Actinobacteria from Arctic and Atlantic deep-sea sediments—Biodiversity and bioactive potential

Abstract

The deep-sea covers over 70% of the Earth’s surface and harbors predominantly uncharacterized bacterial communities. Actinobacteria are the major prokaryotic source of bioactive natural products that find their way into drug discovery programs, and the deep-sea is a promising source of biotechnologically relevant actinobacteria. Previous studies on actinobacteria in deep-sea sediments were either regionally restricted or did not combine a community characterization with the analysis of their bioactive potential. Here we characterized the actinobacterial communities of upper layers of deep-sea sediments from the Arctic and the Atlantic (Azores and Madeira) ocean basins, employing 16S rRNA metabarcoding, and studied the biosynthetic potential of cultivable actinobacteria retrieved from those samples. Metabarcoding analysis showed that the actinobacterial composition varied between the sampled regions, with higher abundance in the Arctic samples but higher diversity in the Atlantic ones. Twenty actinobacterial genera were detected using metabarcoding, as a culture-independent method, while culture-dependent methods only allowed the identification of nine genera. Isolation of actinobacteria resulted on the retrieval of 44 isolates, mainly associated with Brachybacterium, Microbacterium, and Brevibacterium genera. Some of these isolates were only identified on a specific sampled region. Chemical extracts of the actinobacterial isolates were subsequently screened for their antimicrobial, anticancer and anti-inflammatory activities. Extracts from two Streptomyces strains demonstrated activity against Candida albicans. Additionally, eight extracts (obtained from Brachybacterium, Brevibacterium, Microbacterium, Rhodococcus, and Streptomyces isolates) showed significant activity against at least one of the tested cancer cell lines (HepG2 and T-47D). Furthermore, 15 actinobacterial extracts showed anti-inflammatory potential in the RAW 264.4 cell model assay, with no concomitant cytotoxic response. Dereplication and molecular networking analysis of the bioactive actinobacterial extracts showed the presence of some metabolites associated with known natural products, but one of the analyzed clusters did not show any match with the natural products described as responsible for these bioactivities. Overall, we were able to recover taxonomically diverse actinobacteria with different bioactivities from the studied deep-sea samples. The conjugation of culture-dependent and -independent methods allows a better understanding of the actinobacterial diversity of deep-sea environments, which is important for the optimization of approaches to obtain novel chemically-rich isolates.

High Arctic seawater and coastal soil microbiome co-occurrence and composition structure and their potential hydrocarbon biodegradation

“…Ilumatobacter sp. is not endemic to Arctic waters and has been identified in various locations, including coastal sand [ 50 ], estuary sediments [ 51 ], coastal sediments of the Mediterranean Sea [ 52 ], and Arctic deep-sediments [ 53 ]. Our study suggests that cold-adapted marine and sediment bacteria were commonly present during the summer months, but most of the bacteria found in our beach sediment and seawater metagenomes were not the classical marine hydrocarbon-degraders (i.e.…”

Study of marine microorganism metabolites: new resources for bioactive natural products

“…Oxidative stress plays an important role in endothelial dysfunction ( Miksch et al, 2021 ), lung disease, gastrointestinal dysfunction, and atherosclerosis, all of which are associated with inflammatory responses ( Ribeiro et al, 2023 ). The crude extract of pigment was used as an anti-inflammatory agent to induce paw edema in male Wistar rats.…”

“…Chemical extracts of marine Actinobacteria isolates were screened for their antimicrobial and anti-inflammatory activities as described in ( Ribeiro et al, 2023 ). Extracts of two Streptomyces strains showed activity against Candida albicans .…”

Streptomyces profundus sp. nov., a novel marine actinobacterium isolated from deep-sea sediment of Madeira Archipelago, Portugal

“…Several Streptomyces species have been isolated from deep-sea sediments and their contribution to the production of new secondary metabolites has been prolific [9,10]. During the isolation of actinomycetes from deep-sea sediment samples collected in the Madeira Archipelago (Portugal), a previously uncharacterized Streptomyces strain was obtained [11]. In this paper, we characterize this strain using a polyphasic approach, aiming to determine its taxonomic position as a new species.…”