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Estrogens, particularly 17β-estradiol, are prevalent endocrine-disrupting chemicals in aquatic environments, posing risks to ecosystems and human health. Biodegradation is considered one of the most effective and environmentally friendly methods for removing estrogen. In this study, a novel bacterial strain, Microbacterium proteolyticum ZJSU01, was isolated from pig manure. It completely degraded 5 mg/L of 17β-estradiol (E2) within 4 h, as well as its major transformation product, estrone (E1). The strain ZJSU01 displayed strong adaptability to high temperatures (37℃, 42℃) and a broad pH range (6–11), E2 (5 mg/L) could be completely removed by the strain under these conditions. Transformation intermediates were analyzed using UHPLC and HPLC-Q-TOF–MS to identify key metabolites and trace the degradation pathways. Four potential degradation pathways were identified, including the 4,5-seco pathway, which is widely conserved in most E2-degrading bacteria. Whole-genome sequencing predicted a chromosome with a size of 3,828,432 bp, and a series of functional genes, and transcriptomics analysis identified several genes involved in E2 degradation. The budC gene, a member of the short-chain dehydrogenases/reductases (SDRs) family, was identified as critical for E2 degradation and exhibited a nearly 170-fold upregulation. Meanwhile, genes such as fdeE and catA were associated with downstream degradation. Microbacterium proteolyticum ZJSU01 demonstrated strong acid–base and high-temperature resilience, highlighting its strong potential for practical applications due to its degradation capability and adaptability. This strain could be applied in wastewater treatment to effectively remove estrogenic pollutants from contaminated water. Key points • Microbacterium proteolyticum ZJSU01 removed 100% of E2 (10、5、1 mg/L) within 4 h. • Strain ZJSU01 showed great tolerance to high temperature and acid–base conditions. • A novel gene, budC , was identified as the primary driver of E2 degradation by ZJSU01.

There are reports on resistance to metals by the Microbacteriaceae family, although few studies have focused on the Microbacterium genus. The present work is one of the first studies related to arsenic (As) resistance and removal by Microbacterium hydrocarbonoxydans . Growth curves were performed simultaneously as follows: (1) growth kinetics without As, and (2) growth kinetics added with As(III). Incubation conditions were at 30 °C and 120 rpm for 168 h, with an inoculation of bacterial culture, 107 (CFU)/ml. Absorbance was measured at 600 nm in an ultraviolet (UV)–vis spectrophotometer. The As surface adsorption and uptake into bacterial cells, exposed to As(III), were confirmed through SEM, EDX, and FTIR analyses. It was observed that the cellular morphology of M. hydrocarbonoxydans through TEM was deformed when exposed to high concentrations of arsenite. Bacterial cells growing in a rich medium with As(III) were able to oxidize 98% As(III), and the inactivated biomass of the bacterium exhibited a high removal capacity. Likewise, M. hydrocarbonoxydans was employed to test its ability to remove other toxic heavy metals such as lead, cadmium, and chromium. The order of resistance of each metal was as follows: Cr VI (2.08 gL −1 ) > Pb (1.24 gL −1 ) > Cd (0.169 gL −1 ). This work demonstrated that the strain M. hydrocarbonoxydans has high arsenic resistance and removal capacity, as well as significant As(III) oxidation potential, rendering it a promising candidate for biotechnological application in the development of affordable systems for the removal of metals/metalloids from contaminated sites.

Strain M28 T was isolated from subsoil obtained from decaying wheat straw. Cells were Gram-positive, non-motile, short rod-shaped and formed yellowish colonies on lysogeny broth (LB) agar. The strain was able to grow at 0–8% (w/v) NaCl , 15–40 °C and pH 5.5–10.0. Phylogenetic analysis based on 16S rRNA gene sequences, core genes and whole-genome indicated that strain M28 T belonged to the genus Microbacterium but was distinct from all known strains in this genus. Based on phenotypic, genotypic, chemical taxono mic and phylogenetic analyses, strain M28 T is a representative of a new species of Microbacterium , which is proposed to be named Microbacterium triticisoli sp. nov., the type strain is M28 T (=CCTCC AA 2022021 T =JCM 35796 T ). Genomic analysis revealed multiple metal resistance systems, antibiotic resistance determinants and oxidative stress defense genes, explaining its exceptional environmental adaptability. Notably, the strain reduced 99% of 50 mg/L Cr(VI) within 24 h under optimized conditions (37 °C, pH 7.0, 2.5 g/L sucrose) and tolerated Cr(VI) concentrations up to 125 mg/L. This study identifies M. triticisoli as a promising agent for chromium bioremediation, providing a foundation for engineering microbial solutions to heavy metal pollution.

Background Microbacterium paraoxydans is known for its potential in bioremediation and biotechnological applications, including promoting plant growth. However, research on this bacterium in Bangladesh has been limited and until now no reported complete genome of M. paraoxydans is available from this country. In this study, we have reported the complete genome of M. paraoxydans BHS25, the first case in Bangladesh, isolated from arsenic-contaminated soil in Bogura. Results Complete genome analysis revealed that BHS25 was closely related to Microbacterium paraoxydans LTR1 from Russia, which itself showed similarity to a strain found at the International Space Station, reported to be resistant to extreme conditions. BHS25 possessed a genome of 3.49 Mb with a GC content of 70.12%, comprising 3,415 protein-coding genes, 47 tRNA genes, and 5 rRNA genes. It carried various heavy metal resistance genes and gene islands, such as ars C, ars B, and acr 3 for arsenic detoxification/transformation, as well as czc D and cop B for resistance to cadmium, zinc, cobalt, and copper. The arrangement of the arsenic resistance genes showed similarity to that in other reported Microbacterium strains, although pangenome and ANI analyses indicated considerable genetic diversity within the species. Additionally, the presence of van Y within the van B cluster suggested potential vancomycin resistance. Metabolic pathway analyses revealed that BHS25 was well adapted, with different carbohydrate and amino acid metabolism, secondary metabolite biosynthesis, and xenobiotic degradation capabilities. The unique notable anabolic pathways were streptomycin biosynthesis with 14 associated genes, novobiocin biosynthesis and tropane , piperidine , and pyridine alkaloid biosynthesis (8 genes each), as well as monobactam biosynthesis , prodigiosin biosynthesis , and penicillin and cephalosporin biosynthesis , suggesting a potential for production of antimicrobials. Furthermore, it showed an auxin biosynthesis pathway for plant growth, further demonstrating its biotechnological potential. Conclusion This research identified Microbacterium paraoxydans BHS25 as a promising candidate for bioremediation and sustainable environmental management, offering insights into microbial adaptation to challenging environments and potential solutions for pollution encounters.

The genus Microbacterium in the phylum Actinomycetota contains over 100 species to date that little is known about their bioactive metabolites production. In this study, a mangrove sediment-derived strain B2969 T was identified as a novel type strain within the genus Microbacterium due to the low 16S rRNA gene sequence similarity (< 99%), and low overall genome relatedness indices (ANI, 75.4%-79.5%; dDDH, 18.5%-22.7%, AAI, 68.7%-76.3%; POCP, 48.3%-65.0%) with the validly named species of the genus. The type strain B2969 T (= MCCC 1K099113 T  = JCM 36707  T ) is proposed to represent Microbacterium alkaliflavum sp. nov.. The crude extracts of strain B2969 T showed weak cytotoxicity against NPC cell lines TW03 and 5-8F, with IC 50 values of ranging from 3.5 µg/µL to 2.4 µg/µL respectively. Genome analysis of strain B2969 T found 8 clusters of genes responsible for secondary metabolite biosynthesis, including cytotoxic compounds desferrioxamines. In addition, the application of liquid chromatography tandem mass spectrometry (LC–MS/MS)-based molecular networking strategy led to the identification of 10 compounds with potent cytotoxic activity in ethyl acetate extracts of strain B2969 T . Results from the cytotoxicity assay, genome mining, and metabolite profiling based on LC–MS/MS analysis revealed its ability to produce bioactive compounds. Background Mangrove ecosystems are largely unexplored sources of Actinomycetota , which represent potential important reservoirs of bioactive compounds. The genus Microbacterium in the phylum Actinomycetota contains over 100 species to date that little is known about their bioactive metabolites production. In this study, a novel species, namely B2969 T , within the genus Microbacterium that showed cytotoxicity against nasopharyngeal carcinoma (NPC) cell lines was isolated from mangrove sediments. Genome mining and metabolic profiling analyses were explored here to assess its biosynthetic potential of metabolites with cytotoxic properties. Results Here, a mangrove sediment-derived strain B2969 T was identified as a novel species within the genus Microbacterium due to the low 16S rRNA gene sequence similarity (< 99.0%), and low overall genome relatedness indices (ANI, 75.4%-79.5%; dDDH, 18.5%-22.7%, AAI, 68.7%-76.3%; POCP, 48.3%-65.0%) with the type strains of this genus. We proposed that strain B2969 T represents a new species, in which the name Microbacterium alkaliflavum sp. nov. is proposed. The strain showed weak cytotoxicity against NPC cell lines TW03 and 5-8F, with IC 50 values of ranging from 3.512 µg/µL to 2.428 µg/µL respectively. Genome analysis of strain B2969 T found 8 clusters of genes responsible for secondary metabolite biosynthesis, including desferrioxamines. In addition, the application of liquid chromatography tandem mass spectrometry (LC–MS/MS)-based molecular networking strategy led to the identification of 10 potent cytotoxic compounds in ethyl acetate extracts of strain B2969 T . Conclusions This study confirmed the taxonomy status of type strain B2969 T (= MCCC 1K099113 T  = JCM 36707  T ) within the genus Microbacterium , in which the name Microbacterium alkaliflavum sp. nov.. Results from the cytotoxicity assay, genome mining, and metabolite profiling based on LC–MS/MS analysis revealed its ability to produce bioactive substances, providing sufficient evidence for the potential of Microbacterium species in the discovery of novel pharmaceuticals.

A promising bacterial strain for biodegrading dibutyl phthalate (DBP) was successfully isolated from activated sludge and characterized as a potential novel Microbacterium sp. USTB-Y based on 16S rRNA sequence analysis and whole genome average nucleotide identity (ANI). Initial DBP of 50 mg/L could be completely biodegraded by USTB-Y both in mineral salt medium and in DBP artificially contaminated soil within 12 h at the optimal culture conditions of pH 7.5 and 30 ℃, which indicates that USTB-Y has a strong ability in DBP biodegradation. Phthalic acid (PA) was identified as the end-product of DBP biodegraded by USTB-Y using GC/MS. The draft genome of USTB-Y was sequenced by Illumina NovaSeq and 29 and 188 genes encoding for putative esterase/carboxylesterase and hydrolase/alpha/beta hydrolase were annotated based on NR (non redundant protein sequence database) analysis, respectively. Gene3781 and gene3780 from strain USTB-Y showed 100% identity with dpeH and mpeH from Microbacterium sp. PAE-1. But no phthalate catabolic gene (pht) cluster was found in the genome of strain USTB-Y. The results in the present study are valuable for obtaining a more holistic understanding on diverse genetic mechanisms of PAEs biodegrading Microbacterium sp. strains.

Microbacterium sp. C448, isolated from a soil regularly exposed to sulfamethazine (SMZ), can use various sulphonamide antibiotics as the sole carbon source for growth. The basis for the regulation of genes encoding the sulphonamide metabolism pathway, the dihydropteroate synthase sulphonamide target (folP), and the sulphonamide resistance (sul1) genes, is unknown in this organism. In the present study, the response of the transcriptome and proteome of Microbacterium sp. C448 following exposure to subtherapeutic (33 µM) or therapeutic (832 µM) SMZ concentrations was evaluated. Therapeutic concentration induced the highest sad expression and Sad production, consistent with the activity of SMZ degradation observed in cellulo. Following complete SMZ degradation, Sad production tended to return to the basal level observed prior to SMZ exposure. Transcriptomic and proteomic kinetics were concomitant for the resistance genes and proteins. The abundance of Sul1 protein, 100-fold more abundant than FolP protein, did not change in response to SMZ exposure. Moreover, non-targeted analyses highlighted the increase of a deaminase RidA and a putative sulphate exporter expression and production. These two novel factors involved in the 4-aminophenol metabolite degradation and the export of sulphate residues formed during SMZ degradation, respectively, provided new insights into Microbacterium sp. C448 SMZ detoxification process.

Microbacterium deferre sp. nov. A1-JK is a metabolically versatile Gram-positive bacterium isolated from the oxic-anoxic interface of freshwater sediments colonised by cable bacteria. Here, we report the metabolic ability of M. deferre A1-JK to simultaneously reduce oxygen and soluble Fe(III), challenging the long-standing paradigm that microbial Fe(III) reduction is restricted to anaerobic conditions. Electrochemical analyses demonstrate that M. deferre A1-JK is capable of extracellular electron transfer (EET) mediated by secreted flavins. It retains electroactivity under mildly alkaline and halophilic conditions, reflecting its broad environmental tolerance. Genomic analyses reveal a non-canonical system involving cytochrome FccA and flavin reductase FmnA, without the involvement of conventional flavin-based extracellular electron transfer (FLEET) components. The ability to couple oxygen and Fe(III) reduction under oxic conditions demonstrates respiratory flexibility, enabling M. deferre A1-JK to utilize both aerobic and anaerobic processes simultaneously in fluctuating environments. These findings offer insights into microbial adaptation to dynamic geochemical gradients and potentially explain strategies used by bacterial life during oxygenation of Earth's atmosphere.

C-glycosides have a unique structure, in which an anomeric carbon of a sugar is directly bonded to the carbon of an aglycone skeleton. One of the natural C-glycosides, carminic acid, is utilized by the food, cosmetic, and pharmaceutical industries, for a total of more than 200 tons/y worldwide. However, a metabolic pathway of carminic acid has never been identified. In this study, we isolated the previously unknown carminic acid-catabolizing microorganism and discovered a flavoenzyme “C-glycoside 3-oxidase” named CarA that catalyzes oxidation of the sugar moiety of carminic acid. A Basic Local Alignment Search Tool (BLAST) search demonstrated that CarA homologs were distributed in soil microorganisms but not intestinal ones. In addition to CarA, two CarA homologs were cloned and heterologously expressed, and their biochemical properties were determined. Furthermore, a crystal structure of one homolog was determined. Together with the biochemical analysis, the crystal structure and a mutagenesis analysis of CarA revealed the mechanisms underlying their substrate specificity and catalytic reaction. Our study suggests that CarA and its homologs play a crucial role in the metabolism of C-glycosides in nature.

Mesembryanthemum crystallinum L. (common ice plant) is an edible halophyte. However, if ice plants are used to phytoremediate salinity soil, there are problems of slow initial growth, and a long period before active NaCl uptake occurs under higher salinity conditions. Application of endophytic bacteria may improve the problem, but there remain gaps in our understanding of how endophytic bacteria affect the growth and the biochemical and physiological characteristics of ice plants. The aims of this study were to identify growth-promoting endophytic bacteria from the roots of ice plants and to document the metabolomic response of ice plants after application of selected endophytic bacteria. Two plant growth-promoting endophytic bacteria were selected on the basis of their ability to promote ice plant growth. The two strains putatively identified as Microbacterium spp. and Streptomyces spp. significantly promoted ice plant growth, at 2-times and 2.5-times, respectively, compared with the control and also affected the metabolome of ice plants. The strain of Microbacterium spp. resulted in increased contents of metabolites related to the tricarboxylic acid cycle and photosynthesis. The effects of salt stress were alleviated in ice plants inoculated with the endobacterial strains, compared with uninoculated plants. A deeper understanding of the complex interplay among plant metabolites will be useful for developing microbe-assisted soil phytoremediation strategies, using Mesembryanthemum species.