Biology subjects

Kurbessoian, T.

Publications and source records attributed to Kurbessoian, T..

4 recordsLinked to original sources

bioRxiv2025

Unraveling the diversity and functional potential of cyanosphere microbiomes assembled from terrestrial cyanobacteria

The cyanosphere consists of heterotrophic microorganisms residing within the exopolysaccharide sheath of cyanobacteria, acting as a crucial interface between the cyanobacteria and their surrounding environment. Understanding the interactions between cyanobacteria and their cyanospheres is essential for predicting the success of terrestrial cyanobacteria in providing ecosystem services in nutrient-poor environments. However, knowledge of the microbial diversity within the cyanosphere remains limited. In this study, we employed metagenomic sequencing to reconstruct 410 metagenome-assembled genomes (MAGs) from cyanosphere-associated microbes linked to 56 unialgal terrestrial cyanobacteria cultures, representing 12 distinct cyanobacteria orders. Our findings revealed that the composition of cyanosphere microbial communities was unique to each cyanobacterial host and was significantly shaped by environmental factors such as habitat, precipitation, and temperature from which the cultures were originally obtained. Notably, three microbial genera, Brevundimonas, Devosia, and Sphingopyxis, were present in over 30% of the cyanospheres, forming a core cyanosphere microbiome. Functional gene analysis showed a distinction between the cyanobacteria and their associated cyanospheres, with dissimilatory nitrate reduction being the dominant pathway in the cyanosphere, while nitrogen fixation was more common in the cyanobacteria. Three cyanospheres also contained nitrogen fixation genes of which two hosts were nitrogen fixation capable themselves. The cyanosphere harbored genes for polysaccharide lyases, indicating a possible link to the exopolysaccharides produced by the cyanobacteria. Given the observed variability in microbial community composition and function across different cyanobacterial hosts, future ecological assessments and restoration efforts involving cyanobacteria should not only focus on the cyanobacteria themselves but also consider their associated microbial communities. ImportanceOur study identifies members of a highly understudied, and potentially under-valued, microbial community -- the cyanosphere. We used a diversity of terrestrial cyanobacteria to understand how the cyanosphere composition and predicted functions were influenced by the host cyanobacterium and environmental factors using metagenomics. This is a new approach to study the cyanosphere and provides insights into the diversity of terrestrial microbial communities. Importantly, our results underscore the need to consider microbial consortia when assessing the ecological potential of cyanobacteria in terrestrial restoration.

ecology↗

bioRxiv2024

Description of new micro-colonial fungi species Neophaeococcomyces mojavensis, Coniosporium tulheliwenetii, and Taxawa tesnikishii cultured from biological soil crusts

Black yeasts and relatives comprise Micro-Colonial Fungi (MCFs) which are slow-growing stress-tolerant micro-eukaryotes that specialize in extreme environments. MCFs are paraphyletic and found in the Orders Chaetothyriales (Eurotiomycetes) and Dothideales (Dothidiomycetes). We have isolated and described three new MCFs species from desert biological soil crusts (BSCs) collected from two arid land regions: Joshua Tree National Park (Mojave Desert) and UC Natural Reserve at Boyd Deep Canyon (confluence of Mojave and Sonoran Deserts). BSCs are composite assemblages of cyanobacteria, eukaryotic algae, fungi, lichens, and bryophytes embedded into the surface of desert soils, providing a protective buffer against the harsh desert environment. Our work focused on one type of desert BSC, the cyanolichen crust dominated by Collema sp. Using culture-dependent protocols, three MCFs were axenically isolated from their respective samples along with the extracted DNA. Their genomes were sequenced using Illumina and Nanopore, and finally assembled and annotated using hybrid assembly approaches and established bioinformatics pipelines to conduct final taxonomic phylogenetic analysis and placement. The three species described here are unique specimen from desert BSCs, here we introduce, Neophaeococcomyces mojavensis (Chaetothyriales), Cladosporium tulheliwenetii (Dothideales), and Taxawa tesnikishii (Dothideales).

microbiology↗

bioRxiv2023

Mrs4 loss of function in fungi during adaptation to the cystic fibrosis lung

The genetic disease cystic fibrosis (CF) frequently leads to chronic lung infections by bacteria and fungi. We identified three individuals with CF with persistent lung infections dominated by Clavispora (Candida) lusitaniae. Whole genome sequencing analysis of multiple isolates from each infection found evidence for selection for mutants in the gene MRS4 in all three distinct lung-associated populations. In each population, we found one or two unfixed, non-synonymous mutations in MRS4 relative to the reference allele found in multiple environmental and clinical isolates including the type strain. Genetic and phenotypic analyses found that all evolved alleles led to loss of function of Mrs4, a mitochondrial iron transporter. RNA Seq analyses found that Mrs4 variants with decreased activity led to increased expression of genes involved in iron acquisition mechanisms in both low iron and replete iron conditions. Furthermore, surface iron reductase activity and intracellular iron was much higher in strains with Mrs4 loss of function variants. Parallel studies found that a subpopulation of a CF-associated Exophiala dermatiditis infection also had a non-synonymous loss of function mutation in MRS4. Together, these data suggest that MRS4 mutations may be beneficial during chronic CF lung infections in diverse fungi perhaps for the purposes of adaptation to an iron restricted environment with chronic infections.

microbiology↗

bioRxiv2022

In host evolution of Exophiala dermatitidis in cystic fibrosis lung micro-environment

Individuals with cystic fibrosis (CF) are susceptible to chronic lung infections that lead to inflammation and irreversible lung damage. While most respiratory infections that occur in CF are caused by bacteria, some are dominated by fungi such as the slow-growing black yeast Exophiala dermatitidis. Here, we analyze isolates of E. dermatitidis cultured from two samples, collected from a single subject two years apart. One isolate genome was sequenced using long-read Nanopore technology as an in-population reference to use in comparative single nucleotide polymorphism (SNP) and insertion-deletion (INDEL) variant analyses of twenty-three isolates. We then used population genomics and phylo-genomics to compare the isolates to each other as well as the type strain E. dermatitidis NIH/UT8656. Within the CF lung population, three E. dermatitidis clades were detected, each with varying mutation rates. Overall, the isolates were highly similar suggesting that they were recently diverged. All isolates were MAT 1-1, which was consistent with their high relatedness and the absence of evidence for mating or recombination between isolates. Phylogenetic analysis grouped sets of isolates into clades that contained isolates from both early and late time points indicating there are multiple persistent lineages. Functional assessment of variants unique to each clade identified alleles in genes that encode transporters, cytochrome P450 oxidoreductases, iron acquisition and DNA repair processes. Consistent with the genomic heterogeneity, isolates showed some stable phenotype heterogeneity in melanin production, subtle differences in antifungal minimum inhibitory concentrations, growth on different substrates. The persistent population heterogeneity identified in lung-derived isolates is an important factor to consider in the study of chronic fungal infections, and the analysis of changes in fungal pathogens over time may provide important insights into the physiology of black yeasts and other slow-growing fungi in vivo.

microbiology↗