Results suggest that prophage integration and induction are mechanisms that contribute to structuring the Sargassum microbiome and its functional profiles, potentially aiding in microbiome flexibility in changing environmental contexts.
Abstract
Background
Pelagic Sargassum has undergone significant range expansion and dramatic blooms in the Atlantic over the past 15 years. This alga's microbiome provides symbiotic functions that are believed to contribute to its ecological success. Recent research shows that Sargassum-associated bacteria are enriched in integrated prophages compared to the surrounding seawater and that these prophages are inducible by chemical and ultraviolet treatment.
Results
Here, we investigated a Sargassum-derived in vitro multispecies biofilm encompassing the dominant heterotrophic microbial members associated with Sargassum to probe the impacts of prophage induction on the composition of Sargassum microbiomes. Induction was quantified by coverage-based virus-to-host ratios in chemically induced treatments with Mitomycin C and non-induced controls, and the community composition and metabolic profiles were analyzed after Mitomycin C treatment. Chemical induction led to a significant increase in abundance and virus-to-host ratio of viral genomes linked to Vibrio metagenome-assembled genomes. This was accompanied by altered biofilm community composition, with a reduction in Vibrio bacterial abundance that opened niche space for other biofilm members in the genera Pseudoalteromonas, Alteromonas, and Cobetia. The induced Vibrio-associated phages encoded genes involved in quorum sensing, biofilm formation, virulence, and host metabolism. Induction led to the depletion of 17 metabolic modules, including functions related to energy metabolism and nitrogen utilization.
Conclusion
Due to the high frequency of lysogeny in the Sargassum microbiome and the susceptibility of prophages to chemical and ultraviolet light induction, these results suggest that prophage integration and induction are mechanisms that contribute to structuring the Sargassum microbiome and its functional profiles, potentially aiding in microbiome flexibility in changing environmental contexts.
This study demonstrates that Bacillus velezensis SPE2, a low-abundance isolate from the phycosphere of dinoflagellate, exhibits a wide degree of antagonistic activity against multiple marine Flavobacteriaceae strains, a dominant taxonomic group across the phycosphere of diverse phytoplankton species.
Runlin Cai, Hao Feng, Yang Liu et al.· Environmental Microbiome· 0 citations
The enrichment and expression of polyphenol degradation pathways define a previously underappreciated metabolic niche for SAR116 and provides new evidence emphasizing the importance of polyphenol metabolism in the marine carbon cycle.
Jordan T. Coelho, M. Borton, J. Thrash· bioRxiv· 0 citations
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
Solar salt pans are extreme hypersaline environments that represent functionally specialised microbial communities mediating essential biogeochemical transformation. Vedaranyam, a coastal region of the Bay of Bengal containing artificially constructed solar salterns for salt production. There is limited information available on the metagenome diversity and functional profiling of this saltpan, which prompted us to investigate it. Here, we report the first whole metagenome sequencing to explore the dynamics of the functional structure of microbial communities in saltpan during the preharvest and postharvest phases of salt production. Methanobacteriota and Pseudomonadota dominated both phases at the phylum level, while Halobacteria comprised the most abundant class (53.2% preharvest; 48% postharvest). A notable bloom of Dactylococcopsis salina was observed during postharvest (4.28% to 12.67%) and flock doubling of Cyanobacterota relative abundance (5.5% to 10.6%), reflecting photosynthetic primary production following salt removal. Conversely, during postharvest phase sulfur oxidising Guyparkeria halophila reduced 23 fold, while the DMSP accumulating osmolyte producer Salinibaculum marinum dominated preharvest (6.98%). However, functional classification of the metagenome revealed active participation of the microbial community across five major biogeochemical cycles. Encompassing carbon fixation by cyanobacteria and diverse haloarchaea, nitrogen cycling through diazotrophy and denitrification, a cryptic preharvest sulfur cycle coupling sulfate reduction and sulphide oxidation, phase shifted DMSP catabolism, and light driven bacteriorhodopsin through archaeal energy conservation. Metagenomic assembly yielded ten metagenomic assembled genomes (MAGs), revealing the taxonomic diversity and metabolic potential of the dominant halophilic community across biogeochemical cycles. These results provide critical insights into the ecological succession from an anaerobic, chemolithotrophy-rich preharvest microbial community to an aerobic, photosynthetically driven postharvest assemblage, advancing our understanding of microbial biogeochemistry in managed hypersaline ecosystems.
Steffy Joseph, L. Abraham, Krishnamanikumar Premachandran et al.· Microbial Ecology· 0 citations
Estuaries host a rich diversity of microorganisms, creating opportunities for animal–microbe interactions that shape host physiology. The sea anemone Nematostella vectensis spans the eastern coast of North America from Nova Scotia to Florida, and prior work shows that anemones from different regions harbor distinct microbial communities. Although the virome of the standard laboratory population has been characterized, population-level variation in viromes remains largely unknown. To address this gap, we conducted a mesocosm experiment using six N. vectensis populations to test whether geographic origin influences the diversity and functional potential of associated viruses and bacteria. We sampled individuals before mesocosm exposure and 14 days after to sequence their viromes, microbiomes, and host transcriptomes. We also collected anemones from a natural population to compare against experimental animals. Both virome and microbiome analyses revealed increased taxonomic and functional diversity after 14 days, with the strongest increase observed in lower-latitude populations. Notably, experimental anemones did converge toward the natural population’s community composition; however, population-specific interactions with viruses and microbes persisted. Differential gene expression indicated a modest host response overall, whereas WGCNA identified a clear north–south expression pattern. Together, these findings demonstrate that N. vectensis genotypes from locations along a latitudinal gradient maintain distinct viral and microbial associations, highlighting geographically structured host–microbe–virus relationships.
Sydney Birch, Yehu Moran, A. Reitzel· bioRxiv· 0 citations
Previous studies have demonstrated that quorum sensing (QS) can mitigate the impact of antibiotics on environmental microbial communities. Metagenomic analysis was used to examine AHL effects on the resistome in anaerobic fermentation microbiomes under antibiotic stress in this research. AHLs reduced ARGs, MGEs, and phage abundance compared to antibiotic-only samples following the addition of high concentrations (500 nmol/L) of AHLs. Phages and integrons played pivotal roles in shaping the resistome. Escherichia coli, Vibrio cholerae, and Pseudomonas aeruginosa were key targets affected by AHLs. Both the assembled environmental metagenomes and the complete genomes of isolated bacteria consistently support the broad potential of quorum-sensing systems in mediating the dissemination or regulation of resistome spreading. Quorum sensing systems are very likely to affect microbial community resistomes by regulating the phageome. These insights are valuable for refining fermentation and waste management processes, offering potential in environmental restoration and possibly curbing the spread of resistance genes.
Qin Zhou, Xiangyue Xu, Kun Mi et al.· Journal of Environmental Man...· 0 citations
