Jan 2026· ISME Communications· Vol 6 1, pp.
ycag226
· 0 citations
Medicine
TL;DR
These findings deepen the understanding of Microcystis’ phycosphere functioning and demonstrate the value of multi-omics systems biology approaches, while suggesting that metabolic complementarity between species and across phycospheres could play a role in bloom-associated microbiome structure.
Abstract
Favored by global changes, freshwater cyanobacterial harmful blooms generate major ecological, economic, and public health challenges. Microcystis, one of the most widespread cyanobacterial genera, grows within a phycosphere where specialized interactions with its microbiome occur, that are suspected to influence bloom appearance and its potential toxicity. Using a combination of metagenomics, metabolomics, and metabolic modeling, we characterized the culture-associated phycospheres of 12 Microcystis strains isolated from a French pond. The distribution of metabolic reactions within Microcystis was consistent with their genospecies, whereas the metabolic landscape at the community level diverged from cyanobacterial phylogeny, indicating partial functional decoupling between cyanobacteria and their associated microbiomes. Bacteria associated with the simplified phycospheres substantially expanded the metabolic repertoire of the system, while maintaining functional redundancy within and across communities. On the other hand, endometabolomic profiles were largely driven by cyanobacterial metabolic outputs, whereas exometabolomic analysis did not reveal metabolites involved in exchange processes. Metabolic modeling, together with the identification of toxic specialized metabolites produced by specific biosynthetic gene clusters, further highlighted differences in metabolic potential among phycospheres. Together, these findings deepen the understanding of Microcystis' phycosphere functioning and demonstrate the value of multi-omics systems biology approaches, while suggesting that metabolic complementarity between species and across phycospheres could play a role in bloom-associated microbiome structure.
Recognizing the central role of microorganisms in greenhouse gas (GHG) cycling in aquaculture systems, we provide a genome- and gene-centric perspective on the metabolic potential for CO₂ and CH₄ cycling in prawn aquaculture ponds across seasons and contrasting culture practices. Using TaxVAMB, we recovered 78 high- and medium-quality metagenome-assembled genomes (MAGs), including previously underappreciated taxa such as Bathyarchaeia and Terriglobia. Metabolic profiling revealed that CO₂ and CH₄ cycling constitute a minor fraction of the pond’s metabolic potential, dominated instead by heterotrophic processes such as fermentation, oxygen metabolism, and iron reduction. The relative metabolic weight of these carbon-cycling pathways was lower than that reported for permafrost, wetland, peatland, deep-sea, and human gut microbiomes. An integrated metabolic network suggested that genetic potential for CO₂ production is primarily driven by pyruvate and acetyl-CoA oxidation, while methanogenesis and methane oxidation genes together encode the potential for internal carbon-recycling loops via canonical archaeal and bacterial pathways. Seasonal dynamics, rather than management treatment, strongly influenced functional gene abundances, with CO₂ fixation and CH4 oxidation genes increasing toward the late season. Bathyarchaeia emerged as the most versatile taxon for CO₂ cycling and methanogenesis, with stable relative abundance across seasons and treatments. This study underscores the role of seasonally evolving microbial networks in regulating carbon turnover and the potential for CO2 and CH4 emissions in prawn aquaculture ponds.
A. Bashar, A. M. Djurhuus, P. Browne et al.· bioRxiv· 0 citations
A comprehensive genome‑resolved assessment of the taxonomic and functional diversity of the Lake Karum microbiome is provided and microbial taxa with the potential to drive key carbon, nitrogen, and sulfur cycling processes in a hypersaline lake are identified.
M. Macey, Velislava Ilieva, B. Stephens et al.· Environmental Microbiome· 0 citations
Myxococcota are globally distributed bacteria renowned for their remarkable ecological and biotechnological significance due to their complex lifestyles, social behaviour, and secondary metabolite production. Despite their ubiquity in diverse environments, including soil, marine, and extreme habitats, their diversity and ecological roles remain underexplored. Here, we utilized the Microflora Danica dataset, encompassing >10,000 metagenomes and >400 rRNA gene datasets from various environments in Denmark, to investigate the distribution, diversity, and metabolic potential of Myxococcota. We show that Myxococcota are ubiquitous but strongly structured by environment, with soil-associated lineages enriched in predatory and multicellular development traits, whereas aquatic-associated taxa exhibit alternative lifestyles, including anaerobic metabolism and phototrophy. Comparative genomic analysis reveals widespread potential for secondary metabolite production, hydrocarbon degradation, and organohalide transformation, alongside diverse contribution to carbon and nutrient cycling. Together, these findings redefine Myxococcota as a functionally diverse and ecologically differentiated phylum, extending beyond canonical predation and multicellularity, and underscore their promise as large reservoir of unexplored functional potential for biotechnological applications in drug discovery and environmental remediation.
F. Petriglieri, Yu Yang, Z. Kondrotaite et al.· bioRxiv· 0 citations
Cyanobacterial blooms are intensifying globally due to nutrient enrichment and climate change, producing a chemically diverse suite of peptides, in addition to the well-studied microcystins. These cyanopeptides, including anabaenopeptins, cyanopeptolins, aeruginosins, and microginins, frequently co-occur in blooms across freshwater and estuarine systems and exhibit potent protease- and phosphatase-inhibitory activities at environmentally relevant concentrations. This review synthesizes emerging evidence that these compounds may profoundly influence both environmental and host-associated microbiota. Bloom-associated cyanopeptides and related environmental stressors may act as ecological filters in aquatic ecosystems, contributing to microbial dysbiosis, which is characterized by changes in community composition and sometimes reduced diversity. This also leads to the enrichment of toxin-degrading components of microbiota taxa, such as Sphingomonas and Novosphingobium, and metabolic reconfiguration toward xenobiotic degradation. Microbiota exposed to bloom-associated cyanopeptides rich conditions in aquatic ecosystems occur in free and particulate forms in the water column, and these forms often recover and adapt more rapidly than host-associated microbiomes. However, conflicting results have been observed in fish gut microbiota data responses, where some host-associated microbiomes show relatively fast recovery and others show delayed restoration. Multi-omics studies have revealed conserved mechanisms linking cyanopeptide exposure to shifts in microbial structure and metabolic pathways, which together can affect host physiology. However, most studies remain biased toward microcystin-LR, and there is a significant gap in our understanding of how other cyanopeptides alter free-living and host gut microbiota in aquatic ecosystems. Therefore, this review identifies an important next step in research, which should focus on how non-microcystin cyanopeptides affect free and host-gut microbiota, and these studies should include multiomics approaches to unravel these changes under natural field observations and controlled exposure. Recognizing microbiota as both targets and agents of cyanopeptide transformation offers a new framework for understanding bloom ecology, because this knowledge will aid in predicting ecosystem recovery and mitigating the ecological risks of these compounds.
Mathias Ahii Chia, A. Lorenzi, M. K. Cordeiro-Araújo et al.· Science of the Total Environ...· 0 citations
Sulfate-reducing microbiomes (SRMs) have shown strong potential for antibiotic remediation, yet the active microorganisms and community-level strategies associated with sulfamethoxazole (SMX) biotransformation remain poorly understood. In this study, long-term bioreactor operation (269 days; 500-1500 μg/L SMX), DNA-stable isotope probing (DNA-SIP), and metagenomic analyses were integrated to investigate the microbial contributors and functional organization underlying SRM-driven SMX biotransformation. Desulfobacterium, a key SRM member, was co-enriched with Geobacter and Leptolinea in the 13C-labeled heavy fraction, suggesting potential metabolic complementarity during community-level SMX biotransformation. Genome-resolved analyses further revealed structured patterns of inferred horizontal gene transfer (HGT) and predicted metabolite exchange among keystone taxa. The transferred genes were mainly associated with energy conservation, transport, sulfur-associated metabolism, and stress-response functions, whereas the predicted exchanged metabolites included carbon metabolites, amino acid-related sulfur compounds, purine-related intermediates, and cofactor-associated metabolites. Together, these findings suggest that HGT-associated functional redistribution and metabolic complementarity may contribute to the persistence and coordinated activity of sulfate-reducing microbiomes under high SMX stress. This study links SIP-identified active populations with genome-inferred interaction patterns in a sulfate-reducing system and provides new insight into microbiome-based anaerobic strategies for antibiotic-containing wastewater treatment.
Yanyan Jia, Yujian Yan, Ben Chen et al.· Environmental Science and Te...· 0 citations
The findings expand current knowledge of oyster-associated cyanobacteria and highlight their metabolic diversity in the Amazon region, as well as genomic traits that may be associated with adaptation to dynamic estuarine environments.
M. J. Machado, F. R. Jacinavicius, R. B. Dextro et al.· Phycology· 0 citations