Lopez-Chevalier, H. B. | bioRxiv Science

bioRxiv2026

A closed genome of Streptococcus agalactiae ST347/II reveals a composite integrative element coupling nisin P biosynthesis to erm(B) and tet(O) in Dominican group B Streptococcus

Clindamycin is the alternative for intrapartum prophylaxis against group B Streptococcus in penicillin-allergic women, and whether it works depends on which lineages carry the resistance and on the mobile element that moves it. No Dominican group B Streptococcus genome has been closed. A Streptococcus agalactiae isolate from residual diagnostic material was sequenced twice on Oxford Nanopore, annotated, and screened against 83 genomes from a published Dominican maternal colonisation survey. The assembly is one circular chromosome of 2,066,859 bp with all seven rRNA operons resolved: ST347/CC19, serotype II, carrying erm(B), tet(O), mef(J) and msr(I). Two integrative conjugative elements were delimited: one of ~34 kb related to Tn5252 carrying erm(B) and tet(O), another of ~35 kb at a tRNA-Lys gene carrying mef(J) and msr(I). An eleven-gene class I lanthipeptide cluster lies 96 bp from the first element, on the same strand and with no annotated feature between them; its precursor encodes a 31-residue core identical to nisin P. The complete operon was found in 12 of the 83 genomes, 13 of 84 (15.5%) with the isolate. tet(O) was present in all 12 carriers and none of the 71 others (Fisher p = 1.03 x 10^-14), erm(B) in 12 of 12 against 3 of 71 (p = 4.70 x 10^-12). All eleven ST1 genomes lack both the operon and the nisin resistance protein; all 15 ST1010/IV genomes carry aac(6')-Ie/aph(2'')-Ia. Clindamycin resistance is therefore tightly associated with a lantibiotic-encoding element and contiguous with it in the one closed genome; in the drafts the relationship is statistical, and co-occurrence is not linkage. The ST1 absence predicts lineage-wide susceptibility, testable by deferred antagonism.

microbiology↗

bioRxiv2026

Environmental Drivers of Sediment Microbial Community Structure Across Restored, Altered, and Reference Mangroves in Las Calderas Bay, Dominican Republic

Mangrove reforestation is expanding across the Caribbean, but restoration success is still judged almost exclusively by tree survival and canopy cover. Whether the sediment microbiome, which governs carbon burial and nutrient cycling, follows the recovery of the vegetation remains largely unknown. We combined 16S rRNA gene metabarcoding (V4, Illumina MiSeq) with CHNS elemental analysis, pH and salinity measurements to compare sediment prokaryotic communities along 0-100 cm profiles in a reference, a reforested (Rhizophora mangle plantings since 2019) and an altered mangrove within the Las Dunas de Las Calderas Natural Monument, Dominican Republic (39 cores pooled into 28 depth-resolved composite samples). Reference sediments contained 2.5-5.5-fold more organic carbon (median 7.5% vs 3.0% in altered and 1.3% in reforested sediments), had higher C/N ratios and were less alkaline (pH 8.2 vs 8.8). Reference communities were more diverse and even, and differed in composition from both disturbed stands (pairwise PERMANOVA, R^2 ~ 0.09, adjusted P = 0.0015), whereas reforested and altered communities were statistically indistinguishable (R^2 = 0.04, P = 0.25). Disturbed sediments were dominated by Cyanobacteriota (~41-45% of reads), which tracked high pH, whereas reference sediments were enriched in Chloroflexota, Thermodesulfobacteriota and Thermoproteota, lineages linked to anaerobic degradation of complex organic matter and sulfate reduction. Depth structured communities by separating surface from subsurface layers, and sediment organic carbon and nitrogen were the only significant constraints in distance-based redundancy analysis. These results indicate that, within a few years of the first plantings (2019), reforestation had not restored the carbon-rich, anaerobic sediment habitat of the reference forest. We propose sediment organic carbon and microbial community structure as complementary indicators for mangrove restoration monitoring in the Caribbean.

microbiology↗