Mariniluteicoccus flavus gen. nov., sp. nov., a new member of the family Propionibacteriaceae, isolated from a deep-sea sediment

Uncovering the biodiversity and biosynthetic potentials of rare actinomycetes

Background

Antibiotic resistance is on the rise, and new antibiotic research has slowed in recent years, necessitating the discovery of possibly novel microbial resources capable of producing bioactive compounds. Microbial infections are gaining resistance to existing antibiotics, emphasizing the need for novel medicinal molecules to be discovered as soon as possible. Because the possibilities of isolating undiscovered actinomycetes strains have decreased, the quest for novel products has shifted to rare actinomycetes genera from regular environments or the identification of new species identified in unusual habitats.

Main body of the abstract

The non-streptomyces actinobacteria are known as rare actinomycetes that are extremely difficult to cultivate. Rare actinomycetes are known to produce a variety of secondary metabolites with varying medicinal value. In this review, we reported the diversity of rare actinomycetes in several habitat including soil, plants, aquatic environment, caves, insects and extreme environments. We also reported some isolation methods to easily recover rare Actinobacteria from various sources guided with some procedures to identify the rare Actinobacteria isolates. Finally, we reported the biosynthetic potential of rare actinomycetes and its role in the production of unique secondary metabolites that could be used in medicine, agriculture, and industry. These microbial resources will be of interest to humanity, as antibiotics, insecticides, anticancer, antioxidants, to mention but a few.

Short conclusion

Rare actinomycetes are increasingly being investigated for new medicinal compounds that could help to address existing human health challenges such as newly emerging infectious illnesses, antibiotic resistance, and metabolic disorders. The bioactive secondary metabolites from uncommon actinomycetes are the subject of this review, which focuses on their diversity in different habitats, isolation, identification and biosynthetic potentials.

Altererythrobacter flava sp. nov., a new member of the family Erythrobacteraceae, isolated from a surface seawater sample

A Gram-stain-negative, light yellow pigmented, non-motile and aerobic bacterial strain, designated HHU E2-1 ^T, was isolated from a surface seawater sample. The 16S rRNA gene sequence analysis indicated that HHU E2-1 ^T shared the highest sequence similarity to the type strain Qipengyuania gaetbuli DSM 16225 ^T (96.90%), which belongs to the family Erythrobacteraceae. Combined phylogeny of 288 single-copy orthologous gene clusters, analysis of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), average amino acid identity (AAI) and evolutionary distances suggested that HHU E2-1 ^T can be considered as a member of the genus Altererythrobacter based on the recently proposed standard for defining genera of Erythrobacteraceae. Strain HHU E2-1 ^T grew at 15-35 °C and pH 5.0-8.0, with optimum growth at 28 °C and pH 7.0. Tolerance to NaCl was up to 4% (w/v) with optimum growth in 2-3% NaCl. The major fatty acids (> 10%) were C_18:1ω7c11-methyl, summed feature 3 (C_16:1ω7c and/or C_16:1ω6c), and summed feature 8 (C_18:1ω7c and/or C_18:1ω6c). The predominant isoprenoid quinone was ubiquinone-10. The genomic G + C content was 57.40%. On the basis of the phenotypic, phylogenetic and chemotaxonomic characterizations, HHU E2-1 ^T represents a novel species of the genus Altererythrobacter, for which the name Altererythrobacter flava sp. nov. is proposed. The type strain is HHU E2-1 ^T (= CGMCC 1.17394 ^T = KCTC 72835 ^T = MCCC 1K04226^T).

Granulation of halophilic sludge inoculated with estuarine sediments for saline wastewater treatment

As a solution of the sludge loss in the treatment of saline wastewater, the granulation of halophilic sludge was explored in this study. The inoculated estuarine sediment was granulated to an average diameter of 1155 ± 102 μm under the selective settling pressure in the airlift sequencing batch reactor (SBR) when the influent organic loading rate (OLR) was doubled to 0.36 g COD/L·day. The results indicated that the OLR doubled the amount of total extracellular polymeric substance (EPS) and that protein was predominant in the EPS (72.8 ± 2.0%). The correlation between aggregate size and protein content was better than that between aggregate size and polysaccharide content. The amount of alginate-like exopolysaccharides (ALE) increased linearly at the mature granular stage, co-occurring with the compact and elastic structure of the granules. According to the results of 16S rRNA high -throughput sequencing, the Shannon-Weaver index of mature granule decreased by >50% compared to the inoculated sediment. Bacteria of Propionibacteriaceae family constituted 34% of the population in granules and were in symbiotic relationship with halophiles of family Rhodocyclaceae, Vibrionaceae, Flavobacteriaceae, and Cryomorphaceae. The aerobic halophilic granular sludge showed COD removal efficiency of 90.9 ± 0.8% and ammonia removal efficiency of 72.6 ± 4.0% for 30 g/L saline wastewater. An average nitrite accumulation ratio of 94.5 ± 2.9% was observed during nitrification. Granulation of halophilic sludge provides an effective solution to the saline sludge loss problem, which is a step forward to realize the biological treatment of saline wastewater by halophiles.

Desertihabitans aurantiacus gen. nov., sp. nov., a novel member of the family Propionibacteriaceae

The taxonomic position of an actinobacterium isolated from a desert soil sample collected from Badain Jaran Desert, designated as CPCC 204711^T, was established using a polyphasic approach. Cells of the isolate were Gram-staining-positive, aerobic, non-motile cocci. Good growth was observed at 28 °C (range 20-40 °C), pH 7.0 (range pH 6.0-8.0) and 0-1 % NaCl concentration (range 0-5 %, w/v). Galactose, arabinose and ribose were detected as the sugar compositions in the whole cell hydrolysates. The peptidoglycan type was A3gamma (ll-Dpm-Gly). MK-9(H4) was detected as the predominant menaquinone, and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, several unidentified glycolipids, and one unidentified amino-glycolipid were detected as the major polar lipids. The predominant fatty acid was anteiso-C15 : 0. The genomic DNA G+C content was 73.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CPCC 204711^T affiliated to the family Propionibacteriaceae, in which the strain formed a distinct phylogenetic lineage next to the genus Mariniluteicoccus, with the highest 16S rRNA gene sequence similarity of 96.0 % to Mariniluteicoccus endophyticus YIM 2617^T. Both phylogenetic analysis and phenotypic characteristics supported that strain CPCC 204711^T represents a novel species of a new genus in the family Propionibacteriaceae, for which the name Desertihabitans aurantiacus gen. nov., sp. nov. is proposed, with CPCC 204711^T (=KCTC 39977^T=DSM 105431^T) as the type strain.

Marine Rare Actinomycetes: A Promising Source of Structurally Diverse and Unique Novel Natural Products

Rare actinomycetes are prolific in the marine environment; however, knowledge about their diversity, distribution and biochemistry is limited. Marine rare actinomycetes represent a rather untapped source of chemically diverse secondary metabolites and novel bioactive compounds. In this review, we aim to summarize the present knowledge on the isolation, diversity, distribution and natural product discovery of marine rare actinomycetes reported from mid-2013 to 2017. A total of 97 new species, representing 9 novel genera and belonging to 27 families of marine rare actinomycetes have been reported, with the highest numbers of novel isolates from the families Pseudonocardiaceae, Demequinaceae, Micromonosporaceae and Nocardioidaceae. Additionally, this study reviewed 167 new bioactive compounds produced by 58 different rare actinomycete species representing 24 genera. Most of the compounds produced by the marine rare actinomycetes present antibacterial, antifungal, antiparasitic, anticancer or antimalarial activities. The highest numbers of natural products were derived from the genera Nocardiopsis, Micromonospora, Salinispora and Pseudonocardia. Members of the genus Micromonospora were revealed to be the richest source of chemically diverse and unique bioactive natural products.

Mariniluteicoccus endophyticus sp. nov., an endophytic actinobacterium isolated from root of Ocimum basilicum

Two strains of Gram-stain-positive, aerobic, non-motile, irregular coccus-shaped bacteria, designated YIM 2617^T and YIM 2617-2, were isolated from the root of Ocimum basilicum. Phylogenetic analysis on the basis of 16S rRNA gene sequence comparison revealed that the two strains were closely related to Mariniluteicoccus flavus YIM M13146^T (98.1 and 98.0 % similarities, respectively) and formed a robust clade with M. flavus in the neighbour-joining tree. Optimum growth of the strains was observed at 28-32 °C, at pH 7.0-8.0 and in the presence of 0-2 % (w/v) NaCl. The chemotaxonomic profiles of the strains comprised anteiso-C_15 : 0 as the major cellular fatty acid, MK-9(H₄) as the predominant menaquinone, alanine, glycine, glutamic acid and ll-diaminopimelic acid as peptidoglycan components, and phosphatidylcholine and diphosphatidylglycerol as the major polar lipids. The G+C contents of the genomic DNA of strains YIM 2617^T and YIM 2617-2 were 66.4 and 66.6 mol%, respectively. DNA-DNA hybridizations of the two strains with M. flavus YIM M13146^T gave mean relatedness values of 47.6 ± 2.0 and 43.2 ± 1.5 %, respectively, while the relatedness value between them was 92.1 ± 2.2 %. On the basis of the data recorded from the present study, strains YIM 2617^T and YIM 2617-2 represent a novel species of the genus Mariniluteicoccus, for which the name Mariniluteicoccus endophyticus sp. nov. is proposed. The type strain is YIM 2617^T ( = KCTC 29482^T = DSM 28728^T = JCM 30097^T).

Culturable diversity and antimicrobial activity of Actinobacteria from marine sediments in Valparaíso bay, Chile

Marine-derived Actinobacteria are a source of a broad variety of secondary metabolites with diverse biological activities, such as antibiotics and antitumorals; many of which have been developed for clinical use. Rare Actinobacteria represent an untapped source of new bioactive compounds that have been scarcely recognized. In this study, rare Actinobacteria from marine sediments were isolated from the Valparaíso bay, Chile, and their potential to produce antibacterial compounds was evaluated. Different culture conditions and selective media that select the growth of Actinobacteria were used leading to the isolation of 68 bacterial strains. Comparative analysis of the 16S rRNA gene sequences led to identifying isolates that belong to the phylum Actinobacteria with genetic affiliations to 17 genera: Aeromicrobium, Agrococcus, Arthrobacter, Brachybacterium, Corynebacterium, Dietzia, Flaviflexus, Gordonia, Isoptericola, Janibacter, Microbacterium, Mycobacterium, Ornithinimicrobium, Pseudonocardia, Rhodococcus, Streptomyces, and Tessaracoccus. Also, one isolate could not be consistently classified and formed a novel phylogenetic branch related to the Nocardiopsaceae family. The antimicrobial activity of these isolates was evaluated, demonstrating the capability of specific novel isolates to inhibit the growth of Gram-positive and Gram-negative bacteria. In conclusion, this study shows a rich biodiversity of culturable Actinobacteria, associated to marine sediments from Valparaíso bay, highlighting novel rare Actinobacteria, and their potential for the production of biologically active compounds.