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.
Abstract
Hypersaline environments are dynamic ecosystems, the chemistry of which is significantly influenced by climate change, which in turn impacts the microbiota and biogeochemical processes. This study investigates the microbiome of Lake Karum, a hypersaline lake in the Danakil Depression, Ethiopia, with a particular focus on genome-based potential of climate-relevant biogeochemical processes.
The microbiomes of Lake Karum sediments and waters were dominated by halophilic Archaea (Halobacteriota) and Bacteria (Bacteroidota, Pseudomonadota, and Cyanobacteriota), with significant variation in community composition among sites, reflecting geochemical heterogeneity. Despite these taxonomic differences, sediment and water metagenomes exhibited broadly overlapping functional gene profiles. Genes involved in denitrification, carbon monoxide oxidation, osmotic stress tolerance, and utilisation of osmolytes were widespread and predominantly affiliated with Halobacteriales, indicating their pivotal role in nitrogen and carbon cycling. Genome‑resolved analyses revealed substantial intrageneric variation in metabolic potential within dominant halobacterial lineages as well as bacterial candidate phyla, including
Candidatus
Bipolaricaulota and
Candidatus
Salsurabacteriota, which encode genes linked to trace-gas metabolism and nitrogen cycling. Notably, a high‑quality metagenome‑assembled genome assigned to the
Candidatus
Salsurabacteriota was recovered that possesses novel combinations of functional genes not previously reported for this lineage.
This study provides a comprehensive genome‑resolved assessment of the taxonomic and functional diversity of the Lake Karum microbiome and identifies microbial taxa with the potential to drive key carbon, nitrogen, and sulfur cycling processes in a hypersaline lake. By revealing previously unrecognised metabolic capabilities within bacterial candidate phyla and highlighting intrageneric functional heterogeneity among dominant halophilic Archaea, this work advances understanding of how hypersaline microbial communities contribute to biogeochemical cycling in extreme environments.
Soda lakes represent some of the most extreme aquatic ecosystems on Earth, yet their microbial diversity and functional potential remain poorly characterized, particularly in East Africa. This study presents the first shotgun metagenomic analysis of bacterial communities inhabiting both water and sediment of Small Momela Lake, a soda lake in northern Tanzania. Samples were sequenced using Illumina NovaSeq and analyzed with MetaPhlAn4 and HUMAnN3 to resolve taxonomic composition, diversity patterns and predicted metabolic functions. Results showed 27 distinct species within Pseudomonadota, Bacteroidota, Firmicutes, Cyanobacteria and Verrucomicrobia dominated by sulfur-cycling Thioalkalivibrio denitrificans and uncultured Candidatus lineages. Notably, based on currently available literature multiple taxa were detected for the first time in soda lake environments globally, within Africa and East Africa, expanding the known biogeography of extremophiles. Functional profiling revealed a strong enrichment of nucleotide and amino acid biosynthesis pathways, alongside marker genes linked to pH homeostasis, osmotic stress tolerance, sulfur metabolism and carbon fixation. These features suggest pronounced metabolic flexibility supporting microbial persistence under extreme alkaline and saline conditions. These findings underscore Small Momela Lake as a critical reservoir of novel, functional bacterial resources with promising applications in biotechnology and bioprospecting.
A. A. Siima, Sadikiel E. Kaale, F. Mpenda et al.· Discover Life· 0 citations
The Eboliang Hu saline lakes in the hyper-arid Qaidam Basin is a high-altitude, weakly acidic hypersaline system with strong environmental gradients and limited nitrogen availability. To resolve its microbial ecology and evolutionary context, we performed genome-resolved metagenomic sequencing across four distinct habitats, reconstructing 46 medium- to high-quality metagenome-assembled genomes (MAGs) and a comprehensive gene catalog. The community shows pronounced spatial heterogeneity and is dominated by Thermodesulfobacteriota, Pseudomonadota, Bacteroidota, and archaeal lineages. Phylogenomic placement and large-scale sequence comparisons indicate that multiple dominant taxa exhibit affinity to marine- and subsurface-associated reference lineages, consistent with long-term isolation of a marine-derived ecosystem about 10–11 million years ago. Functional reconstruction reveals a distributed metabolic system in which carbon, nitrogen, and sulfur cycling are partitioned across taxa. Notably, hydrogen oxidation and arsenite oxidation are recurrent energy-producing strategies across dominant lineages, indicating redox flexibility under oligotrophic conditions. Comparative genomics further suggests lineage-specific adaptations to osmotic stress, UV exposure, and nutrient limitation. Horizontal gene transfer and phylogenetic incongruence among key metabolic genes indicate that co-evolutionary processes and gene exchange have contributed to functional innovation. These findings provide a framework for understanding microbial persistence and evolution in isolated extreme environments and offer potential analogs for extraterrestrial habitability.
Haoran Wang, Chunhui Ai, A. Barcan et al.· bioRxiv· 0 citations
Mangrove ecosystems play a critical ecological role in coastal protection, habitat provision, and the maintenance of biogeochemical cycles, thereby contributing to climate change mitigation and adaptation while reducing the impacts of ecosystem degradation in coastal environments. This study aimed to characterize the community structure and relative abundance of soil bacteria in mangrove ecosystems along the northern coast of Kendal across different anthropogenic disturbance conditions. To address this, we performed 16S rRNA amplicon sequencing on the Illumina MiSeq platform at four sites representing contrasting environmental conditions. Results showed microbial communities were dominated by the phyla Pseudomonadota, Bacillota, and Bacteroidota, with halotolerant coastal genera such as
Vibrio
,
Marinomonas
, and
Microbulbifer
being abundant. Lower bacterial diversity in more disturbed sites suggests potential environmental stress associated with settlement activities, aquaculture influence, and organic pollution inputs that may alter mangrove sediment conditions. By describing the taxonomic structure of bacterial communities, this study provides baseline information on mangrove soil microbiota and contributes to a better understanding of microbial diversity in coastal ecosystem. These findings contribute to SDG 13 (Climate Action) and SDG 14 (Life Below Water) by improving understanding of microbial components supporting mangrove ecosystem resilience.
R. Atunnisa, Alya Aisyah Fadhilla, Sitty Nur Syafa Bakri et al.· E3S Web of Conferences· 0 citations
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
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.
Juliette Audemard, Nicolas Creusot, Julie Leloup et al.· ISME Communications· 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