Oligotrophy is Helpful for the Isolation of Bioactive Actinomycetes

Streptomyces meridianus sp. nov. isolated from brackish water of the Tagus estuary in Alcochete, Portugal

An isolation effort focused on sporogenous Actinomycetota from the Tagus estuary in Alcochete, Portugal, yielded a novel actinomycetal strain, designated MTZ3.1T, which was subjected to a polyphasic taxonomic study. MTZ3.1T is characterised by morphology typical of members of the genus Streptomyces, with light beige coloured substrate mycelium, which does not release pigments to the culture medium and with helicoidal aerial hyphae that differentiate into spores with a light-grey colour. The phylogeny of MTZ3.1T, based on the full 16S rRNA gene sequence, indicated that its closest relatives were Streptomyces alkaliterrae OF1T (98.48 %), Streptomyces chumphonensis KK1-2T (98.41 %), Streptomyces albofaciens JCM 4342T (98.34 %), Streoptomyces paromomycinus NBRC 15454T (98.34 %) and Streptomyces chrestomyceticus NRBC 13444T (98.34 %). Moreover, average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridisation (dDDH) are below the species cutoff values (ANI 67.70 and 68.35 %, AAI 77.06 and 76.71 % and dDDH 22.10 and 21.50 % for S. alkaliterrae OF1T and S. chumphonensis KK1-2T, respectively). Whole genome sequencing revealed that MTZ3.1T has a genome of 5 644 485 bp with a DNA G+C content of 71.29 mol% and 5044 coding sequences. Physiologically, MTZ3.1T is strictly aerobic, able to grow at 15-37 °C, optimally at 25 °C and between pH5 and 8 and showed high salinity tolerance, growing with 0-10 %(w/v) NaCl. Major cellular fatty acids are C15 : 0, iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0. Furthermore, it was able to utilise a variety of nitrogen and carbon sources. Antimicrobial screening indicated that MTZ3.1T has potent anti-Staphylococcus aureus activity. On the basis of the polyphasic data, MTZ3.1T is proposed to represent a novel species, Streptomyces meridianus sp. nov. (= CECT 30416T = DSM 114037T=LMG 32463T).

iChip-Inspired Isolation, Bioactivities and Dereplication of Actinomycetota from Portuguese Beach Sediments

Oceans hold a stunning number of unique microorganisms, which remain unstudied by culture-dependent methods due to failures in establishing the right conditions for these organisms to grow. In this work, an isolation effort inspired by the iChip was performed using marine sediments from Memoria beach, Portugal. The isolates obtained were identified by 16S rRNA gene analysis, fingerprinted using BOX-PCR and ERIC-PCR, searched for the putative presence of secondary metabolism genes associated with polyketide synthase I (PKS-I) and non-ribosomal peptide synthetases (NRPS), screened for antimicrobial activity against Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 29213, and had bioactive extracts dereplicated by LC/HRMS. Of the 158 isolated strains, 96 were affiliated with the phylum Actinomycetota, PKS-I and NRPS genes were detected in 53 actinomycetotal strains, and 11 proved to be bioactive (10 against E. coli, 1 against S. aureus and 1 against both pathogens). Further bioactivities were explored using an "one strain many compounds" approach, with six strains showing continued bioactivity and one showing a novel one. Extract dereplication showed the presence of several known bioactive molecules and potential novel ones in the bioactive extracts. These results indicate the use of the bacteria isolated here as sources of new bioactive natural products.

Recent methods for discovering novel bioactive metabolites, specifically antimicrobial agents, from marine-associated microorganisms

Marine microorganisms are a promising source for novel natural compounds with many medical and biotechnological applications. Here we demonstrate limitations and recent strategies for investigating the marine microbial community for novel bioactive metabolites, specifically those of antimicrobial potential. These strategies include culture-dependent methods such as modifying the standard culture media, including changing the gelling agent, dissolving vehicle, media supplementation, and preparation to access a broader range of bacterial diversity from marine samples. Furthermore, we discuss strategies like in situ cultivation, dilution-to-extinction cultivation, and long-term incubation. We are presenting recent applications of culture-independent methods such as genome mining, proteomics profiling, and the application of metagenomics as a novel strategy for structure confirmation in the discovery of the marine microorganism for novel antimicrobial metabolites. We present this review as a simple guide and a helpful resource for those who seek to enter the challenging field of applied marine microbiology.

In Vitro Antitumor Activity of Endophytic and Rhizosphere Gram-Positive Bacteria from Ibervillea sonorae (S. Watson) Greene against L5178Y-R Lymphoma Cells

Plant-associated microorganisms represent a potential source of new antitumor compounds. The aim of the present study was to isolate endophytic and rhizosphere Gram-positive bacteria from Ibervillea sonorae and produce extracts with antitumor activity. Methanol and ethyl acetate extracts were obtained from 28 d bacterial fermentation, after which murine L5178Y-R lymphoma cells growth inhibition was evaluated at concentrations ranging from 15.62 µg/mL to 500 µg/mL by the 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide reduction colorimetric assay. IC₅₀ and the selectivity index (SI) were calculated and compared with healthy control human peripheral blood mononuclear cells (PBMC). Identification of the isolated strains was performed using the 16S ribosomal gene and by MALDI-TOF MS mass spectrometry. The endophytic and rhizosphere bacterial extracts from strains ISE-B22, ISE-B26, ISE-B27, ISS-A01, ISS-A06, and ISS-A16 showed significant (p < 0.05) L5178Y-R cell growth inhibition, compared with an untreated control. The rhizosphere Micromonospora echinospora isolate ISS-A16 showed the highest (90.48%) percentage of lymphoma cells growth inhibition and SI (19.1) for PBMC, whereas the Bacillus subtilis ISE-B26 isolate caused significant (p < 0.01) growth inhibition (84.32%) and a SI of 5.2. Taken together, results of the present study evidenced antitumor effects by I. sonorae endophytic and rhizosphere bacteria culture extracts. Further research will involve the elucidation of the compounds that exert the antitumor activity and their evaluation in pre-clinical studies.

Streptomyces arboris sp. nov., isolated from Populus euphratica wetland soil

A novel actinobacterial strain (TRM 68085T) was isolated from soil ofPopulus euphraticawetland. A polyphasic approach was used to study the taxonomy of TRM 68085Tand the results showed a range of phylogenetic and chemotaxonomic properties consistent with those of the genusStreptomyces. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain TRM 68085Tshowed the highest similarity value toStreptomyces capitiformicae1H-SSA4T(98.6 %), and phylogenetically clustered withStreptomyces kanasensisZX01T(97.5 %) andStreptomyces ipomoeaeNBRC 13050T(97.4 %). The genomic DNA G+C content of strain TRM 68085Tbased on the genome sequence was 71.4 mol%. The levels of DNA–DNA relatedness between the genome of the isolate and its nearest phylogenetic neighbours,S. capitiformicae1H-SSA4T,S. kanasensisZX01TandS. ipomoeaeNBRC 13050T, were 19.2±0.4, 21.8±0.5 and 19.3±0.6 %, respectively. Chemotaxonomic data revealed that strain TRM 68085Tpossessed MK-9(H6) and MK-9(H8) as the predominant menaquinones.ll-Diaminopimelic acid and a small amount ofmeso-diaminopimelic acid were the diagnostic diamino acids. Ribose, xylose, glucose and galactose were the whole-cell sugars. The major cellular fatty acids were C16 : 0(25.4 %) and iso-C16 : 0(18.3 %). On the basis of these genotypic and phenotypic data, it is concluded that strain TRM 68085Trepresents a novel species of the genusStreptomyces, for which the nameStreptomyces arborissp. nov. is proposed. The type strain is TRM 68085T(=CCTCC AA2019031T=LMG 31492T).

Bryophytes Harbor Cultivable Actinobacteria With Plant Growth Promoting Potential

This study was designed to investigate the cultivable actinobacteria associated with bryophytes and their plant growth promoting ability. Thirteen actinobacteria were isolated and tested for their ability to promote growth of plant in vitro and in planta. All isolates were able to produce IAA and siderophores. Six isolates were identified as members of the genus Micromonospora. Five isolates belonged to the genus Streptomyces and one each of Microbispora and Mycobacterium. Micromonospora sp. CMU55-4 was inoculated to rare moss [Physcomitrium sphaericum (C. Ludw.) Fürnr.] and could increase the amount of carotenoid, fresh weight, and dry weight of this moss. In addition, this strain promoted capsule production, and rescued P. sphaericum’s gametophytes during acclimatization to land. Strain CMU55-4 was identified as Micromonospora chalcea based on whole genome sequence analysis. Its plant growth promoting potential was further characterized through genome mining. The draft genome size was 6.6 Mb (73% GC). The genome contained 5,933 coding sequences. Functional annotation predicted encoded genes essential for siderophore production, phosphate solubilization that enable bacteria to survive under nutrient limited environment. Glycine-betaine accumulation and trehalose biosynthesis also aid plants under drought stress. M. chalcea CMU55-4 also exhibited genes for various carbohydrate metabolic pathways indicating those for efficient utilization of carbohydrates inside plant cells. Additionally, predictive genes for heat shock proteins, cold shock proteins, and oxidative stress such as glutathione biosynthesis were identified. In conclusion, our results demonstrate that bryophytes harbor plant growth promoting actinobacteria. A representative isolate, M. chalcea CMU55-4 promotes the growth of P. sphaericum moss and contains protein coding sequences related to plant growth promoting activities in its genome.

The Microbiomes of Seven Lichen Genera Reveal Host Specificity, a Reduced Core Community and Potential as Source of Antimicrobials

The High Andean Paramo ecosystem is a unique neotropical mountain biome considered a diversity and evolutionary hotspot. Lichens, which are complex symbiotic structures that contain diverse commensal microbial communities, are prevalent in Paramos. There they play vital roles in soil formation and mineral fixation. In this study we analyzed the microbiomes of seven lichen genera in Colombian Paramos using 16S rRNA gene amplicon sequencing and provide the first description of the bacterial communities associated with Cora and Hypotrachyna lichens. Paramo lichen microbiomes varied in diversity indexes and number of OTUs, but were composed predominantly by the phyla Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria, and Verrucomicrobia. In the case of Cora and Cladonia, the microbiomes were distinguished based on the identity of the lichen host. While the majority of the lichen-associated microorganisms were not present in all lichens sampled, sixteen taxa shared among this diverse group of lichens suggest a core lichen microbiome that broadens our concept of these symbiotic structures. Additionally, we identified strains producing compounds active against clinically relevant microbial strains. These results indicate that lichen microbiomes from the Paramo ecosystem are diverse and host-specific but share a taxonomic core and can be a source of new bacterial taxa and antimicrobials.

Biocontrol effects of Penicillium griseofulvum against monkshood (Aconitum carmichaelii Debx.) root diseases caused by Sclerotium rolfsiii and Fusarium spp

AIMS

The aims of this study were to investigate the biocontrol effects of Penicillium griseofulvum strain CF3 and its mechanisms against soil-borne root pathogens (Fusarium oxysporum and Sclerotium rolfsii) of the medical plant Aconitum carmichaelii Debx.

METHODS AND RESULTS

The effects of P. griseofulvum strain CF3 were evaluated with regard to the hyphal growth of S. rolfsii and F. oxysporum, the sclerotial formation and germination of S. rolfsii and its expression of sclerotia-formation-related genes. A field experiment was conducted to explore how strain CF3 controls the severity of soil-borne diseases, promotes the growth of A. carmichaelii plants and mediates shifts in the culturable rhizosphere microbial populations. The results showed that treatment with a cell-free culture filtrate of strain CF3 considerably inhibited the hyphal growth of both S. rolfsii and F. oxysporum, in addition to limiting the sclerotial formation and germination of S. rolfsii. Three genes related to sclerotial formation (ArsclR, ArnsdD1 and ArnsdD2) were predicted in S. rolfsii and their expression was found suppressed by the CF3 treatment. Field application of the CF3 biocontrol agent in a powder form (1·9 × 10¹⁰ conidia per gram of substrate) reduced soil-borne disease severity by 15·0%. The shoot and root growth of A. carmichaelii plants was promoted by 61·6 and 83·1% respectively, as the biocontrol strain massively colonized the rhizosphere soil. The CF3 treatment also markedly reduced the density of some known species harmful to plants while increasing the density of some beneficial species in the rhizosphere soil.

SIGNIFICANCE AND IMPACT OF THE STUDY

Genes related to sclerotia formation of S. rolfsii are predicted for the first time and their expression patterns in the presence of P. griseofulvum strain CF3 are evaluated. This comprehensive study provides a candidate fungal biocontrol strain and reveals its potential mechanisms against S. rolfsii and F. oxysporum in A. carmichaelii plants.

Aislamiento y caracterización parcial de actinomicetos de suelos con actividad antimicrobiana contra bacterias multidrogo-resistentes

Con el objetivo de evaluar la actividad antimicrobiana frente a bacterias multi-drogo resistentes, se estudiaron 234 cepas de actinobacterias aisladas de suelo de Argentina y Perú. Se seleccionaron 13 cepas sobre la base de su actividad antagonista contra Staphylococcus aureus meticilina-resistente (SAMR) y Enterococcus resistente a vancomicina (EVR-van A y van B). La presencia de los genes NRPS, PKS-I y PKS-II fueron investigados por técnicas de PCR. Entre las 13 actinobacterias seleccionadas, la cepa AC69C mostró la mayor actividad en las pruebas de difusión en medio sólido y se evaluó posteriormente la producción de metabolitos antagonistas en medios líquidos. Los mejores resultados se lograron en caldo de fermentación con carbohidratos, al usarse en combinación almidón y glucosa. Se obtuvieron actividades antimicrobianas de 640 unidades arbitrarias (UA), 320 UA, 320 UA y 80 UA contra EVR-van A, EVR-van B, Listeria monocytogenes ATCC7644 y SAMR, respectivamente. La amplificación por PCR del gen ARNr 16S y el análisis filogenético subsecuente de la cepa AC69C exhibieron una homología del 100 % con Streptomyces antibioticus NRRL B-1701. No fue posible establecer una correlación entre los genes amplificados y la actividad antimicrobiana de las 13 cepas seleccionadas. Los resultados de este trabajo demuestran la amplia distribución de las actinobacterias en suelo y la importancia del aislamiento de cepas para la búsqueda de nuevos metabolitos activos contra bacterias multi-drogo resistentes de origen clínico.