Environmental filtering shapes biosynthetic potential and resistome of antarctic microbiomes

Diverse biosynthetic pathways in Arctic hydrothermal biofilms

Biosynthetic gene clusters (BGCs) which encode diverse secondary metabolites are ubiquitous across microbiomes and support critical ecological functions. They also serve as attractive targets for new drug discovery. Here we combined genome-resolved metagenomics with long-read Nanopore RNA sequencing, yielding 1016 bacterial and 124 archaeal medium-to-high quality MAGs from previously unchartered microbial communities in Arctic hydrothermal vent biofilms. We identified 2965 BGCs from 870 metagenome-assembled genomes (MAGs) comprising a distinctive and rich diversity of BGCs, with ribosomally synthesized and post-translationally modified peptides (RiPPs) predominating across all samples. RiPPs and non-ribosomal peptide synthetases (NRPs), also known to encode metabolites with antimicrobial potential, are represented among the most expressed transcripts. Terpenes, though less expressed, contribute to microbial signaling and defense. Notably, we identify hydrogen cyanide (HCN) synthesis pathways in archaeal genomes, challenging the view that cyanogenesis is restricted to bacteria and eukaryotes. Our findings demonstrate that microbial adaptation to extreme environments favors RiPP-based biosynthesis and that HCN may play a role in archaeal ecological interactions. Moreover, microbial communities in Arctic hydrothermal vent biofilms provide a rich reservoir of unique bioactive compounds, with implications for drug discovery.

Metagenomic insights into biogeochemical functional potential and resistome dynamics of PM2.5 microbial communities.

Atmospheric particulate matter harbors diverse microorganisms, yet their functional potential in biogeochemical cycling and the associated risks of resistome remain poorly understood. Here, we performed metagenomic sequencing on PM2.5 samples collected across four months to unravel the microbial genetic repertoire involved in methane, nitrogen, phosphorus, and sulfur cycling, as well as the resistome, and pathogen composition. A broad range of functional genes was detected for each biogeochemical cycle, with more than 65% of gene subtypes shared across all months, indicating conserved functional signatures. In contrast, more than 80% of the resistome showed temporal variation in abundance, with the lowest richness observed in March. Temporal shifts were also observed in resistome composition, with several resistance determinants reaching higher abundances in April and May. Network analysis indicated frequent co-occurrence among several pathogenic and opportunistic taxa. Contig-based profiling identified 51 potential pathogenic taxa, including 32 human- or animal-associated taxa. In addition, both PM10 and PM2.5 concentrations were associated with pathogen abundance and functional gene richness (e.g., antibiotic resistance genes and virulence factors). Together, this metagenomic survey suggests contrasting temporal patterns between conserved biogeochemical functional potential and more variable resistome-related traits in PM2.5 microbial communities. While constrained by limited temporal coverage and sample size, this study provides preliminary insights into the ecological and potential public health relevance of airborne microbial communities in urban environments.

Siwa spring microbiomes as reservoirs of biosynthetic gene clusters: Unlocking natural product potential

The integrated bioinformatics pipeline enabled the reconstruction of 37 medium-to-high-quality metagenome-assembled genomes (MAGs), and recovered 147 BGCs mostly from Pseudomonadota, Actinomycetota, and Acidobacteriota phyla, highlighting the Siwa Oasis as a promising reservoir of unexplored biosynthetic potential and a valuable resource for natural product discovery to address global health challenges.

Markers of biosynthetic innovation in the Cyanobacteria

Genome mining of coastal cenote sediment-associated Streptomyces sp. NCA360 strain uncovers novel biosynthetic gene clusters and their regulatory architecture

The rise of antibiotic resistance has intensified the search for novel antimicrobial compounds, and bioprospecting of natural products from underexplored environments remains an effective strategy. The genus Streptomyces is one of the most prolific sources of pharmacologically active secondary metabolites, whose biosynthetic information is encoded in biosynthetic gene clusters (BGCs). However, many BGCs remain transcriptionally silent under standard laboratory conditions, underscoring the need to characterize the regulatory mechanisms governing their activation. In this study, we sequenced and analyzed the genome of Streptomyces sp. NCA360. The strain was isolated from sediments of the coastal cenote (a natural sinkhole) in the Yucatán Peninsula and selected for its antimicrobial and enzymatic activities. The high- quality genome assembly (89.7% completeness, <1% contamination) encoded 26 BGCs, of which 11 showed low similarity to characterized clusters and were classified as putatively novel (nBGCs). Resistance-guided prioritization identified duplicated resistance determinants, including an additional glyceraldehyde-3-phosphate dehydrogenase copy within a PKS-II cluster and Biotin_lipoyl/Carboxyl_trans domains within two divergent NRPS/PKS-I clusters, that were classified as candidate chemotherapeutic gene clusters. Biosynthetic pathways associated with clinically relevant antibiotics, including monobactams, carbapenems, and cephalosporins, were also detected. The regulatory architecture of the nBGCs revealed 26 regulatory genes, 20 transcription factor binding sites, and 20 rare TTA codons, reflecting heterogeneous and often multifactorial regulatory schemes. In silico protein-protein interaction analysis further revealed a coordinated cross-cluster regulation. The analysis of Streptomyces sp. NCA360 genome expands our understanding of the biosynthetic and regulatory diversity of Streptomyces and highlights the potential of cenotes as unique environments and reservoirs of new bioactive compounds with pharmaceutical relevance.

Unveiling active microbial processes in Earth's deepest seawater.

Analysis of microbiome samples collected from hadal seawaters via in situ filtration during 12 human-occupied vehicle dives identifies 135,073 non-redundant active proteins, with over 95% being hadal-specific.