Biology subjects

Causevic, S.

Publications and source records attributed to Causevic, S..

5 recordsLinked to original sources

bioRxiv2026

Genome-scale metabolic models for a synthetic soil microbial community as a path for understanding community functioning

Microbial communities drive essential ecosystem processes, yet community-level behavior often deviates from predictions based on single-species studies. This mismatch reflects the context-dependent nature of nutrient dependencies, metabolic interactions, and resource availability in complex environments. Here, we present a mechanistic, species-resolved framework to dissect metabolism and nutrient exchange in a defined 21-member soil synthetic community spanning five bacterial phyla. For each isolate, we reconstructed and manually curated thermodynamically constrained genome-scale metabolic models, reconciling predictions with growth phenotypes across rich and minimal media. We mapped minimal nutrient requirements, cataloged environment-specific uptake and secretion profiles, and compared metabolic pathways to identify potential competitive and cooperative interactions. Using community-scale metabolomics, we assigned putative producers and consumers for detected metabolites and revealed medium-dependent shifts in niche overlap. This approach exposes metabolic strategies that govern community function and resilience, offering a predictive basis for understanding and manipulating microbiomes. Our findings highlight how species-level metabolic maps can clarify why microbial interventions succeed or fail and guide targeted manipulations in soil ecosystems.

systems biology↗

bioRxiv2024

Habitat filtering but not microbiota origin controls microbiome transplant outcomes in soil

Human activities cause global losses of soil microbiome diversity and functionality. Microbiota transplants offer a potential solution, but the factors influencing transplant success remain unclear. We investigated how microbiota origin affects microbiome mergers, hypothesizing that native strains through niche preference are better adapted to their habitat and will outcompete non-native ones. To test this, we contrasted transplants between soil microcosm-cultured topsoil or lakewater communities with a community of 21 soil bacteria (SynCom). In both cases, SynCom transplant increased resident productivity but permanently shifted compositions, although its abundance dropped from an initial 50-80% to <1% within two months. Both merged and non-merged communities resembled natural soil microbiota in comparisons with over 81,000 soil, sediment and lake compositional data. Our results show that habitat filtering and niche competition, more than microbiota origin, determine transplant outcomes. Despite the limited proliferation of SynCom transplants, their capacity to instill lasting community trajectory changes opens new paths for microbiome engineering. TEASEREven transiently present microbiota transplants can alter resident microbiome composition through processes governed by habitat filtering.

microbiology↗

bioRxiv2023

Niche Availability and Competitive Facilitation Control Proliferation of Bacterial Strains Intended for Soil Microbiome Interventions

Microbiome engineering, the rational manipulation of microbial communities and their habitats, is considered a crucial strategy to revert dysbiosis. However, the concept is in its infancy and lacks experimental support. Here we study the ecological factors controlling the proliferation of focal bacterial inoculants into taxa-complex soil communities and their impact on resident microbiota. We demonstrate using standardized soil microbiomes with different growth phases that the proliferation of typical soil inoculants depends on niche competition. By adding an artificial, inoculant selective niche to soil we improve inoculant proliferation and show by metatranscriptomics to give rise to a conjoint metabolic network in the soil microbiome. Furthermore, using random paired growth assays we demonstrate that, in addition to direct competition, inoculants lose competitiveness with soil bacteria because of metabolite sharing. Thus, the fate of inoculants in soil is controlled by niche availability and competitive facilitation, which may be manipulated by selective niche generation. TeaserTypical bacterial inoculants for soil microbiome engineering suffer from facilitating growth of native resident microorganisms

ecology↗

bioRxiv2021

Reproducible Propagation of Species-Rich Soil Microbiomes Suggests Robust Underlying Deterministic Principles of Community Formation

Microbiomes are typically characterised by high species diversity but it is poorly understood how such system-level complexity can be generated and propagated. Here, we used soils as a relevant model to study microbiome development. Despite inherent stochastic variation in manipulating species-rich communities, both laboratory-mixed medium complexity (21 soil bacterial isolates in equal proportions) and high-diversity natural top-soil communities followed highly reproducible succession paths, maintaining distinct soil microbiome signatures. Development trajectories and compositional states were different for communities propagated in soils than in liquid suspension. Microbiome states were maintained over multiple renewed growth cycles but could be diverged by short-term pollutant exposure. The different but robust trajectories demonstrated that deterministic taxa-inherent characteristics underlie reproducible development and self-organized complexity of soil microbiomes within their environmental boundary conditions. Our findings also have direct implications for potential strategies to achieve controlled restoration of desertified land. TEASERSpecies-rich soil microbiomes grow and propagate reproducibly despite inherent stochastic complexity, paving the way for soil restoration.

microbiology↗

bioRxiv2020

Characterization of the antimicrobial activity of the cell-penetrating peptide TAT-RasGAP317-326

Antibiotic resistance is an increasing threat for public health, underscoring the need for new antibacterial agents. Antimicrobial peptides (AMPs) represent an alternative to classical antibiotics. TAT-RasGAP317-326 is a recently described AMP effective against a broad range of bacteria, but little is known about the conditions that may influence its activity. Using RNA-sequencing and screening of mutant libraries, we show that Escherichia coli and Pseudomonas aeruginosa respond to TAT-RasGAP317-326 by regulating metabolic and stress response pathways, possibly implicating two-component systems. Our results also indicate that bacterial surface properties, in particular integrity of the lipopolysaccharide layer, influence peptide binding and entry. Finally, we found differences between bacterial species with respect to their rate of resistance emergence against this peptide. Our findings provide the basis for future investigation on the mode of action of this peptide and its potential clinical use as an antibacterial agent.

microbiology↗