Biology subjects

Bizic, M.

Publications and source records attributed to Bizic, M..

6 recordsLinked to original sources

bioRxiv2026

Giant bacteria in gut microbiomes

The advent of sequencing-based omics has transformed our understanding of the gut microbiome, enabling microbial communities to be characterised at unprecedented scale and resolution. However, these approaches provide limited information about cellular traits such as size and morphology. Giant bacteria remain largely overlooked in gut microbiome research, despite their extraordinary cell size, extreme polyploidy and unusual reproductive strategies. Epulopiscium, one of the largest known heterotrophic bacteria, has been studied primarily as an intestinal symbiont of surgeonfish, leaving its broader host range unresolved. Here we show, by a large-scale analysis of publicly available 16S ribosomal RNA amplicon samples, alongside locally collected human samples, that Epulopiscium spp. occur across diverse hosts, including humans and a broad diversity of animals. Full-length 16S rRNA gene phylogenies resolved multiple Epulopiscium-related lineages with distinct host compositions. Among human samples, Epulopiscium sequences were most abundant during the first year of life. In adults, abundance varied across disease states, increasing in inflammatory bowel disease and colorectal cancer while decreasing in neurological conditions compared with a healthy adult baseline. Similar patterns were also observed in mouse models. Our study broadens the known host range of Epulopiscium and establishes giant bacteria as an overlooked component of gut microbiome diversity. These findings highlight the need to combine sequence-based studies with classical microbiological techniques to identify organisms with unique traits, otherwise hidden by taxonomy or phylogeny.

microbiology↗

bioRxiv2026

Intracellular genomic variability driven by cellular compartmentalization in the giant bacterium Achromatium spp

Bacteria of the genus Achromatium harbor hundreds of chromosomes that were previously suggested to be genetically diverse. By sequencing multiple regions from individual cells, we demonstrate that chromosomes within a single cell differ in nucleotide and amino acid sequence, reaching levels of divergence well below accepted bacterial species boundaries and below the range associated with homologous recombination. Sequencing of dividing cells further revealed that daughter cells inherit distinct chromosome populations, a mode of inheritance previously associated with sexual reproduction in eukaryotes. Combining subcellular sequencing with high-resolution microscopy, we reconstruct the three-dimensional cellular architecture of Achromatium and show that extensive intracellular heterogeneity arises from the spatial segregation of chromosome populations by the cells internal structure, which limits genome-wide recombination. Our findings establish cellular architecture as a determinant of genome evolution in giant polyploid bacteria and identify spatial genome segregation as a mechanism enabling the maintenance and inheritance of divergent chromosome populations in bacteria.

microbiology↗

bioRxiv2024

Phenotypic variability between closely related Trichodesmium strains as a means to making the most out of heterogeneous microenvironments

The cynobacteria Trichodesmium spp., play an important role in oceanic carbon and nitrogen cycles. Forming colonies that host diverse microorganisms likely enhances Trichodesmiums metabolic flexibility and resilience. Combining single-colony metagenomics and metatranscriptomics with a novel bioinformatic approach we investigated the community composition and transcriptional activity of 69 individual Trichodesmium thiebautii colonies collected from the northern Red Sea, Israel. Three Trichodesmium strains were detected in all colonies, each with a heterogenous yet distinct transcriptional-activity profile. N-fixation, superoxide dismutase, and ATPase activities were similar among colonies, while P and Fe uptake, as well as photosynthesis, were high in only few colonies. Colonies had no core microbiome with >70% dissimilarity in the associated microbial communities, yet, the abundance of some species was correlated with the activity of specific Trichodesmium strains. We propose Trichodesmium occupies heterogeneous microenvironments with which it deals through inter-strain phenotypic variability further fine-tuned through interactions with beneficial, non-fixed, heterotrophic colonizers.

microbiology↗

bioRxiv2022

From microbes to mammals: pond biodiversity homogenization across different land-use types in an agricultural landscape

Local biodiversity patterns are expected to strongly reflect variation in topography, land use, dispersal boundaries, nutrient supplies, contaminant spread, management practices and other anthropogenic influences. In contrast, studies focusing on specific taxa revealed a biodiversity homogenization effect in areas subjected to long-term intensive industrial agriculture. We investigated whether land use affects biodiversity and metacommunity structure in 67 kettle holes (KH) representing small aquatic islands embedded in the patchwork matrix of a largely agricultural landscape comprising grassland, forest, and arable fields. These KH, similar to millions of standing water bodies of glacial origin, spread across northern Europe, Asia, and North America, are physico-chemically diverse, differ in the degree of coupling with their surroundings. We assessed biodiversity patterns of eukaryotes, Bacteria and Archaea in relation to environmental features of the KH, using deep-amplicon-sequencing of eDNA. First, we asked whether deep sequencing of eDNA provides a representative picture of KH biodiversity across the three domains of life. Second, we investigated if and to what extent KH biodiversity is influenced by the surrounding land-use. Our data shows that deep eDNA amplicon sequencing is useful for in-depth assessments of cross-domain biodiversity comprising both micro- and macro-organisms, but, has limitations with respect to single-taxa conservation studies. Using this broad method, we show that sediment eDNA, integrating several years to decades, depicts the history of agricultural land-use intensification. The latter, coupled with landscape wide nutrient enrichment (including by atmospheric deposition), groundwater connectivity between KH and organismal movement in the tight network of ponds, resulted in a biodiversity homogenization in the KH water, levelling off todays detectable differences in KH biodiversity between land-use types.

ecology↗

bioRxiv2020

Genomic and morphologic characterization of a planktonic Thiovulum (Campylobacterota) dominating the surface waters of the sulfidic Movile Cave, Romania

Life in Movile Cave (Romania) relies entirely on carbon fixation by bacteria. The microbial community in the surface water of Movile Caves hypoxic air bells is dominated by large spherical-ovoid bacteria we identified as Thiovulum sp. (Campylobacterota). These form a separate phylogenetic cluster within the Thiovulaceae, consisting mostly of freshwater cave bacteria. We compared the closed genome of this Thiovulum to that of the marine strain Thiovulum ES, and to a genome we assembled from public data from the sulfidic Frasassi caves. The Movile and Frasassi Thiovulum were very similar, differing greatly from the marine strain. Based on their genomes, cave Thiovulum can switch between aerobic and anaerobic sulfide oxidation using O2 and NO3- as electron acceptors, respectively. NO3-, is likely reduced to NH3 via dissimilatory nitrate reduction to ammonia using periplasmic nitrate reductase (Nap) and hydroxylamine oxidoreductase. Thus, Thiovulum, is likely important to both S and N cycles in sulfidic subterranean aquatic ecosystems. Additionally, we suggest that the short peritrichous flagella-like structures typical of Thiovulum are type IV pili, for which genes were found in all Thiovulum genomes. These pili may play a role in veil formation, connecting adjacent cells and the exceptionally fast swimming of these bacteria.

microbiology↗

bioRxiv2020

Heterozygous, polyploid, giant bacterium, Achromatium, possesses an identical functional inventory worldwide across drastically different ecosystems

Achromatium is large, hyperpolyploid and the only known heterozygous bacterium. Single cells contain ca. 300 different chromosomes with allelic diversity typical of entire bacterial communities. Surveying all publicly available sediment sequence archives, we show Achromatia are common worldwide, spanning temperature, salinity, pH, and depth ranges normally resulting in bacterial speciation. Nevertheless, Achromatia display no ecotypic phylogenetic signal and contain a, globally identical, complete functional inventory. Achromatia cells from differing ecosystems (e.g. freshwater vs. saline) are, unexpectedly, equally functionally equipped but differ in gene expression patterns by transcribing only relevant genes. We suggest environmental adaptation occurs by increasing the copy number of relevant genes across the cells hundreds of chromosomes, without losing irrelevant ones, thus maintaining the ability to survive in any ecosystem type. The functional versatility of Achromatium, and its genomic features, reveal alternative genetic and evolutionary mechanisms, expanding our understanding of the role and evolution of polyploidy in bacteria while challenging the bacterial species concept and drivers of bacterial speciation.

microbiology↗