonas (4), Pseudomonas (2), Marinobacter (2), and Rheinheimera (1)), seven to the α-proteobacteria (Thalassospira, Qipengyuania, Salipiger, Seohaeicola, Martelella, Citromicrobium, and Aurantimonas), and one to the Actinobacteria (Agromyces), as determined by their 16S rRNA and genome sequences. The physiological characterization of these isolates revealed wide versatility in electron donors (Fe(II) and Mn(II), or thiosulfate) and a variety of lifestyles as lithotrophic or heterotrophic, microaerobic, or anaerobic. As a representative strain, Pseudomonas sp. IOP_13 showed its autotrophic gowth from 105 cells/ml to 107 cells/ml;carbon dioxide fixation capacity with the δ13CVPDB in the biomass increased from −27.42‰ to 3460.06‰; the thiosulfate-oxidizing ability with produced SO42− increased from 60 mg/L to 287 mg/L; and the iron-oxidizing ability with Fe(II) decreased from 10 mM to 5.2 mM. In addition, iron-oxide crust formed outside the cells. Gene coding for energy metabolism involved in possible iron, manganese, and sulfur oxidation, and denitrification was identified by their genome analysis. This study sheds light on the function of the mixotrophic microbial community in the iron/manganese/sulfur cycles and the carbon fixation of the hydrothermal fields.