The filamentous actinomycete Actinomadura namibiensis has attracted increasing interest as the only known natural producer of the carbocyclic lantibiotic labyrinthopeptin A1, a secondary metabolite with a broad antiviral spectrum of activity. Developing a model of microbial growth and product formation at the pellet level requires a deeper mechanistic understanding of the interactions between cultivation conditions, substrate availability, and oxygen limitation. These factors influence the cultivation process and product formation. As part of this work, a predictive model in the form of diffusion-reaction equations is developed to quantitatively describe nutrient uptake, oxygen diffusion limitation, and pellet growth. This framework couples the consumption kinetics of carbon sources, such as glucose and glycerol, to pellet growth, maintenance metabolism, and the formation of the secondary metabolite labyrinthopeptin A1. The model is calibrated based on the results of multiscale experiments, i.e., offline analysis of shake flask cultures and oxygen profiling of pellets at different time points under various conditions. This forms the basis for understanding nutrient uptake, metabolic heterogeneity, and mass transfer limitations within the pellets. Thus, the model provides a quantitative basis for predicting productivity. The validated multiscale model reproduces the experimental results well and can be used to predict pellet growth, substrate uptake, and product formation.

Evolving genomic diversity of Mycobacterium tuberculosis complex pathogens is poorly known in French Polynesia, a remote archipelago in the southern Pacific Ocean. A total of 321 mycobacteria sampled from 321 patients presenting pulmonary tuberculosis between 1998 and 2010 at the microbiology laboratory of the French Polynesia Hospital Centre in Tahiti were whole genome sequenced (WGS), disclosing three major M. tuberculosis sensu stricto sublineages: L4.4.1.1 S-type, L4.1.1.3 X-Type, and L4.1.2.1 Haarlem. Furthermore, 20 isolates were identified as nontuberculous mycobacteria, including Mycobacterium fortuitum, which accounted for 65% of the identified nontuberculous mycobacteria, as well as Mycobacterium paragordonae and Mycobacterium gordonae identified with M. tuberculosis in two samples. Two further isolates were potentially representative of novel species in the Mycobacterium and Actinomadura genera. In total, 43 isolates exhibited in silico predicted antibiotic resistance to first- and second-line antibiotics. Combined with previously published data, the data reported here indicate a 12-year trend of decreasing diversity among the M. tuberculosis population circulating in Tahiti and the seemingly unsuccessful implantation of a recently imported of East African-Indian sublineage (L1.2.1.2.1). These findings contrast with the long-term persistence and predominance of the X-type family with L4.1.1.3; the S-type family with L4.4.1.1 and L4.4.2; the Haarlem family with L4.1.2 and L4.1.2.1, and the LAM family with L4.3.3, L4.3.2, and L4.3.4.2. These observations suggest that in remote territories such as the French Polynesia archipelago M. tuberculosis may rapidly adapt to local ecosystems.

The application of microbial inoculants during composting represents a promising strategy to mitigate antibiotic residues and antibiotic resistance genes (ARGs) in organic wastes. However, the dose-dependent effects of inoculation on antibiotic degradation and ARG fate remain poorly understood. This study investigated the impacts of low (0.03%, w/w; T2) and high (0.15%; T3) dosages of a microbial consortium on the fate of three antibiotic (oxytetracycline [OTC], ciprofloxacin [CIP], and sulfamerazine [SM1]) and their corresponding ARGs during 43-day sludge composting. Results showed that T2 achieved superior removal of all three antibiotics (78.62% for OTC, 78.73% for SM1, 42.83% for CIP) compared to T3 (72.31%, 73.24%, and 31.14%, respectively). However, ARG dynamics exhibited gene-specific responses: T2 unexpectedly caused poor sul2 removal (28.13%) and substantial tetX enrichment (657.61%), whereas T3 enhanced the removal of tetA (75.12%), tetG (59.06%), and intI1 (96.09%). In CK, T1, and T3, sul2 removal was efficient (91.2-95.9%). Mechanistic analyses revealed that T3's brief but intense thermophilic peak (65.2 °C for 8 days) potentially inactivated mesophilic degrading bacteria and reduced antibiotic bioavailability, while its stable enrichment of Bacillus and Actinomadura facilitated ARG host suppression. Degradation pathway analysis identified multiple intermediates for each antibiotic, confirming complex, multi-step transformation processes. Redundancy analysis and structural equation modeling identified temperature, Actinobacteria abundance, and MGEs as key drivers of ARG dynamics. These findings demonstrate that antibiotic removal and ARG attenuation are not necessarily coupled during composting, highlighting the critical need for optimizing inoculant dosage to simultaneously achieve efficient pollutant degradation and effective resistance control.

To enhance the quality of chicken manure and corn straw mixed compost, we evaluated the changes in physical, chemical indicators, and bacterial community diversity throughout the composting process. Three experimental groups were established with varying ratios of chicken manure to corn straw. The compost temperature was monitored daily, and samples were routinely collected to assess physical and chemical indicators. The results indicated that Group A (with a 6:4 ratio) entered the thermophilic phase earlier, sustained this phase for 20 days, exhibited faster organic matter degradation rates, and had a significantly higher total nutrient content by the end of composting compared to the other groups. The 16S rRNA high-throughput sequencing technology was utilized to investigate the alterations and distinctions in the bacterial community across 5 sampling layers of Group A samples on days 5, 15, 25 and 45. It was found that the diversity of bacterial communities initially increased, then decreased, followed by a slow increase and eventually stabilized. The predominant bacterial phyla during composting were Firmicutes, followed by Actinobacteria and Proteobacteria. The distribution ratio of bacteria in each sampling layer at each stage was small, while the main bacterial genera included Bacillus, Corynebacterium, Tepidimicrobium, Halocella, Planifilum, Luteimonas, and Actinomadura. Linear discriminant analysis revealed that the bacterial community with the greatest impact on organic matter degradation was the genus Bacillus (Firmicutes).

Evolutionary functional innovations can occur while gene families expand and two homologous (or analogous) genes co-occur. PriA is a dual-substrate enzyme family exclusive to Actinomycetota, with activities in l-histidine and l-tryptophan biosynthesis (HisA and TrpF activities) that evolved after the loss of the trpF gene. Since this gene loss, PriA has undergone multiple functional gain and loss events in central metabolism. Here, we report further evolutionary scenarios of PriA. First, in Ornithimicrobiaceae, a rare Actinomycetota family, PriA coexists with HisA, concomitant with the loss of its HisA but not TrpF activity, and is recruited in a physiological genome context. Second, a priA homologue, adeK, is located in the biosynthetic gene cluster of the specialized metabolites adechlorin and 2'-amino-2'-deoxyadenosine. The adeK gene is encoded in several genomes of the Streptosporangiaceae family and coexists with the expected and conserved priA. In this scenario, the PriA enzymes conserve both activities, whereas AdeK has only detectable levels of HisA activity, which might be related to specificity for a chlorinated intermediary during adechlorin biosynthesis. The adeK gene was first identified in strain ATCC-39365, previously designated as Actinomadura sp., but reclassified here as Nonomuraea sp. We further identified unprecedented adechlorin/2'-amino-2'-deoxyadenosine/pentostatin producers within the Microbispora and Streptosporangium genera. Phylogenomic analysis revealed additional recruitments of priA and hisG homologues into diverse uncharacterized biosynthetic gene clusters taxonomically related to the nucleoside antibiotics adechlorin, pentostatin and pyrazomycin. These findings highlight how enzyme family expansions and recruitment drive metabolic functional innovation in Actinomycetota, involving both gene loss and gain throughout central and specialized metabolism, and how evolutionary genome mining allows unbiased natural product discovery.

Coupling membrane-covered composting with vermicomposting is an emerging strategy for livestock manure management. However, crop straw, the conventional bulking agent, poses challenges due to inconsistent supply and slow biodegradation, prolonging the composting cycle. Therefore, identifying readily available and biodegradable alternative bulking agents is crucial. This study evaluated the effects of the solid fraction of cattle slurry (SCM), the solid fraction of pig slurry, and water hyacinth as alternative bulking agents on the combined composting process, using wheat straw as the control. The results demonstrated that SCM outperformed other bulking agents. Compared with the control, SCM not only increased cocoon production and average weight gain by 72.3% and 76.6%, respectively, but also maintained the highest survival rate and substrate reduction efficiency. Moreover, SCM enhanced lignin degradation and the humification index to 12.4% and 2.0, respectively. It also enhanced bacterial diversity and lignocellulose-degrading genera like Actinomadura. Additionally, SCM reduced copper content and bioavailability and improved final product quality, characterized by high total nutrient content (54.5 mg/g), low electrical conductivity (2.7 mS/cm), and low bulk density (0.3 g/cm[3]). Finally, SCM reduced greenhouse gas emissions (carbon dioxide equivalents) by 13.1% relative to the control group (P < 0.05). These findings provide theoretical support and technical guidance for livestock waste management and vermicomposting.

There is considerable interest in harnessing bacterial catabolic activities to valorize lignin-derived compounds. One such class of compounds, hydroxyphenylethanones (HPEs), includes acetovanillone (AV), 4-hydroxyacetophenone (HAP), and acetosyringone (AS). Despite occurring in various industrial streams of lignin, there are few reports on their microbiological degradation. Here, we report that Rhodococcus aromaticirovans RHA1 cometabolizes, but does not grow on, AV and HAP, converting them to 3,4-dihydroxyacetophenone (3,4-DHAP), a catechol with pharmacological properties. Molecular genetics studies revealed that AgcAB, a cytochrome P450 alkylguaiacol O-demethylase, catalyzes AV O-demethylation and AphAB, an alkylphenol hydroxylase, catalyzes HAP hydroxylation. Additionally, AV induced the expression of AgcA and the alkylcatechol extradiol dioxygenase, AphC. The specificity (kcat/KM) of AgcAB for AV was ~7% that of 4-propylguaiacol, while AphC cleaved 3,4-DHAP at ~8% the rate of 4-methylcatechol. We also compared the activity of HPE catabolic pathways from three strains by integrating their genes into RHA1. In resting cell assays, a strain expressing the hpe genes of Rhodococcus rhodochrous GD02 converted AV 43- and 97-fold faster than strains expressing pathways from Actinomadura macra sp. NBRC-14102 and Sphingobium lignivorans SYK-6, respectively. All three pathways preferentially converted AV and HAP over AS. However, the strain expressing the SYK-6 pathway had the highest relative activity for AS, 18% its activity on AV. The GD02 hpe genes enabled the growth of RHA1 on HPEs, and it grew faster on AV than on GD02. Overall, this work provides insight into the substrate preference of aromatic catabolic enzymes, highlights the value of cometabolism for biocatalysis, and facilitates the engineering of microbial cell factories to valorize HPEs.

A detailed chemical investigation of the Australian pasture soil-derived Actinomadura sp. S4S-00069B10, utilizing optimized cultivation on four different solid-phase media (M1, IMA, D400, and YEME), yielded the new isoindolinone goondicones I-K (1-3) and anthra-γ-pyrone cratermycins A-D (4-7). Structures were assigned to 1-7 on the basis of detailed spectroscopic, ECD, and X-ray analyses as well as chemical transformations and biosynthetic considerations. The goondicones 1-3 are especially noteworthy in that they feature an unprecedented carbo-heterocyclic framework, with 1 and 2 undergoing a facile keto-enol-mediated equilibration to a 1:3 mixture (of C-13 epimers) that exhibits promising anthelmintic properties against the dog heartworm Dirofilaria immitis microfilariae (EC50 1.1 μM) and L4 larvae (EC50 1.3 μM). Notably, this activity is accompanied by measurable mammalian cytotoxicity, indicating a narrow therapeutic window. Together, these findings highlight the chemical novelty of Actinomadura-derived metabolites, and their value as structurally unique anthelmintics leads to further optimization.

The excretion of the anthelmintic drug albendazole (ALB) from treated animals into the soil, as well as its widespread application as a fungicide, poses a serious ecological risk to the soil environment. In this study, we investigated the degradation of ALB in soil and its bioaccumulation in earthworms, changes in the microbiome and degradation genes, and the effect of zinc oxide nanoparticles on the degradation and enrichment behaviors of ALB and microbial community structure and function. Our findings showed that ALB selectively enriched specific albendazole degradation genes (i.e., hmr and ami) in the earthworm, preferentially activating the pathways associated with sulfur reduction, amination of ALB sulfone, and hydroxylation of ALB. Metagenomic analysis revealed that the relative abundances of ppo, xylA, cutC, and nfsl in the earthworm gut were 0.19-52.64-fold higher in the ALB treatment than in the control, indicating their potential dominance in ALB biodegradation. Network analysis further identified potential bacterial hosts carrying biodegradation genes and albendazole degradation genes. Notably, Sphaerobacter, Saccharothrix, Actinomadura, and Nocardia were recognized as potential dual hosts of biodegradation genes and albendazole degradation genes, displaying a 0.05-1.32-fold elevation in relative abundance in ALB-treated earthworm guts compared to the control. Additionally, ZnO nanoparticles were found to reduce ALB bioaccumulation in earthworms and accelerate its dissipation in soil. These findings provide novel insights into the bioremediation mechanisms of pesticides in soil-earthworm ecosystems.

A critical barrier to optimizing straw composting is the lack of a defined dose-response relationship between input and biosafety outcomes. Here this study investigated the effects of low (10%, carbon-to-nitrogen (C/N) ratio: 15), medium (30%, C/N ratio: 25) and high (50%, C/N ratio: 35) corn straw additions on pathogen elimination. By integrating eco-modeling and multi-omics, we quantified the microbial community contribution and explored their biological mechanisms. The medium addition ratio showed an optimal performance on pathogen elimination, achieving a 94.6% reduction in pathogen abundance without regrowth. Structural equation modeling indicated that microbial community composition (path coefficient: -0.638) surpassed thermal effects (path coefficient of temperature: -0.534). Under this optimal condition, a specific straw-degrading core microbiota (e.g., Actinomadura, Thermobifida; relative abundance 66.8%) was enriched, exhibiting a significantly broader niche width. This functional consortium exhibited a significant shift in metabolic activity, characterized by the upregulation of lipid/organic acid metabolism and secondary metabolite (such as antibiotics) biosynthesis pathways. These metabolic changes facilitated a combined strategy of competitive exclusion and potential antagonistic interactions, ultimately driving pathogen elimination. This work elucidates a novel mechanism for ensuring compost biosafety by regulating microbial function through resource manipulation, providing a feasible strategy for the simultaneous realization of efficient straw conversion and compost biosafety.

Chemical investigation of an Australian pasture soil-derived Actinomadura sp. prioritized for anthelmintic properties, led to the isolation and characterization of four new triamide-hydroxamates, goondastatins A1-D1 (1-4), with structures assigned on the basis of detailed spectroscopic analysis and chemical degradations/derivatization (Marfey's and Mosher analyses). The corresponding oxazoles, goondastatins A2-D2 (1a-4a) were also detected and tentatively identified. An expanded investigation of four additional Australian pasture soil-derived Streptomyces spp., also prioritized for anthelmintic properties, led to the discovery of goondastatin E2 (5) as a hydrolysis handling artifact of the known cometabolite kasichelin C (5a), two new piperazines, goondazines A (6) and B (9), and the known piperazines XR334 (7) and piperafizine A (8) with structures assigned by detailed spectroscopic and chemical analysis. While much of the anthelmintic properties of the pasture soil actinomycete could be attributed to known natural product classes (e.g., maduramicins and piericidins), goondastatin E1 (5) exhibited moderate and selective inhibition of dog heartworm Dirofilaria immitis microfilariae motility (EC50 = 4.1 μg/mL). Goondazine A (6), in contrast, exhibited moderate inhibition of livestock (ruminant) gastrointestinal nematode Hemonchus contortus L1-L3 larval development (EC50 = 1.2 μg/mL) and weak inhibition of D. immitis microfilariae motility (EC50 = 15 μg/mL).

This study explores the taxonomic diversity, metabolic profile, and bioactivity of marine-derived actinomycetes isolated from sediments collected off the coast of Lisbon and Setúbal Peninsula, Portugal. The combined use of two sediment pre-treatments (heat shock and dry overnight) and four growth media with varying nutrient concentrations revealed that formulations 10% A1 and SWA were most effective for recovering diverse actinomycetes, including rare Actinomadura, resulting in a total of 142 cultivable strains closely related to 47 phylogenetic distinct species dominated by Streptomyces and Micromonospora. Antimicrobial screening against methicillin-resistant Staphylococcus aureus (MRSA, COL) and Escherichia coli (K12) identified 22 bioactive strains, with strain PTS-083 exhibiting the strongest activity against MRSA (MIC = 1.95 µg/mL) and a 98.30% 16S rRNA gene identity to S. chumphonensis, highlighting it as a strong candidate for further metabolite and genomic studies. Cytotoxicity assays against HCT-116 human colorectal adenocarcinoma cells revealed eight bioactive strains with potent anticancer activity for extracts from strains related to S. sundarbansensis, S. violaceorubidus, and S. aculeolatus (IC50 < 0.005-5.08 µg/mL). Untargeted LC-MS/MS metabolomic analysis uncovered a wide array of secondary metabolites, including macrolides, siderophores, fatty acids, and cyclic peptides. Comparative analyses with other Portuguese coastal studies revealed both shared and distinctive metabolomic profiles, emphasizing the importance of exhaustive sampling, even at nearby locations, since localized environmental conditions can influence metabolic diversity and are crucial for uncovering unique metabolites with potential biotechnological value. These findings highlight Portugal's coastal sediments as a rich and underexplored source of novel actinomycetes and bioactive compounds with promising pharmaceutical applications.

BACKGROUND: Fusarium oxysporum f. sp. albedinis (Foa) is a destructive soil-borne fungal pathogen responsible for bayoud disease, which threatens date palm cultivation in North Africa. This disease has caused significant agricultural losses, particularly in Morocco, where the Zagora oasis is a key region for date palm production. Within this oasis, two cultivars—Black Bousthammi and Jihel—are mainly cultivated and exhibit complete resistance and high susceptibility to Foa, respectively. Thus, this study aimed to identify and compare the bacterial and fungal communities associated with the two cultivars and understand their assemblage regarding the disease resistance or susceptibility. Moreover, we explored the influence of each cultivar on the composition and structure of its root-associated microbiome and examined its relationship with the microbial populations present in the surrounding bulk soil, to better understand the recruitment dynamics that shape the microbiome in the roots. RESULTS: The results revealed significant differences in microbiome composition between the bulk soil and roots of the two date palm cultivars, and between the microbiome of the resistant and susceptible cultivars as well. Moreover, we observed that date palm cultivars had a greater effect on bacterial community composition than on fungal population. Interestingly, the susceptible cultivar exhibited a higher enrichment of several beneficial genera, such as Pseudomonas, Lysinibacillus, Actinomadura, Halomonas, Kocuria, Serratia, Phyllobacterium, Bacillus, Streptomyces, and Trichoderma. CONCLUSION: The presence of these beneficial genera, known for their antagonistic activity against phytopathogens, may reflect a recruitment pattern associated with pathogen pressure in the susceptible cultivar. This study is the first to compare the microbial communities between a bayoud-resistant and susceptible cultivar and provides insights into the potential role of the root microbiome when plants are under pathogen pressure. This reinforces the need to further elucidate the genetic and biological mechanisms that trigger microbiome assembly, which could be a key step in developing effective methods to manage the bayoud disease.