Mining Indonesian Microbial Biodiversity for Novel Natural Compounds by a Combined Genome Mining and Molecular Networking Approach

Indonesia is one of the most biodiverse countries in the world and a promising resource for novel natural compound producers. Actinomycetes produce about two thirds of all clinically used antibiotics. Thus, exploiting Indonesia's microbial diversity for actinomycetes may lead to the discovery of novel antibiotics. A total of 422 actinomycete strains were isolated from three different unique areas in Indonesia and tested for their antimicrobial activity. Nine potent bioactive strains were prioritized for further drug screening approaches. The nine strains were cultivated in different solid and liquid media, and a combination of genome mining analysis and mass spectrometry (MS)-based molecular networking was employed to identify potential novel compounds. By correlating secondary metabolite gene cluster data with MS-based molecular networking results, we identified several gene cluster-encoded biosynthetic products from the nine strains, including naphthyridinomycin, amicetin, echinomycin, tirandamycin, antimycin, and desferrioxamine B. Moreover, 16 putative ion clusters and numerous gene clusters were detected that could not be associated with any known compound, indicating that the strains can produce novel secondary metabolites. Our results demonstrate that sampling of actinomycetes from unique and biodiversity-rich habitats, such as Indonesia, along with a combination of gene cluster networking and molecular networking approaches, accelerates natural product identification.

Serinibacter arcticus sp. nov., isolated from a thawing ancient ice wedge

A novel actinobacterium, strain K3-2^T, was isolated in pure culture from a thawing ancient ice wedge at Mammoth Mountain (Eastern Siberia, Russia). Colonies of strain K3-2^T were yellowish orange; cells had the fine structure typical of Gram-positive bacteria, were non-motile short rods and were non-spore-forming. Strain K3-2^T was mesophilic (optimum growth at 28 °С), but capable of growing at 4 °С. The cell-wall peptidoglycan of strain K3-2^T contained lysine (the diagnostic diamino acid), glutamic acid, alanine, ornithine, glycine and serine. The polar lipids were phosphatidylglycerol, lysophosphatidylserine, three unidentified phospholipids and glycolipids. The major fatty acids were anteiso-C_15 : 0 and C_16 : 0. The only menaquinone detected was MK-8(H₄). 16S rRNA gene analysis indicated that strain K3-2^T belongs to the genus Serinibacter. The closest taxonomically described relatives were Serinibacter salmoneus Kis4-28^T and Serinibacter tropicus PS-14-7^T, with 97.20 and 97.20 % 16 s rRNA gene sequence similarity, respectively. The average nucleotide identity value of the whole genome sequence between strain K3-2^T and S. salmoneus Kis4-28^T was 78.9 %. DNA-DNA relatedness values between strain K3-2^T and S. salmoneus DSM 21801^T (=Kis4-28^T) and S. tropicus VKPM Ac 2044^T (=PS-14-7^T) were 41 and 47 %. Thus, strain K3-2^T represents a novel species of the genus Serinibacter for which the name Serinibacter arcticus sp. nov. is proposed. The type strain is K3-2^T (DSM 103859^T=VKM Ас-2719^T).

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.

Phenolic metabolism and related heavy metal tolerance mechanism in Kandelia Obovata under Cd and Zn stress

In the present study, a set of pot culture experiments was conducted to reveal how the metabolism process of phenolic compounds was affected by cadmium (Cd) and zinc (Zn) and to further uncover heavy metal tolerance mechanisms in Kandelia obovata. After 60d of treatment, the biomass and chlorophyll a content in the leaves were suppressed, but total phenolic compounds in roots and leaves were improved by the increasing gradient of Cd or Zn concentrations; Total phenolic compounds significantly increased by 3.6-44.6% in the roots, and by 0.4-126.6% in the leaves. At the meantime, the activity of Shikimate dehydrogenase (SKDH), cinnamyl alcohol dehydrogenase (CAD), and polyphenol oxidase (PPO) in the roots increased by 11.2-307.6%, 12.4-175.4% and - 2.7-392.8%, and the results were 3.4-69.5%, 1.7-40.0%, 16.0-99.7% in the leaves. Higher toxicity of Cd than Zn, as well as slight alleviating effect of 100 mg kg^-1 Zn on 2.5 mg kg^-1 Cd were found. Additionally, a significantly positive correlation coefficients for relationship between phenolic metabolism related enzyme activity and Cd/Zn contamination levels was found, and leaf SKDH, leaf CAD, and leaf PPO activities were moderately correlated with leaf Cd (r = 0.39, r = 0.43, and r = 0.57, respectively) and leaf Zn (r = 0.44, r = 0.41, r = 0.19, respectively) content, which indicate that Cd and Zn play a previously unrecognized but major role in phenolic compounds synthesis, transport, and metabolism in K. obovata. The results also provided evidence that the application of high levels of Cd and Zn was accompanied by three phenolic metabolism pathways participating in heavy metal tolerance process.

Litorihabitans aurantiacus gen. nov., sp. nov., an actinobacterium of the family Beutenbergiaceae isolated from beach sand

A novel actinobacterium, designated HIsM16-52^T, was isolated from beach sand collected from Ishigaki Island in Japan and its taxonomic position was investigated by a polyphasic approach. Strain HIsM16-52^T contained both lysine and ornithine as the diagnostic diamino acids of the peptidoglycan. The predominant isoprenoid quinone was MK-8(H4) and the major fatty acids were anteiso-C15 : 0, C16 : 0 and C14 : 0. The detected polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and two unidentified phospholipids. The DNA G+C content was determined to be 73.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequence comparison revealed that strain HIsM16-52^T fell within the cluster of the family Beutenbergiaceae and formed a reliable cluster with the members of the genus Serinibacter. The highest 16S rRNA gene sequence similarities were obtained to species of the genus Serinibacter(97.8-97.9 %), followed by the genera Miniimonas (97.0 %), Beutenbergia (96.4 %) and Salana (95.9 %). However, strain HIsM16-52^T differed from the members of the genus Serinibacter and the other genera within the family Beutenbergiaceae in terms of chemotaxonomic characteristics. Therefore, strain HIsM16-52^T is concluded to represent a novel genus and species of the family Beutenbergiaceae, for which the name Litorihabitans aurantiacus gen. nov., sp. nov. is proposed. The type strain of L. aurantiacus is HIsM16-52^T (=NBRC 112290^T=TBRC 7759^T).

Kocuria pelophila sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove

A novel spherical actinobacterium, designated RS-2-3T, was isolated from the rhizosphere of a mangrove growing on Rambut Island, Indonesia, and its taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that strain RS-2-3T was related to the members of the genus Kocuria. The highest 16S rRNA gene sequence similarity value was observed with Kocuria marina KMM 3905T (97.0 %). The peptidoglycan type of strain RS-2-3T was found to be A3α with an interpeptide bridge comprising l-Ala4-5. The predominant menaquinone was MK-7(H2) and the major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The DNA G+C content was 71.8 mol%. These characteristics were consistent with those of members of the genus Kocuria. Meanwhile, physiological and biochemical characteristics revealed that strain RS-2-3T differed from the species of the genus Kocuria with validly published names. Therefore, strain RS-2-3T represents a novel species of the genus Kocuria, for which the name Kocuria pelophila sp. nov. is proposed. The type strain is RS-2-3T (=NBRC 110990T=InaCC A704T).