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High-level terpene production via a novel Actinomycetota-derived MVA pathway in E. coli.

The heterologous production of terpene in microbial hosts is often limited by inefficient and unstable pathway expression, creating a major bottleneck for industrial-scale synthesis. While E. coli as a chassis offers significant advantages, such as rapid growth, ease of cultivation, and genetic tractability. Its endogenous supply of terpenoid precursors remains a critical constraint, fundamentally restricting high-yield production. To address this challenge, we developed a genomically integrated Mevalonate (MVA) pathway from Actinomycetota in E. coli BL21(DE3) to enhance terpene precursor supply. Our approach began with an in silico multi-layer global genome mining analysis of 25,261 Actinomycetota genomes to identify a series of MVA pathway enzymes with potentially high catalytic efficiency, created a high-efficiency chassis E. coli MVA platform (ecMVA-1 and ecMVA-2) for terpene precursor synthesis. Its functionality was validated by testing eight distinct TSs. Among them, the fermentation of artemisinin precursor amorphadiene using a 5-liter bioreactor yielded 947.80 mg/L. These results indicated that E. coli (MVA) is well-suited for TS studies in the laboratory as well as holding significant promise for industrial applications. In addition, this in silico approach offers a new perspective for metabolic engineering and provides potential reservoir of diverse chassis for the industrial production of terpenoid-derived compounds.

Actinomycetota

Rhodoglobus galactosidasius sp. nov., a psychrophilic Actinomycetota producing a cold-active β-galactosidase isolated from Cape Hallett, Antarctica.

A novel psychrophilic member of the phylum Actinomycetota, designated strain CPHL_1T, was isolated from the shoreline of Cape Hallett, Antarctica. Cells were Gram-positive, aerobic, non-motile, non-spore-forming rods (0.7-1.0 µm in length) with orange to yellow pigmentation. Optimal growth occurred at 15 °C, pH 8.0, with NaCl tolerance up to 3% (w/v). Strain CPHL_1T exhibited cytosolic cold-active β-galactosidase activity, with an optimum at 15 °C and pH 7.0 and formed non-adherent biofilms. Phylogenetic analysis based on 16S rRNA gene sequence placed the strain within the genus Rhodoglobus, showing high similarity to Rhodoglobus vestalii LV3T (99.4%) and Rhodoglobus aureus CMS 81yT (97.6%). Chemotaxonomic characteristics, including the predominance of anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 fatty acids, the presence of MK-11, MK-10 and MK-12 as the major respiratory quinones, and genomic G+C content of 60%, further supported its assignment to the genus Rhodoglobus. Whole-genome comparisons revealed clear taxonomic distinction, with strain CPHL_1T sharing 88.9% average nucleotide identity (ANI) and 38.3% digital DNA-DNA hybridization (dDDH) values with R. aureus, and 81.7% ANI and 25.1% dDDH with R. vestalii, confirming its status as a novel species. Phylogenetic analysis revealed that the β-galactosidases from these Rhodoglobus strains form a well-supported clade with high sequence similarity. Based on these data, a novel species is proposed: Rhodoglobus galactosidasius sp. nov. (type strain CPHL_1T =ITEM 19986T =KCTC 59592T). Genomic analyses also highlighted its biosynthetic potential for specialized metabolites, consistent with the recognized metabolic diversity of the genus.

Phylogeny

Fast-growing Bacillus sensu lato rhizosphere populations are constrained by antagonistic Pseudomonadota, Actinomycetota and other Bacillus sensu lato.

Copiotrophic Bacillus and related taxa grow rapidly and are commonly isolated from soil. Despite their growth rate, Bacillus sensu lato (BSL) constitute less than one percent of soil bacterial communities, and the nutrient-enriched rhizosphere contains even fewer. Amendment of bulk soil with synthetic root exudate did not lead to increase in Bacillus culturable counts. We hypothesized that BSL populations in soil enriched with growth-supporting carbon are suppressed by various soil microbes. A screen using B. pseudomycoides as tester strain yielded 124 growth inhibiting isolates, aligning by 16S rRNA genes to 3 Alphaproteobacteria, 6 Betaproteobacteria, 5 Gammaproteobacteria, 3 Streptomyces, and 19 Bacillaceae. Most antagonists also suppressed four other BSL, and over 70% of the BSL isolates suppressed each other. The 11 sequenced BSL genomes encoded between 2 and 10 antibiotic biosynthetic gene clusters. Incubation of multiple isolates in artificial soil microcosms resulted in population growth restraint through a high percentage of endospores formed. This indicated that growth suppression by antagonists was due primarily to induction of sporulation. These results support our hypothesis that Bacillus populations in soil enriched with growth-supporting carbon are suppressed by various soil microbes.

Bacillus

Exploration of the antibacterial function of the Eutherian LEG1s.

Liver-enriched gene 1 (LEG1) encodes a novel protein family whose functions are not fully explored. LEG1 was first reported and characterized in zebrafish, where it encodes secreted proteins involved in liver development. In contrast, mammalian LEG1s exhibit a different expression pattern. The platypus monotreme lactation protein (platMLP) was uncovered in milk with antibacterial function. Studies in mouse and pig have shown that LEG1s are specifically expressed in the salivary glands; however, their function remains unclear. Evolutionarily, LEG1s are present in vertebrates and form three major clades, LEG1a, LEG1b, and LEG1c. Only a few invertebrates, protists, and bacteria retain LEG1 homologs, making the evolutionary origin of LEG1 obscure. In the current study, we conducted a thorough exploration of prokaryotic reference genomes and found that LEG1 predominantly exists in Actinomycetota. Given that Actinomycetota are well known for producing antibacterial compounds, and that platMLP can inhibit the growth of certain bacteria, we hypothesized that LEG1 is a conserved antibacterial protein. Recombinant LEG1s from each of the three clades were then purified and subjected to antibacterial tests, which showed that pig LEG1c and platMLP have divergent antibacterial activities. These findings support the hypothesis that the antibacterial function of LEG1 is conserved in eutherians but has undergone functional diversification following gene duplication events.

Animals

Discovery of Sphaeriaurantins as Rapid-Acting Antiplasmodials with Dual Activity in Blood and Liver Stages.

The rapid emergence of resistance in the malaria-causing protozoan Plasmodium falciparum has heightened the demand for treatments with novel modes of action. Having evolved to produce a myriad of structurally diverse natural products (NPs) as defenses against soil-dwelling parasites including protozoa, Actinomycetota strains are a promising source for the discovery of NPs as antiplasmodial drug leads. Herein, the selective inhibition of P. falciparum is reported for five distinct NP families from Actinomycetota, including an unprecedented family of glycosylated type II polyketides termed sphaeriaurantins (SPAs). The structures of SPAs were established through the combination of MS and NMR spectroscopic data analysis, derivatization and comparison of the deoxyhexose moieties to authentic standards, and quantum chemical calculations, including 1H and 13C NMR chemical shifts and electronic circular dichroism (ECD) spectra. The three isolated SPA congeners reveal that the characteristic pseudodimeric structure of the SPA family of NPs, likely introduced at a late stage of the SPA biosynthesis, is highly relevant for the observed low nanomolar activity. SPA A exhibits a rapid killing profile, with activities across all intraerythrocytic stages, and potent liver stage efficacy, as well as a low propensity for resistance development. Taken together, these results suggest a mode of action that most likely is distinct from the existing antimalarials, supporting SPA A as a promising antimalarial drug lead for further development.

Plasmodium falciparum

The selective culture and enrichment of major rumen bacteria on three distinct anaerobic culture media.

Ruminants play an important part in global food security, but also emit methane, which contributes to global warming. Rumen microbes strongly influence the energy retention efficiency from the host's plant-based diet and produce methane as a by-product. While thousands of novel microbial genomes have been assembled from metagenomic sequence data, their culturability is ill-defined. Here, different media (Med10, Med2, and MedTC) were used to isolate co-cultures of microbes from rumen fluid. Thirty-four OTUs were identified belonging to the phyla Bacillota (75.28 ± 6.34%), Bacteroidota (19.99 ± 4.85%), Pseudomonadota (2.46 ± 2.01%), and Actinomycetota (2.09 ± 1.07%). The most abundant genera were Selenomonas (28.08 ± 11.71%), Streptococcus (22.67 ± 6.06%), Prevotella (18.71 ± 4.02%), and unclassified Lachnospiraceae (11.50 ± 2.54%), and 31 significantly enriched on at least one medium, with each medium successfully culturing a distinct range of microbes. The composition of the source rumen fluid was vastly different from those cultured. Bacteroidota (52.53 ± 5.10%) predominated, with Bacillota (41.00 ± 3.96%), Methanobacteriota (5.12 ± 1.94%), Pseudomonadota (1.22 ± 0.78%), and Actinomycetota (0.12 ± 0.08%) comprising the rest. The most abundant genera were Prevotella (29.13 ± 4.16%), Butyrivibrio (18.21 ± 2.08%), Succiniclasticum (15.57 ± 5.03%), unclassified Bacteroidetes (13.91 ± 1.67%), and unclassified Prevotellaceae (9.50 ± 2.01%). These data further emphasize the importance of using defined media to select for different microbial taxa. This is essential to understand the complex workings of the rumen microbes to enhance digestion efficiency and reduce the loss of energy that could potentially be utilized by the host.IMPORTANCEThis research demonstrates that using a range of culture media, containing a wide variety of substrates, can lead to the culture of key rumen microbes. The knowledge of which of these microbes is selectively enriched on each medium is essential to understand how to grow these microbes in co-culture and isolate them in pure culture for further investigation. In addition, this research shows the stark disparity between the population of rumen microbes grown in co-culture and those found in the rumen itself. This further demonstrates the need for a targeted approach to growing and isolating these microbes. Learning how these microbes respond to culture media with different nutritional compositions will lead to a better understanding of the rumen microbiota, and this research provides a valuable insight into how selective media can target the enrichment of different microbes. This knowledge will contribute to increasing ruminant digestion efficiency and reducing methane production.

Rumen

Microbial decaprenoxanthin: From understanding an extremophile-derived C50 carotenoid to its bioprocessing for large-scale applications.

Decaprenoxanthin (DPXT) is an unusual bacterial C50 carotenoid that has historically received limited attention despite its well-defined structure. For decades, carotenoid research and industrial development have been dominated by C40 carotenoids, leaving longer-chain carotenoids largely overlooked. Recent discoveries, particularly from microorganisms inhabiting Antarctic and other extreme environments, have repositioned DPXT as an adaptive pigment shaped by intense environmental pressures. Its extended polyene chain and membrane-associated behavior suggest roles in membrane stabilization and protection against ultraviolet radiation and oxidative stress, features that may hold relevance for food and biotechnological applications. This review integrates historical and recent knowledge on DPXT, covering its structural characteristics, biosynthetic pathways, ecological function, and emerging technological relevance. Special attention is given to microbial sources, particularly Actinomycetota from extreme environments, and to recent advances in microbial genomics, metabolic engineering, and sustainable bioprocess development that enable the production and exploration of C50 carotenoids beyond their native extremophilic context. The analysis highlights DPXT as a representative example of stress-resilient carotenoids, with physicochemical and membrane-interacting properties that may offer advantages for future food and biotechnological systems. Although significant challenges remain in cultivation strategies, yield optimization, and downstream recovery, advances in microbial cell factories and green extraction technologies open new opportunities for valorizing C50 carotenoids. This review bridges extremophile microbiology, carotenoid biochemistry, and sustainable food innovation, positioning DPXT as an emerging molecule that may expand the functional and structural landscape of carotenoids relevant to food science.

Carotenoids

Manipulation of rhizosphere microbiome by Microbacterium sp. GB16_1_BI to promote plant growth.

AIM: The bioinoculant properties of a newly identified ammonium-releasing novel strain of Actinomycetota-Microbacterium bengalense sp. nov. GB16_1_BI (Accession number: SRX9280401) on the microbiome structure of rice rhizosphere were assessed. METHODS AND RESULT: GB16_1_BI may inhibit most bacteria present in the rice rhizosphere as well as encouraged the growth of rare bacteria specific to the waterlogged rice rhizosphere. The genome sequence as well as untargeted metabolome analyses of GB16_1_BI showed abundance of secondary metabolites with probable antimicrobial activity. Amplicon sequencing of the 16S rRNA V3-V4 region from the rhizosphere of the black rice showed inhibition of most bacteria by GB16_1_BI. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) analysis showed increased abundance in the marker genes for nitrogen cycling (nifH, nrfA, and nrt) but not for nifD or nifK, which was also reflected in the ANOSIM analysis in the OTUs of the N-fixing bacteria. Higher abundance of the nitrogen-fixing methanotrophs, Methylosinus and Methylocystis in inoculated plants also led to study of the marker genes for methane metabolism. CONCLUSION: Microbes present in the rhizosphere contribute to the biogeochemical cycle by transforming unavailable minerals and by retaining nutrients for their growth, which get released after death for plant adsorption. However, not all microbes contribute positively to plant growth. Microbes compete with plants for nutrients, cause disease, or produce harmful greenhouse gases. Hence, GB16_1_BI could influence plant growth predominantly by suppressing microbes and encouraged niche-specific microbes specifically involved in nitrogen cycling.

Rhizosphere

Species-specific structuring of gut bacterial and fungal communities in honey bees Apis cerana and Apis mellifera.

Honey bee gut microbiome studies have primarily emphasized bacteria, leaving fungal communities comparatively overlooked despite their ecological and functional importance. Whole-genome shotgun metagenomics of Apis cerana and Apis mellifera revealed fungal assemblages dominated by Ascomycota, with Basidiomycota and Microsporidia in minor proportions, alongside gut bacterial communities composed mainly of Pseudomonadota, Bacillota, and Actinomycetota. The bacterial diversity was markedly higher in A. mellifera (Shannon = 5.90; Simpson = 0.98) than in A. cerana (Shannon = 4.01; Simpson = 0.94; p > 0.05), while fungal diversity remained comparable between species (p > 0.05). Beta-diversity analyses revealed strong host-specific clustering for both bacterial (PERMANOVA R2 = 0.7989, p > 0.05) and fungal communities (R2 = 0.7218, p > 0.05), indicating distinct microbial organization driven by host species. Bacterial-fungal co-occurrence patterns exhibited host-specific structuring, suggesting differential inter-kingdom community organization between A. cerana and A. mellifera. Linear Discriminant Analysis Effect Size (LEfSe) identified 93 discriminatory fungal taxa (45 enriched in A. cerana, 48 in A. mellifera), highlighting yeast-dominated signatures in A. mellifera and Basidiomycota-affiliated enrichments in A. cerana. KEGG and CAZy profiling revealed host- and kingdom-specific functional differences, with bacterial communities of A. mellifera showing distinct representation of carbohydrate metabolism and nutrient-cycling functions, while fungal communities exhibited a comparatively narrower functional repertoire. Together, these findings provide a high-resolution view of honey bee bacterial and fungal microbiomes, highlighting strong host-driven divergence in taxonomy, function, and cross-kingdom interactions.

Animals

Genomic and biosynthetic landscape of high-temperature Daqu microbiome.

As the core starter for Chinese Baijiu, high-temperature Daqu is produced through open solid-state fermentation with recurrent inoculation by mature Daqu, forming a rich yet largely untapped reservoir of genomes and bioactive compounds. This study constructs the High-temperature Daqu Fermentation Microbiome catalog using 463 metagenomes spanning the full fermentation cycle. The catalog comprises 4,264 metagenome-assembled genomes that are dereplicated into 252 representative genome-based species, 82 % of which are absent from current global food microbiome databases. It further contains 14.3 million non-redundant genes, of which 17.3 % are novel, and 17,031 biosynthetic gene clusters, of which 62.63 % are novel, thereby substantially expanding the known genomic and biosynthetic space of food microbiomes. Genome-resolved analyses revealed a U-shaped ecological trajectory, shifting from early Bacillus velezensis-enriched assemblages to transient dominance of lactic acid bacteria during peak thermogenesis, before returning in late fermentation to thermotolerant, spore-forming Bacillota and Actinomycetota. In parallel, biosynthetic potential was further organized into four recurrent, stage-enriched profiles, from RiPP-rich thermogenic states to mature-state assemblages enriched in PKS-, NRPS-, and terpene-related capacities, with Bacillus, Kroppenstedtia, and Saccharopolyspora constituting the principal biosynthetic reservoir. Together, this work uncovers a largely unexplored genomic and biosynthetic reservoir in high-temperature Daqu fermentation, providing a target resource for mining thermotolerant industrial enzymes, flavor-related genes, and bioactive metabolites with biotechnological potential.

Microbiota

Compost microbiomes as reservoirs of cellulolytic microorganisms for cellulosic textile degradation.

Cellulosic textiles, constituting over 30% of global fibre production, are biodegradable but remain challenging to recycle at scale owing to their high crystallinity, chemical finishes, and heterogeneous waste streams. Although microorganisms drive cellulose turnover in natural ecosystems, their potential for transforming anthropogenic cellulosic waste remains largely unexplored. In this study, composting was evaluated both as a sustainable approach to textile biodegradation and a reservoir of cellulolytic microorganisms with biotechnological potential. Biodegradation assays of cotton and lyocell were integrated with shotgun metagenomics and targeted cultivation to identify microbial taxa and enzymes involved in cellulose degradation. Composting trials showed that degradation was strongly influenced by both composting system and fibre composition. Community composting achieved near-complete textile disintegration, while shredded textiles exhibited the highest degradation rates, reaching up to 97%. Shotgun metagenomic revealed a bacterial-dominated community enriched in Actinomycetota and Bacillota and characterised by an abundance of glycoside hydrolases. Culture-based screening recovered 62 microbial isolates, of which Neurospora and Aspergillus exhibited the highest cellulolytic activity (>60%). In vitro assays further showed that cotton was more readily degraded than lyocell, with several isolates achieving >70% mass loss. Metagenomic approach revealed a predominantly bacterial composting community at the sampled stage, whereas cultivation preferentially recovered fungi that, despite their low relative abundance in situ, exhibited strong cellulolytic potential. These findings highlight the potential of composting as a sustainable end-of-life strategy for cellulosic textiles and identify compost microbiomes as valuable reservoirs of cellulolytic microorganisms for the development of sustainable bioprocesses for textile waste treatment.

Cellulose

Seawater type shapes larval development, intestinal microbiota, and water quality in Macrobrachium rosenbergii.

Giant freshwater prawn (Macrobrachium rosenbergii) has high economic value and extensive aquaculture prospects, and larval quality critically restricts the sustainable development of the industry. To investigate the effects of different seawater sources on larval survival and growth, artificial seawater, natural seawater from Beibu Gulf (China) and East China Sea (China) were used as culture media to compare their influences on larval development and intestinal microbiota of M. rosenbergii. Significant intergroup differences were observed in cultivation outcomes. The larval emergence rate reached the maximum value of 52.1% in Group G (Beibu Gulf natural seawater), followed by 43.57% in Group R (artificial seawater), and only 36.4% in Group Z (East China Sea natural seawater), indicating distinct larval emergence gaps and a gradual decline in larval development efficiency. Intestinal microbiota analysis indicated that Pseudomonadota, Actinomycetota and Bacillota were the dominant phyla in all three groups. The relative abundance of Bacillota increased significantly in Group G on day 10. LEfSe analysis proved that this group owned the most stable microbial structure and highest community diversity, and pronounced structural fluctuations occurred in Group R, suggesting that intestinal microbial profiles can reflect larval developmental conditions. Correlation analysis showed that gut microbial composition was closely correlated with water environmental parameters, and microbial metabolic pathways were strongly associated with larval growth and development. This study indicates that natural seawater from the Beibu Gulf of China is more suitable for healthy larval cultivation of M. rosenbergii. Structural stability and diversity of intestinal microbiota are key factors affecting larval growth. The results offer theoretical references for optimizing artificial seawater formula and improving larval rearing efficiency.

16S rRNA

Draft genome sequence data of Streptomyces antibioticus SCBA4 isolated from the Soils of Surigao del Sur, Philippines.

The draft genome of Streptomyces antibioticus SCBA4 isolated from the soils of Surigao del Sur, Philippines is reported here. S. antibioticus is a member of the phylum Actinomycetota, a diverse group of Gram positive, high G+C content bacteria well known for their production of a variety of bioactive compounds. Sequencing using the Illumina NovaSeq 6000 platform yielded a 8,616,999 bp genome across 36 contigs with 7621 coding sequences, 87 tRNA, and 1 tmRNA. Consistent with the members of the same phylum, the GC content was 71.83% and was found to contain putative gene clusters of secondary metabolites such as NRPs, terpenes and polyketides. The genome sequence has been deposited at NCBI under the accession number JBSWZT020000000.

Actinobacteria

Phyllosphere microbiomes in grassland plants harbor a vast reservoir of novel antimicrobial peptides and biosynthetic diversity.

INTRODUCTION: The phyllosphere microorganisms colonizing plant surface harbor capacities to synthesize diverse specialized metabolites that mediate communication and interactions with environment and host. However, most known metabolites are derived from a few culturable microorganisms, and the genomic diversity and biosynthetic potential of the vast majority of bacteria associated with plants remain largely unexplored. OBJECTIVES: Here, we aim to explore the genome architecture, biosynthetic ability, and host specific adaptability of grassland ecosystems, uncovering new perspectives on grassland phyllosphere microbial resources. METHODS: We employed ultra-deep metagenomic sequencing, functional analysis, host-associated characterization, and bioactivity assays to explore the phyllosphere microbiome across 221 grassland plant samples representing 45 families. This approach revealed host preference in biosynthetic gene clusters (BGCs) and validated the antimicrobial efficacy of phyllosphere-derived antimicrobial peptides (AMPs). RESULTS: Grassland plant phyllosphere microbiomes encode diverse BGCs. We identified 885,396 potential AMPs from over 68 million non-redundant gene sequences. Then, we reconstructed hundreds of near-complete genomes from phyllosphere metagenomes, and 32.61 % of reconstructed genomes were identified as unclassified genomes, primarily within Pseudomonadota, Actinomycetota, Bacillota and Bacteroidota phyla. Of the near-complete genomes, 91.97 % of the BGCs and 99.76 % of the identified AMPs were previously uncharacterized. Host phylogenetic analysis revealed functional divergence. Poaceae-associated Pseudomonas genomes contain an average of 28 BGCs, significantly higher than those in Asteraceae-associated genomes (mean = 14.76, P = 0.033). Similarly, Poaceae-associated Pantoea genomes carried an average of 9 BGCs, exhibiting significant enrichment compared to genomes from Asteraceae (mean = 7.13, P = 6.1e-05), Lamiaceae (mean = 7, P = 0.015), Ranunculaceae (mean = 8.22, P = 0.0053), and Rosaceae (mean = 7.75, P = 0.00069). ParaFit analyses further confirmed that host phylogeny significantly structures microbial functional repertoires, with intra-family hosts sharing more KEGG pathways than inter-family hosts. These results suggest that host evolutionary relationships are associated with metabolic specialization in phyllosphere microbiomes. All 13 AMPs synthesized via solid-phase peptide synthesis demonstrated antimicrobial activity, inhibiting the growth of at least one tested bacterial strain. CONCLUSION: This study demonstrates the promise of grassland plant phyllosphere microbiome as a rich source for novel antimicrobial agents.

Antimicrobial Peptides

Long-term petroleum pollution alters soil microbial communities via electron transfer capacity: Evidence from a 35-year chronosequence.

Petroleum pollution poses a serious threat to soil ecosystems, especially in areas surrounding oil wells, where contamination should not be overlooked. Through a 35-year longitudinal study of soils surrounding oil wells, we demonstrate that petroleum hydrocarbons accumulate predominantly in the top 10 cm of soil, reducing the electron acceptor capacity (EAC) by 61.59 % (from 12.68 to 4.87 μmole-/gC) and decreasing the electron transfer capacity (ETC) by 43 %. Structural equation modeling identified ETC as the critical mediator of microbial community shifts, with EAC playing a pivotal role in sustaining redox processes. Notably, hydrocarbon accumulation triggered a microbial succession: The abundance of Actinomycetota (including genera Rhodococcus, Arthrobacter, and Rubrobacter) showed the most significant fluctuations within 2 years, while Pseudomonadota (genera Methylobacter, Thiobacillus, and Pseudomonas), which were dominant in uncontaminated soils, decreased markedly during this period. This transition coincided with peak microbial dysbiosis (microbial dysbiosis index in 2022 reached 31.41 times that of controls). Within two to four years following mild petroleum stress, the bacterial community established a new structural configuration, revealing a crucial window for ecological recovery. The coupling between ETC reduction and microbial succession highlights the pivotal role of electron flux in soil recovery. Our findings establish a mechanistic framework for ETC-targeted restoration strategies to enhance bioremediation in petroleum-contaminated soils.

Soil Microbiology

Microplastic aging drives convergence of the plastisphere microbiome and resistome toward agricultural soils.

The degree of microplastic (MP) aging varies substantially in agricultural soils; however, how this common aging gradient influences the plastisphere microbiome and resistome remains largely unknown. We therefore collected polyethylene MPs from long‑term mulched farmlands and classified them into low‑aged plastispheres (LAPs) and high‑aged plastispheres (HAPs). Bacterial community dissimilarity to soil decreased progressively from LAPs to HAPs, accompanied by broadening niche breadth, increasing bacterial diversity, and a shift toward more stochastic community assembly. The diversity and abundance of antibiotic resistance genes (ARGs) declined significantly along the aging gradient, with clinically relevant high-risk ARGs (e.g., vanR, ugd, and aac(6')-I) decreasing by 53.34-84.01%. Furthermore, the ARG hosts shifted from Actinomycetota in LAPs to Pseudomonadota in soils. Variance partitioning showed that the carbonyl index uniquely explained 57.03% of the variation in plastisphere ARG profile distance toward soil, identifying MP aging as the primary driver of resistome convergence. Collectively, these findings demonstrate that natural MP aging drives a progressive convergence of the plastisphere resistome toward that of the surrounding soil, indicating that aged MPs may pose a reduced risk of antibiotic resistance compared to newly formed MPs. This convergence underscores the need to incorporate plastic aging into future risk assessment frameworks for plastisphere-associated ARGs.

Soil Microbiology

The Pseudomonas aeruginosa Type VI secretion system toxin Tse8 evolved from a novel N-carbamoylputrescine amidohydrolase.

The polyamine putrescine is synthesized primarily from L-arginine via agmatine in bacteria. There are currently three known routes from agmatine to putrescine, including direct conversion by agmatinase. The other two routes use agmatine deiminase to produce N-carbamoylputrescine from agmatine, then one of two nonhomologous enzymes, putrescine transcarbamylase or N-carbamoylputrescine amidohydrolase (NCPAH), converts N-carbamoylputrescine to putrescine. Here, we functionally identify enzymes from phylogenetically distant bacteria, the ɣ-proteobacterium Shewanella oneidensis, and the actinomycetota species Microterricola gilva, that are novel alternative, nonhomologous, noncanonical NCPAHs that we term AguY, which have emerged by convergent evolution. Kinetic analysis indicates that the AguY enzymes are as efficient as the canonical NCPAH from Pseudomonas aeruginosa in converting N-carbamoylputrescine to putrescine. Genomic evidence suggests that the AguY enzymes may participate in putrescine biosynthetic or agmatine catabolic pathways and are occasionally encoded in genomes that also encode agmatinase. We show that the Type VI secretion system toxin Tse8 from P. aeruginosa has evolved from AguY. It is formally possible that AguY evolved directly or indirectly from the ancient glutamine amidohydrolase GatA, a component of the transamidosome, an RNA/protein complex required for the production of glutamine-charged tRNA. Our study provides a further example of the prevalence of convergent evolution and horizontal gene transfer in polyamine biosynthesis, suggesting pervasive selective pressure to evolve polyamine metabolism in bacteria.

Pseudomonas aeruginosa

Eco-evolutionary dynamics sustain a potent yet rare antibiotic gene cluster in Streptomyces.

Microbial secondary metabolites have been recognized and utilized for nearly a century. Nevertheless, the eco-evolutionary mechanisms governing their distribution among microorganisms remain largely unresolved. In this study, we examined intraspecific interactions within Streptomyces albidoflavus and identified a strain exhibiting potent antagonistic activity against conspecifics. This "killer" phenotype was attributed to the production of kosinostatin, a hybrid aromatic polyketide antibiotic. Evolutionary genomic analyses provided strong evidence that the kosinostatin biosynthetic gene cluster was horizontally acquired in S. albidoflavus over a relatively short evolutionary timescale, a finding consistent with its sparse distribution within this species, across the genus Streptomyces, and even throughout the phylum Actinomycetota. Using microcosm assays, we demonstrated that the kosinostatin producer outcompeted sensitive conspecifics in liquid culture but not in soil, indicating that environmental context plays a key role in altering the fitness benefits of this cluster. Moreover, the competitive advantage was observed only in the presence of sensitive strains, revealing a trade-off between fitness benefits and metabolic costs. These results highlight the role of context-dependent selection in shaping the evolutionary persistence of the kosinostatin cluster. The current distribution pattern of this cluster in S. albidoflavus likely results from a dynamic interplay of intraspecific horizontal gene transfer, vertical inheritance, and recurrent gene loss. Overall, our findings establish an eco-evolutionary framework that explains the rarity of a potent antibiotic gene cluster in Streptomyces, illustrating how environmental constraints, fitness trade-offs, and gene flux collectively orchestrate the biosynthetic architecture of Streptomyces species.

Streptomyces