Structural diversification of vitamin D using microbial biotransformations.

Vitamin D deficiencies are linked to multiple human diseases. Optimizing its synthesis, physicochemical properties, and delivery systems while minimizing side effects is of clinical relevance and is of great medical and industrial interest. Biotechnological techniques may render new modified forms of vitamin D that may exhibit improved absorption, stability, or targeted physiological effects. Novel modified vitamin D derivatives hold promise for developing future therapeutic approaches and addressing specific health concerns related to vitamin D deficiency or impaired metabolism, such as avoiding hypercalcemic effects. Identifying and engineering key enzymes and biosynthetic pathways involved, as well as developing efficient cultures, are therefore of outmost importance and subject of intense research. Moreover, we elaborate on the critical role that microbial bioconversions might play in the a la carte design, synthesis, and production of novel, more efficient, and safer forms of vitamin D and its analogs. In summary, the novelty of this work resides in the detailed description of the physiological, medical, biochemical, and epidemiological aspects of vitamin D supplementation and the steps towards the enhanced and simplified industrial production of this family of bioactives relying on microbial enzymes. KEY POINTS: • Liver or kidney pathologies may hamper vitamin D biosynthesis • Actinomycetes are able to carry out 1α- or 25-hydroxylation on vitamin D precursors.

Demequina capsici sp. nov., a novel plant growth-promoting actinomycete isolated from the rhizosphere of bell pepper (Capsicum annuum).

Demequina, commonly found in coastal and marine environments, represents a genus of Actinomycetes. In this study, strains Demequina PMTSA13T and OYTSA14 were isolated from the rhizosphere of Capsicum annuum, leading to the discovery of a novel species, Demequina capsici. Bacteria play a significant role in plant growth, yet there have been no reports of the genus Demequina acting as plant growth-promoting bacteria (PGPB). Comparative genomics analysis revealed ANI similarity values of 74.05-80.63% for PMTSA13T and 74.02-80.54% for OYTSA14, in comparison to various Demequina species. The digital DNA-DNA hybridization (dDDH) values for PMTSA13T ranged from 19 to 39%, and 19.1-38.6% for OYTSA14. Genome annotation revealed the presence of genes associated with carbohydrate metabolism and transport, suggesting a potential role in nutrient cycling and availability for plants. These strains were notably rich in genes related to 'carbohydrate metabolism and transport (G)', according to their Cluster of Orthologous Groups (COG) classification. Additionally, both strains were capable of producing auxin (IAA) and exhibited enzymatic activities for cellulose degradation and catalase. Furthermore, PMTSA13T and OYTSA14 significantly induced the growth of Arabidopsis thaliana seedlings primarily attributed to their capacity to produce IAA, which plays a crucial role in stimulating plant growth and development. These findings shed light on the potential roles of Demequina strains in plant-microbe interactions and agricultural applications. The type strain is Demequina capsici PMTSA13T (= KCTC 59028T = GDMCC 1.4451T), meanwhile OYTSA14 is identified as different strains of Demequina capsici.

Endophytic actinomycetes promote growth and fruits quality of tomato (Solanum lycopersicum): an approach for sustainable tomato production.

Background: Tomato, a fruit with a high vitamin content, is popular for consumption and economically important in Thailand. However, in the past year, the extensive usage of chemicals has significantly decreased tomato yields. Plant Growth-Promoting Rhizobacteria (PGPR) is an alternative that can help improve tomato production system growth and yield quality while using fewer chemicals. The present study aimed to determine whether endophytic actinomycetes promote growth and fruit quality of tomato (Solanum lycopersicum). Methods: The experiment was conducted in a net-houses at the Center for Agricultural Resource System Research, Faculty of Agriculture, Chiang Mai University, Chiang Mai province, Thailand. The randomized completely block design (RCBD) was carried out for four treatments with three replications, which was control, inoculation with TGsR-03-04, TGsL-02-05 and TGsR-03-04 with TGsL-02-05 in tomato plant. Isolated Actinomycetes spp. of each treatment was then inoculated into the root zone of tomato seedlings and analyzed by Scanning Electron Microscopy (SEM). The height of tomato plants was measured at 14, 28, 56, and 112 days after transplanting. Final yield and yield quality of tomato was assessed at the maturity phase. Results: The SEM result illustrated that the roots of tomato seedlings from all treatments were colonized by endophytic actinomycetes species. This contributed to a significant increase in plant height at 14 days after transplanting (DAT), as found in the TGsR-03-04 treatment (19.40 cm) compared to the control. Besides, all inoculated treatments enhanced tomato yield and yield quality. The highest weight per fruit (47.38 g), fruit length (52.37 mm), vitamin C content (23.30 mg 100 g-1), and lycopene content (145.92 µg g-1) were obtained by inoculation with TGsR-03-04. Moreover, the highest yield (1.47 kg plant-1) was obtained by inoculation with TGsL-02-05. There was no statistically significant difference in the number of fruits per plant, fruit width, brix, and antioxidant activity when various inoculations of endophytic actinomycetes were applied. Therefore, the use of endophytic actinomycetes in tomato cultivation may be an alternative to increase tomato yield and yield quality.

Molecular characterization of vaginal microbiota using a new 22-species qRT-PCR test to achieve a relative-abundance and species-based diagnosis of bacterial vaginosis.

Background: Numerous bacteria are involved in the etiology of bacterial vaginosis (BV). Yet, current tests only focus on a select few. We therefore designed a new test targeting 22 BV-relevant species. Methods: Using 946 stored vaginal samples, a new qPCR test that quantitatively identifies 22 bacterial species was designed. The distribution and relative abundance of each species, α- and ß-diversities, correlation, and species co-existence were determined per sample. A diagnostic index was modeled from the data, trained, and tested to classify samples into BV-positive, BV-negative, or transitional BV. Results: The qPCR test identified all 22 targeted species with 95 - 100% sensitivity and specificity within 8 hours (from sample reception). Across most samples, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensenii, Gardnerella vaginalis, Fannyhessea (Atopobium) vaginae, Prevotella bivia, and Megasphaera sp. type 1 were relatively abundant. BVAB-1 was more abundant and distributed than BVAB-2 and BVAB-3. No Mycoplasma genitalium was found. The inter-sample similarity was very low, and correlations existed between key species, which were used to model, train, and test a diagnostic index: MDL-BV index. The MDL-BV index, using both species and relative abundance markers, classified samples into three vaginal microbiome states. Testing this index on our samples, 491 were BV-positive, 318 were BV-negative, and 137 were transitional BV. Although important differences in BV status were observed between different age groups, races, and pregnancy status, they were statistically insignificant. Conclusion: Using a diverse and large number of vaginal samples from different races and age groups, including pregnant women, the new qRT-PCR test and MDL-BV index efficiently diagnosed BV within 8 hours (from sample reception), using 22 BV-associated species.

[Vertical Distribution Characteristics and Driving Factors of Bacterioplankton and Nitrogen Phosphorus Cycle Genes in Danjiangkou Reservoir].

Danjiangkou Reservoir is a critical water source for the South-to-North Water Diversion Project, which harbors a diverse bacterioplankton community with varying depths, and the understanding of its nitrogen and phosphorus cycle and associated driving factors remains limited. In this study, we selected five ecological sites within Danjiangkou Reservoir and conducted metagenomics analysis to investigate the vertical distribution of bacterioplankton communities in the surface, middle, and bottom layers. Furthermore, we analyzed and predicted the function of nitrogen and phosphorus cycles, along with their driving factors. Our findings revealed the dominance of Proteobacteria, Actinobacteria, and Planctomycetes in the Danjiangkou Reservoir. Significant differences were observed in the structure of bacterioplankton communities across different depths, with temperature （T）, oxidation-reduction potential （ORP）, dissolved oxygen （DO）, and Chla identified as primary factors influencing the bacterioplankton composition. Analysis of nitrogen cycle functional genes identified 39 genes, including gltB, glnA, gltD, gdhA, NRT, etc., which were involved in seven main pathways, encompassing nitrogen fixation, nitrification, denitrification, and dissimilatory nitrate reduction. Phosphorus cycle function gene analysis identified 54 genes, including pstS, ppx-gppA, glpQ, ppk1, etc., primarily participating in six main pathways, including organic P mineralization, inorganic P solubilization, and regulatory. Cluster analysis indicated that different depths were significant factors influencing the composition and abundance of nitrogen and phosphorus cycle functional genes. The composition and abundance of nitrogen and phosphorus cycle functional genes in the surface and bottom layers differed and were generally higher than those in the middle layer. Deinococcus, Hydrogenophaga, Limnohabitans, Clavibacter, and others were identified as key species involved in the nitrogen and phosphorus cycle. Additionally, we found significant correlations between nitrogen and phosphorus cycle functional genes and environmental factors such as DO, pH, T, total dissolved solids （TDS）, electrical conductivity （EC）, and Chla. Furthermore, the content of these environmental factors exhibited depth-related changes in the Danjiangkou Reservoir, resulting in a distinct vertical distribution pattern of bacterioplankton nitrogen and phosphorus cycle functional genes. Overall, this study sheds light on the composition, function, and influencing factors of bacterioplankton communities across different layers of Danjiangkou Reservoir, offering valuable insights for the ecological function and diversity protection of bacterioplankton in this crucial reservoir ecosystem.

Alternative protocol leading to rapid identification of Actinomycetes isolated from Algerian desertic soil by MALDI-TOF mass spectrometry.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is the first-line method for the rapid identification of most cultured microorganisms. As for Streptomyces strains, MALDI-TOF MS identification is complicated by the characteristic incrustation of colonies in agar and the strong cell wall of Actinomycetes cells requiring the use of alternative protein extraction protocols. In this study, we developed a specific protocol to overcome these difficulties for the MALDI-TOF MS identification of Actinomycetes made on solid medium. This protocol includes incubation of colony removed from agar plate with the beta-agarase enzyme, followed by a mechanical lysis and two washes by phosphate buffer and ethanol. Twenty-four Streptomyces and two Lentzea strains isolated from Algerian desertic soils were first identified by 16S rRNA sequencing as gold standard method, rpoB gene was used as a secondary gene target when 16S rRNA did not allow species identification. In parallel the isolates were identified by using the MALDI-TOF MS protocol as reported. After the expansion of the database with the inclusion of this MSPS, the strains were analyzed again in MALDI Biotyper, and all were identified. This work demonstrates that the rapid identification of Actinomycetes can be obtained without protein extraction step frequently used in MALDI-TOF mass spectrometry with this type of microorganisms.

Cellulamides: A New Family of Marine-Sourced Linear Peptides from the Underexplored Cellulosimicrobium Genus.

Bioprospecting the secondary metabolism of underexplored Actinomycetota taxa is a prolific route to uncover novel chemistry. In this work, we report the isolation, structure elucidation, and bioactivity screening of cellulamides A and B (1 and 2), two novel linear peptides obtained from the culture of the macroalga-associated Cellulosimicrobium funkei CT-R177. The host of this microorganism, the Chlorophyta Codium tomentosum, was collected in the northern Portuguese coast and, in the scope of a bioprospecting study focused on its associated actinobacterial community, strain CT-R177 was isolated, taxonomically identified, and screened for the production of antimicrobial and anticancer compounds. Dereplication of a crude extract of this strain using LC-HRMS(/MS) analysis unveiled a putative novel natural product, cellulamide A (1), that was isolated following mass spectrometry-guided fractionation. An additional analog, cellulamide B (2) was obtained during the chromatographic process and chemically characterized. The chemical structures of the novel linear peptides, including their absolute configurations, were elucidated using a combination of HRMS, 1D/2D NMR spectroscopy, and Marfey's analysis. Cellulamide A (1) was subjected to a set of bioactivity screenings, but no significant biological activity was observed. The cellulamides represent the first family of natural products reported from the Actinomycetota genus Cellulosimicrobium, showcasing not only the potential of less-explored taxa but also of host-associated marine strains for novel chemistry discovery.

Characterization and Biosynthetic Regulation of Isoflavone Genistein in Deep-Sea Actinomycetes Microbacterium sp. B1075.

Deep-sea environments, as relatively unexplored extremes within the Earth's biosphere, exhibit notable distinctions from terrestrial habitats. To thrive in these extreme conditions, deep-sea actinomycetes have evolved unique biochemical metabolisms and physiological capabilities to ensure their survival in this niche. In this study, five actinomycetes strains were isolated and identified from the Mariana Trench via the culture-dependent method and 16S rRNA sequencing approach. The antimicrobial activity of Microbacterium sp. B1075 was found to be the most potent, and therefore, it was selected as the target strain. Molecular networking analysis via the Global Natural Products Social Molecular Networking (GNPS) platform identified 25 flavonoid compounds as flavonoid secondary metabolites. Among these, genistein was purified and identified as a bioactive compound with significant antibacterial activity. The complete synthesis pathway for genistein was proposed within strain B1075 based on whole-genome sequencing data, with the key gene being CHS (encoding chalcone synthase). The expression of the gene CHS was significantly regulated by high hydrostatic pressure, with a consequent impact on the production of flavonoid compounds in strain B1075, revealing the relationship between actinomycetes' synthesis of flavonoid-like secondary metabolites and their adaptation to high-pressure environments at the molecular level. These results not only expand our understanding of deep-sea microorganisms but also hold promise for providing valuable insights into the development of novel pharmaceuticals in the field of biopharmaceuticals.

Evaluating the low-rank coal degradation efficiency bioaugmented with activated sludge.

Microbial bioaugmentation of coal is considered as a viable and ecologically sustainable approach for the utilization of low-rank coals (LRC). The search for novel techniques to derive high-value products from LRC is currently of great importance. In response to this demand, endeavors have been undertaken to develop microbially based coal solubilization and degradation techniques. The impact of supplementing activated sludge (AS) as a microbial augmentation to enhance LRC biodegradation was investigated in this study. The LRC and their biodegradation products were characterized using the following methods: excitation-emission Matrices detected fluorophores at specific wavelength positions (O, E, and K peaks), revealing the presence of organic complexes with humic properties. FTIR indicated the increased amount of carboxyl groups in the bioaugmented coals, likely due to aerobic oxidation of peripheral non-aromatic structural components of coal. The bacterial communities of LRC samples are primarily composed of Actinobacteria (up to 36.2%) and Proteobacteria (up to 25.8%), whereas the Firmicutes (63.04%) was the most abundant phylum for AS. The community-level physiological profile analysis showed that the microbial community AS had high metabolic activity of compared to those of coal. Overall, the results demonstrated successful stimulation of LRC transformation through supplementation of exogenous microflora in the form of AS.

Volatile communication in Actinobacteria: a language for secondary metabolism regulation.

BACKGROUND: Volatile compounds are key elements in the interaction and communication between organisms at both interspecific and intraspecific levels. In complex bacterial communities, the emission of these fast-acting chemical messengers allows an exchange of information even at a certain distance that can cause different types of responses in the receiving organisms. The changes in secondary metabolism as a consequence of this interaction arouse great interest in the field of searching for bioactive compounds since they can be used as a tool to activate silenced metabolic pathways. Regarding the great metabolic potential that the Actinobacteria group presents in the production of compounds with attractive properties, we evaluated the reply the emitted volatile compounds can generate in other individuals of the same group. RESULTS: We recently reported that volatile compounds released by different streptomycete species trigger the modulation of biosynthetic gene clusters in Streptomyces spp. which finally leads to the activation/repression of the production of secondary metabolites in the recipient strains. Here we present the application of this rationale in a broader bacterial community to evaluate volatiles as signaling effectors that drive the activation of biosynthesis of bioactive compounds in other members of the Actinobacteria group. Using cocultures of different actinobacteria (where only the volatile compounds reach the recipient strain) we were able to modify the bacterial secondary metabolism that drives overproduction (e.g., granaticins, actiphenol, chromomycins) and/or de novo production (e.g., collismycins, skyllamycins, cosmomycins) of compounds belonging to different chemical species that present important biological activities. CONCLUSIONS: This work shows how the secondary metabolism of different Actinobacteria species can vary significantly when exposed in co-culture to the volatile compounds of other phylum-shared bacteria, these effects being variable depending on strains and culture media. This approach can be applied to the field of new drug discovery to increase the battery of bioactive compounds produced by bacteria that can potentially be used in treatments for humans and animals.

[Altitude Distribution Characteristics of Farmland Soil Bacteria in Loess Hilly Region of Ningxia].

It is of great significance for the conservation of biodiversity in farmland ecosystems to study the diversity, structure, functions, and biogeographical distribution of soil microbes in farmland and their influencing factors. High-throughput sequencing technology was used to analyze the distribution characteristics of soil bacterial diversity, community structure, and metabolic function along elevation and their responses to soil physicochemical properties in farmland in the loess hilly areas of Ningxia. The results showed that:① The Alpha diversity index of soil bacterial was significantly negatively correlated with elevation (P < 0.05) and showed a trend of decreasing and then slightly increasing along the elevation. ② Seven phyla, including Proteobacteria, Actinobacteria, and Acidobacteria, were the dominant groups, and five of them showed highly significant differences between altitudes (P < 0.01). ③ At the secondary classification level, there were 36 metabolic functions of bacteria, including membrane transport, carbohydrate metabolism, and amino acid metabolism, of which 22 showed significant differences, and 12 showed extremely significant differences among different altitudes. ④ Pearson correlation analysis showed that soil water content, bulk density, pH, and carbon-nitrogen ratio had the most significant effects on bacterial Alpha diversity, whereas soil nutrients such as total organic carbon, total nitrogen, and total phosphorus had significant effects on bacterial Beta diversity. ⑤ Mantel test analysis showed that the soil water content, total organic carbon, and carbon-nitrogen ratio affected bacterial community structure at the phylum level, and soil pH, total organic carbon, total nitrogen, total phosphorus, and carbon-nitrogen ratio were significantly correlated with bacterial metabolic function. Variance partitioning analysis showed that soil water content had the highest explanation for the community structure of soil bacteria, whereas soil pH had the highest explanation for metabolic function. In conclusion, soil water content and pH were the main factors affecting the diversity, community composition, and metabolic function of soil bacteria in farmland in the loess hilly region of Ningxia.

Isoptericola haloaureus sp. nov., a dimorphic actinobacterium isolated from mangrove sediments of southeast India, implicating biosaline agricultural significance through nitrogen fixation and salt tolerance genes.

Strain MP-1014T, an obligate halophilic actinobacterium, was isolated from the mangrove soil of Thandavarayancholanganpettai, Tamil Nadu, India. A polyphasic approach was utilized to explore its phylogenetic position completely. The isolate was Gram-positive, filamentous, non-motile, and coccoid in older cultures. Ideal growth conditions were seen at 30 °C and pH 7.0, with 5% NaCl (W/V), and the DNA G + C content was 73.3%. The phylogenic analysis of this strain based upon 16S rRNA gene sequence revealed 97-99.8% similarity to the recognized species of the genus Isoptericola. Strain MP-1014T exhibits the highest similarity to I. sediminis JC619T (99.7%), I. chiayiensis KCTC19740T (98.9%), and subsequently to I. halotolerans KCTC19646T (98.6%), when compared with other members within the Isoptericola genus (< 98%). ANI scores of strain MP-1014T are 86.4%, 84.2%, and 81.5% and dDDH values are 59.7%, 53.6%, and 34.8% with I. sediminis JC619T, I. chiayiensis KCTC19740T and I. halotolerans KCTC19646T respectively. The major polar lipids of the strain MP-1014T were phosphatidylinositol, phosphatidylglycerol, diphosphotidylglycerol, two unknown phospholipids, and glycolipids. The predominant respiratory menaquinones were MK9 (H4) and MK9 (H2). The major fatty acids were anteiso-C15:0, anteiso-C17:0, iso-C14:0, C15:0, and C16:0. Also, initial genome analysis of the organism suggests it as a biostimulant for enhancing agriculture in saline environments. Based on phenotypic and genetic distinctiveness, the strain MP-1014 T represents the novel species of the genus Isoptericola assigned Isoptericola haloaureus sp. nov., is addressed by the strain MP-1014 T, given its phenotypic, phylogenetic, and hereditary uniqueness. The type strain is MP-1014T [(NCBI = OP672482.1 = GCA_036689775.1) ATCC = BAA 2646T; DSMZ = 29325T; MTCC = 13246T].

Biological activities and metabolomic profiles of extracts from the marine sediment bacterium Nocardiopsis alba DP1B cultivated in different media.

The soil bacterium DP1B was isolated from a marine sediment collected off the coast of Randayan Island, Kalimantan Barat, Indonesia and identified based on 16S rDNA as Nocardiopsis alba. The bacterium was cultivated in seven different media (A1, ISP1, ISP2, ISP4, PDB, PC-1, and SCB) with three different solvents [distilled water, 5 % NaCl solution, artificial seawater (ASW)] combinations, shaken at 200 rpm, 30 °C, for 7 days. The culture broths were extracted with ethyl acetate and each extract was tested for its antimicrobial activity and brine shrimp lethality, and the chemical diversity was assessed using thin-layer chromatography (TLC), gas chromatography (GC), and liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). The result showed that almost all extracts showed antibacterial but not antifungal activity, whereas their brine shrimp toxicity levels vary from high to low. The best medium/solvent combinations for antibacterial activity and toxicity were PC-1 (in either distilled water, 5% NaCl solution, or ASW) and SCB in ASW. Different chemical diversity profiles were observed on TLC, GC-MS, and LC-MS/MS. Extracts from the PC-1 cultures seem to contain a significant number of cyclic dipeptides, whereas those from the SCB cultures contain sesquiterpenes, indicating that media and solvent compositions can affect the secondary metabolite profiles of DP1B. In addition, untargeted metabolomic analyses using LC-MS/MS showed many molecular ions that did not match with those in the Global Natural Products Social Molecular Networking (GNPS) database, suggesting that DP1B has great potential as a source of new natural products.

Tessaracoccus lacteus sp. nov., Isolated from the Sludge of a Wastewater Treatment Plant.

A bacterium, designated strain T21T, that is non-motile, rod-shaped, and formed pale white colonies, was isolated from the sludge of a wastewater treatment plant's secondary sedimentation tank in China. Strain T21T could grow at 20-40 °C (optimum growth at 30 °C), pH 3.0-10.0 (optimum growth at pH 5.0) and in the presence of 0-8.0% (w/v) NaCl (optimum growth at 2.0%). Based on phylogenetic analysis of 16S rRNA gene sequences and genome sequences, the isolate belongs to the genus Tessaracoccus in the phylum Actinomycetota. It exhibited a close relationship with Tessaracoccus palaemonis J1M15T, Tessaracoccus defluvii LNB-140T, Tessaracoccus flavescens SST-39T, and Tessaracoccus coleopterorum HDW20T. The 16S rRNA gene sequence similarities are 99.8%, 97.9%, 97.9%, and 97.8%, respectively. The major cellular fatty acids were anteiso-C15:0 and C16:0. The main respiratory quinone was MK-9(H4). The polar lipids included phosphatidylglycerol, diphosphatidylglycerol, glycolipid, and phospholipid. Genome annotation of strain T21T predicted the presence of 2829 genes, of which 2754 are coding proteins and 59 are RNA genes. The genomic DNA G+C content was 69.2%. Based on the results of phylogenetic, phenotypic, chemotaxonomic, and genotypic analyses, we propose the name Tessaracoccus lacteus sp. nov. for this novel species within the genus Tessaracoccus. The type strain is T21T (=CCTCC AB 2023031T = KCTC 49936T).

Structures, biosynthesis and biological activities of benastatins, anthrabenzoxocinones and fredericamycins.

The fast spread of antibiotic resistance results in the requirement for a constant introduction of new candidates. Pentangular polyphenols, a growing family of actinomycetes-derived aromatic type II polyketides, have attracted considerable attention due to their intriguing polycyclic systems and potent antimicrobial activity. Among them, benastatins, anthrabenzoxocinones (ABXs), and fredericamycins, display unique variations in their polycyclic frameworks, yet concurrently share structural commonalities within their substitutions. The present review summarizes advances in the isolation, spectroscopic characteristics, biosynthesis, and biological activities of pentangular polyphenols benastatins (1-16), ABXs (17-39), and fredericamycins (40-42) from actinomycetes. The information presented here thus prompts researchers to further explore and discover additional congeners within these three small classes of pentangular polyphenols.

A treasure trove of 1034 actinomycete genomes.

Filamentous Actinobacteria, recently renamed Actinomycetia, are the most prolific source of microbial bioactive natural products. Studies on biosynthetic gene clusters benefit from or require chromosome-level assemblies. Here, we provide DNA sequences from >1000 isolates: 881 complete genomes and 153 near-complete genomes, representing 28 genera and 389 species, including 244 likely novel species. All genomes are from filamentous isolates of the class Actinomycetia from the NBC culture collection. The largest genus is Streptomyces with 886 genomes including 742 complete assemblies. We use this data to show that analysis of complete genomes can bring biological understanding not previously derived from more fragmented sequences or less systematic datasets. We document the central and structured location of core genes and distal location of specialized metabolite biosynthetic gene clusters and duplicate core genes on the linear Streptomyces chromosome, and analyze the content and length of the terminal inverted repeats which are characteristic for Streptomyces. We then analyze the diversity of trans-AT polyketide synthase biosynthetic gene clusters, which encodes the machinery of a biotechnologically highly interesting compound class. These insights have both ecological and biotechnological implications in understanding the importance of high quality genomic resources and the complex role synteny plays in Actinomycetia biology.

Microalgae growth-promoting bacteria for cultivation strategies: Recent updates and progress.

Microalgae growth-promoting bacteria (MGPB), both actinobacteria and non-actinobacteria, have received considerable attention recently because of their potential to develop microalgae-bacteria co-culture strategies for improved efficiency and sustainability of the water-energy-environment nexus. Owing to their diverse metabolic pathways and ability to adapt to diverse conditions, microalgal-MGPB co-cultures could be promising biological systems under uncertain environmental and nutrient conditions. This review proposes the recent updates and progress on MGPB for microalgae cultivation through co-culture strategies. Firstly, potential MGPB strains for microalgae cultivation are introduced. Following, microalgal-MGPB interaction mechanisms and applications of their co-cultures for biomass production and wastewater treatment are reviewed. Moreover, state-of-the-art studies on synthetic biology and metabolic network analysis, along with the challenges and prospects of opting these approaches for microalgal-MGPB co-cultures are presented. It is anticipated that these strategies may significantly improve the sustainability of microalgal-MGPB co-cultures for wastewater treatment, biomass valorization, and bioproducts synthesis in a circular bioeconomy paradigm.

Characteristics and kinetics of thermophilic actinomycetes' amylase production on agro-wastes and its application for ethanol fermentation.

Thermophilic actinomycetes are commonly found in extreme environments and can thrive and adapt to extreme conditions. These organisms exhibit substantial variation and garnered significant interest due to their remarkable enzymatic activities. This study evaluated the potential of Streptomyces griseorubens NBR14 and Nocardiopsis synnemataformans NBRM9 strains to produce thermo-stable amylase via submerged fermentation using wheat and bean straw. The Box-Behnken design was utilized to determine the optimum parameters for amylase biosynthesis. Subsequently, amylase underwent partial purification and characterization. Furthermore, the obtained hydrolysate was applied for ethanol fermentation using Saccharomyces cerevisiae. The optimal parameters for obtaining the highest amylase activity by NBR14 (7.72 U/mL) and NBRM9 (26.54 U/mL) strains were found to be 40 and 30 °C, pH values of 7, incubation time of 7 days, and substrate concentration (3 and 2 g/100 mL), respectively. The NBR14 and NBRM9 amylase were partially purified, resulting in specific activities of 251.15 and 144.84 U/mg, as well as purification factors of 3.91 and 2.69-fold, respectively. After partial purification, the amylase extracted from NBR14 and NBRM9 showed the highest activity level at pH values of 9 and 7 and temperatures of 50 and 60 °C, respectively. The findings also indicated that the maximum velocity (Vmax) for NBR14 and NBRM9 amylase were 57.80 and 59.88 U/mL, respectively, with Km constants of 1.39 and 1.479 mM. After 48 h, bioethanol was produced at concentrations of 5.95 mg/mL and 9.29 mg/mL from hydrolyzed wheat and bean straw, respectively, through fermentation with S. cerevisiae. Thermophilic actinomycetes and their α-amylase yield demonstrated promising potential for sustainable bio-ethanol production from agro-byproducts.

Actinobacteria as Promising Biocontrol Agents for In Vitro and In Planta Degradation and Detoxification of Zearalenone.

Zearalenone (ZEN) is a prevalent mycotoxin found in grains and grain-derived products, inducing adverse health effects in both animals and humans. The in-field application of microorganisms to degrade and detoxify ZEN is a promising strategy to enhance the safety of food and feed. In this study, we investigated the potential of three actinobacterial strains to degrade and detoxify ZEN in vitro and in planta on wheat ears. The residual ZEN concentration and toxicity in the samples were analysed with UHPLC-MS/MS and a bioluminescence BLYES assay, respectively. Streptomyces rimosus subsp. rimosus LMG19352 could completely degrade and detoxify 5 mg/L ZEN in LB broth within 24 h, along with significant reductions in ZEN concentration both in a minimal medium (MM) and on wheat ears. Additionally, it was the only strain that showed a significant colonisation of these ears. Rhodococcus sp. R25614 exhibited partial but significant degradation in LB broth and MM, whereas Streptomyces sp. LMG16995 degraded and detoxified ZEN in LB broth after 72 h by 39% and 33%, respectively. Although all three actinobacterial strains demonstrated the metabolic capability to degrade and detoxify ZEN in vitro, only S. rimosus subsp. rimosus LMG19352 showed promising potential to mitigate ZEN in planta. This distinction underscores the importance of incorporating in planta screening assays for assessing the potential of mycotoxin-biotransforming microorganisms as biocontrol agents.

Discovering type I cis-AT polyketides through computational mass spectrometry and genome mining with Seq2PKS.

Type 1 polyketides are a major class of natural products used as antiviral, antibiotic, antifungal, antiparasitic, immunosuppressive, and antitumor drugs. Analysis of public microbial genomes leads to the discovery of over sixty thousand type 1 polyketide gene clusters. However, the molecular products of only about a hundred of these clusters are characterized, leaving most metabolites unknown. Characterizing polyketides relies on bioactivity-guided purification, which is expensive and time-consuming. To address this, we present Seq2PKS, a machine learning algorithm that predicts chemical structures derived from Type 1 polyketide synthases. Seq2PKS predicts numerous putative structures for each gene cluster to enhance accuracy. The correct structure is identified using a variable mass spectral database search. Benchmarks show that Seq2PKS outperforms existing methods. Applying Seq2PKS to Actinobacteria datasets, we discover biosynthetic gene clusters for monazomycin, oasomycin A, and 2-aminobenzamide-actiphenol.