Biology subjects

Barcan, A. S.

Publications and source records attributed to Barcan, A. S..

3 recordsLinked to original sources

bioRxiv2026

Microbial evolution, biogeochemical functions, and environmental adaptations in a desert saline lake on the Qinghai-Tibet Plateau

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.

ecology↗

bioRxiv2026

Feed Composition and Antibiotic Supplements Modulate Digestive Enzyme Activities and Alter Gut Microbiome of Pacific White Shrimp

The transition from fishmeal to sustainable alternatives in aquaculture is essential, however the physiological and microbial impacts of alternative diets in shrimp remain poorly understood. Here, we examine how substituting fishmeal with plant-based proteins such as guar and soybean meals, the inclusion of feather meal, and the use of a commonly used antibiotic (gentamicin) influence digestive enzyme function, protein digestibility, and gut microbial assemblages in Litopenaeus vannamei (Pacific white shrimp). The guar-based diet notably altered gut microbiota composition and decreased leucine aminopeptidase activity while maintaining high protein digestibility (>90%). In contrast, the soya/feather diet caused greater disruption to enzyme activity and microbial communities, resulting in reduced digestibility ([~]75%). The gent/guar diet showed comparable digestibility and microbial stability to the guar diet, with only minor shifts at the genus level. Although digestibility data for the acclimation diet were unavailable, these findings highlight diet-specific physiological and microbial responses to fishmeal substitutes. This emphasizes the need to consider dietary formulation, digestive function, and microbiome dynamics when developing sustainable aquafeeds for shrimp farming. ImportanceThe Pacific white shrimp (Litopenaeus vannamei) is a cornerstone of global aquaculture, yet optimizing its diet remains challenging. Current shrimp farming heavily depends on fishmeal, an unsustainable protein source, and antibiotic use to maintain shrimp health raises concerns about antimicrobial resistance and environmental impacts. This study highlights how alternative dietary formulations, including plant-based proteins and antibiotic supplements, influence shrimp digestive physiology and reshape gut microbiomes. Understanding these interactions is crucial to developing feed formulations that support robust shrimp growth and health without excessive reliance on antibiotics or fishmeal. By demonstrating how specific dietary ingredients affect both shrimp digestion and beneficial gut bacteria, this research provides valuable insights that can inform sustainable and responsible shrimp aquaculture practices globally.

microbiology↗

bioRxiv2024

Understanding the Transfer and Persistence of Antimicrobial Resistance in Aquaculture Using a Model Teleost Gut System

The development, progression, and dissemination of antimicrobial resistance (AMR) is determined by interlinked human, animal, and environmental drivers, posing severe risks to human health. Conjugative plasmid transfer drives the rapid dissemination of AMR among bacteria. Besides antibiotic judicious use and implementation of antibiotic stewardship programs, mitigating antibiotic resistance spread requires an understanding of the dynamics of AMR transfer among microbial communities, as well as the role of various microbial taxa as potential reservoirs that promote long term AMR persistence. Here, we employed Hi-C, a high-throughput, culture-free technique, combined with qPCR, to monitor carriage and transfer of a multidrug-resistant plasmid within an Atlantic salmon in vitro gut model during florfenicol treatment, a benzenesulfonyl antibiotic widely deployed in fin-fish aquaculture. Microbial communities from the pyloric ceaca of three healthy adult farmed salmon were inoculated into three bioreactors developed for the SalmoSim gut system. The model system was then inoculated with an Escherichia coli strain ATCC 25922 carrying plasmid pM07-1 and treated with florfenicol at a concentration of 150 mg/L fish feed media for five days prior to a washout/recovery phase. Hi-C and metagenomic sequencing identified numerous transfer events, including to gram-negative and gram-positive taxa and, crucially, continuing transfer and persistence of the plasmid once florfenicol treatment had been withdrawn. Our findings highlight the role of commensal teleost gut flora as a reservoir for AMR, and our system provides a model to study how different treatment regimes and interventions may be deployed to mitigate AMR persistence.

microbiology↗