Skatole, primarily generated via the anaerobic metabolism of tryptophan, is a pervasive nitrogenous heterocyclic malodorant. While ubiquitous in various environments, its microbial remediation in saline ecosystems remains poorly documented. In this study, a skatole-degrading microbial consortium was enriched from marine sediments. High-throughput sequencing revealed distinct successional dynamics during domestication, with Pseudomonas becoming predominant (89.23%) and Rhodococcus persisting as a potential functional taxon (1.98%). An efficient isolate, Rhodococcus sp. SJ-2, was successfully obtained from the consortium. SJ-2 could completely remove 100 mg/L of skatole within 24 h in 2216E medium and 60 h in marine mineral culture medium, with optimal activity at 30-35 °C and pH 6.0-9.0. It also maintained skatole-removing activity across a broad salinity range of 0-45‰ NaCl. 3-Methyloxindole was identified as a detectable intermediate, and the enzymes involved in skatole degradation were inducible. Genomic analysis revealed a 5.77 Mb circular chromosome and two plasmids, but no previously reported skaA homologs, suggesting an as-yet-uncharacterized oxidative system. Bioaugmentation experiments in freshwater and marine sediment microcosms demonstrated that SJ-2 inoculation accelerated skatole removal, shortening the complete removal time to 6 h and 12 h, respectively. Amplicon sequencing showed that bioaugmentation was associated with an increased relative abundance of Rhodococcus and with predicted functional shifts related to aromatic compound degradation. These findings identify Rhodococcus sp. SJ-2 as a promising marine-derived candidate for skatole removal in saline odor-control settings and provide a useful foundation for future studies on the molecular basis of skatole catabolism.
The behaviour of M.thermautotrophicus under suboptimal conditions is described and the need for further optimization to improve methane production yields is highlighted.
N. Hanišáková, Anna Štaud, Eva Kotrlová et al.· Bioresource Technology· 0 citations
Hypersaline soils are poly-extreme terrestrial habitats characterized by high salinity, in some cases heavy-metal contamination, temperature fluctuations, and nutrient limitation. These conditions impose strong selective pressures, and many prokaryotic inhabitants still remain uncultured. Here, we conducted an extensive culturomics study of 549 isolates from the hypersaline soils of the Odiel Saltmarshes Natural Area (Southwest Spain) and compared the results with previously generated shotgun metagenomic datasets from the same environment in order to evaluate taxonomic composition, functional potential, and ecological representativeness. Cultivation across media containing 7.5%, 15%, and 25% (w/v) total salts yielded microorganisms belonging to three major phyla: Pseudomonadota, Bacillota (Bacteria) and Halobacteriota (Archaea). At the genus level, bacterial isolates were dominated by Marinobacter, Halomonas, and Aquibacillus at 7.5% (w/v) salinity, whereas extremely halophilic archaea, including Halorubrum, Halogeometricum, and Haloarcula, were predominantly recovered from media containing 25% (w/v) salts. Among the isolates, 57 strains displayed identity values < 98.65% for 16S rRNA gene sequence comparison, suggesting their putative status as new taxa. Comparison with metagenomic datasets showed that culture-dependent approaches successfully recovered the dominant haloarchaeal groups but missed some abundant bacterial phyla, such as Gemmatimonadota. Conversely, culturomics enabled the isolation of unknown species from the rare biosphere, including representatives of the novel genus Terrihalobacillus, which are typically detected at low abundance in metagenomic datasets. Together, these results demonstrate the complementarity of culturomics and metagenomics and provide an insight into the microbial communities inhabiting the hypersaline soils of the Odiel Saltmarshes.
Rhodococcus ruber MSA14, isolated from oil-polluted coastal sediments in Baja California, Mexico, has previously been shown to degrade pyrene, highlighting its potential for polycyclic aromatic hydrocarbons (PAH) bioremediation. In the present study, MSA14 was subjected to adaptive laboratory evolution using progressively increasing concentrations of pyrene as the sole carbon and energy source, resulting in the isolation of a high-pyrene-adapted strain, R. ruber AD0911. Compared with the parental strain, AD0911 displayed improved growth and pyrene tolerance, modified colony morphology, enhanced biofilm biomass, altered biosurfactant production patterns, and increased oxidative stress tolerance. Whole-genome sequencing and breseq-based variant calling identified 75 mutations in AD0911 relative to MSA14, affecting membrane-associated proteins, transcriptional regulators, cell signaling, and stress-response components. These adaptive mechanisms identified in AD0911 provide new insight into the evolution of bacterial tolerance under high hydrocarbon stress and suggest that adaptation to extreme pyrene exposure was driven primarily by physiological optimization rather than changes in PAH catabolic enzymes.
Gabriela Calcáneo-Hernández, S. Embarcadero-Jiménez, Hortencia Silva-Jiménez et al.· Current Microbiology· 0 citations
