Biology subjects

Rubin Blum, M.

Publications and source records attributed to Rubin Blum, M..

6 recordsLinked to original sources

bioRxiv2026

Cysteine-rich repeats trace past horizontal gene transfers in eukaryotes

Movement of genetic material between non-parental organisms, called horizontal gene transfer (HGT), is well recognized in prokaryotes but represents an underestimated force for the acquisition of novel traits in eukaryotes. The mechanisms of cross-domain HGT remain poorly understood despite numerous reports of its occurrence. Thus, progress in the field remains limited by the lack of targeted approaches for detecting HGT events. Using BLASTp search and sequence identity, we describe an HGT-derived protein from the chytridiomycete fungus Neocallimastix californiae. This protein has two cysteine-rich repeats (CysRReps) and other functional domains that are highly similar to those of prokaryotes. Based on the alignment of several CysRReps, we identified 859 additional eukaryotic proteins spanning 43 protein families, each with at least one match to bacterial, archaeal, or viral proteins. HGT-derived proteins with CysRReps belong to multiple eukaryotic taxa, some of which are well-known HGT models. Bacterial, archaeal, and viral proteins comprise the prokaryotic counterparts. Bacteria belong to 15 phyla, spanning a diverse array of physiologies, habitats, and lifestyles. Viral diversity is largely restricted to Caudoviricetes, suggesting a virus-mediated mechanism of DNA integration underlying these transfers. Although the function of CysRReps remains unclear, their association with HGT events across diverse eukaryotic and prokaryotic taxa suggests the existence of a universal molecular mechanism that facilitates gene transfer across phylogenetic boundaries.

evolutionary biology↗

bioRxiv2024

Switch in parasitic and autotrophic-dominated protist assemblages coupled to seasonal oligotrophic-mesotrophic gradients in the sunlit layer of a subtropical marine ecosystem

Protists are major functional players in the oceans. Time-resolved epipelagic protist successions remain poorly described in subtropical ecosystems, limiting current understanding of food web dynamics and responses to environmental changes in these major world-ocean regions. Here, we used amplicon sequencing data and their trait-based annotation to examine the seasonality of planktonic protists in the subtropical Gulf of Aqaba (northern Red Sea). Temperature and nutrients were identified as major drivers of succession. Marked seasonal shifts in protists were detected. The warm, stratified oligotrophic period spanning through spring and summer were dominated by heterotrophs, including parasitic Syndiniales. By contrast, nutrient influx during deep convective-mixing in winter triggered a progressive shift to photoautotrophic communities dominated by few chlorophyte genera. Ephemeral phytoplankton blooms were detected during the mixing-to-stratification transition. Deeper winter mixing resulted in larger blooms dominated by diatoms and coccolithophores relative to chlorophytes prevalent during shallower mixing. This illustrates the impact of mixing-depth in the development and compostion of blooms. Comparisons with oceanwide rDNA datasets indicate that the oligotrophic protist assemblages from the Gulf of Aqaba resemble those from warm, open-oceans. This work provides a detailed assessment of the seasonality in protist communities and dominant functional strategies in a coastal subtropical planktonic ecosystem.

ecology↗

bioRxiv2023

Metabolic adaptations and aquifer connectivity underpin the high productivity rates in the relict subsurface water

BackgroundDiverse microbes catalyze biogeochemical cycles in the terrestrial subsurface, yet the corresponding ecophysiology was only estimated in a limited number of subterrestrial, often shallow aquifers. Here, we detrained the productivity, diversity, and functions of active microbial communities in the Judea Group carbonate and the underlying deep (up to 1.5 km below ground) Kurnub Group Nubian sandstone aquifers. These pristine oligotrophic aquifers, recharged more than tens to hundreds of thousands years ago, contain fresh/brackish, hypoxic/anoxic, often hot (up to 60{degrees}C) water and serve as habitats for key microbial producers. ResultsWe show that recent groundwater recharge, inorganic carbon and ammonium strongly influence chemosynthetic primary productivity in carbonate and sandstone aquifers (4.4-21.9 {micro}g C d-1 L-1 and 1.2-2.7 {micro}g C d-1 L-1, respectively). These high values indicate the possibility that the global aquifer productivity rates may be underestimated. Metagenome analysis revealed the prevalence of chemoautotrophic pathways, particularly the Calvin-Benson-Bassham cycle. The key chemosynthetic lineages in the carbonate aquifer were Halothiobacillales, whereas Burkholderiales and Rhizobiales occupied the sandstone aquifer. Most chemosynthetic microbes may oxidize sulfur compounds or ammonium, using oxygen or oxidized nitrogen as electron acceptors. Abundant sulfate reducers in the anoxic deeper aquifer have the potential to catabolize various organics, fix carbon via the Wood Ljungdahl pathway, and often possess nitrogenase, indicating diazotrophic capabilities. Our data suggest that connectivity between the aquifers and their exposure to energy inputs and surface water may play a key role in shaping these communities, altering physicochemical parameters and selecting taxa and functions. We highlight the metabolic versatility in the deep subsurface that underpins their efficient harnessing of carbon and energy from different sources.

microbiology↗

bioRxiv2022

Metagenomes of Red Sea subpopulations challenge the use of morphology and marker genes to assess Trichodesmium diversity

The bloom forming Trichodesmium are filamentous cyanobacteria of key interest due to their ability to fix carbon and nitrogen within an oligotrophic marine environment. Trichodesmium blooms typically comprise a complex assemblage of subpopulations and colony-morphologies that are predicted to exhibit distinct ecological lifestyles. Here, we assessed the poorly studied diversity of Trichodesmium in the Red Sea, based on metagenome-assembled genomes (MAGs) and hetR gene-based phylotyping. We assembled four non-redundant MAGs from morphologically distinct Trichodesmium colonies (tufts, dense and thin puffs). T. thiebautii (puffs) and T. erythraeum (tufts) were the dominant species within these morphotypes. While subspecies diversity is present for both T. thiebautii and T. erythraeum, a single T. thiebautii genotype comprised both thin and dense puff morphotypes, and we therefore hypothesize that the phenotypic variation between these morphologies is likely attributed to gene regulation. Additionally, we found the rare non-diazotrophic clade IV and V genotypes, related to T. nobis and T. miru respectively, that likely occurred as single filaments. HetR gene phylogeny indicates that the genotype in clade IV could represent the species T. contortum. We further show that hetR phylotyping can overestimate the taxonomic diversity of Trichodesmium, as two copies of the hetR gene were present within T. thiebautii genomes, one of which misidentified this lineage as T. aureum. Taken together, our results highlight the importance of re-assessing Trichodesmium taxonomy while showing the ability of genomics to capture the complex diversity and distribution of Trichodesmium populations.

microbiology↗

bioRxiv2019

Horizontal acquisition followed by expansion and diversification of toxin-related genes in deep-sea bivalve symbionts

Deep-sea bathymodioline mussels gain their nutrition from intracellular bacterial symbionts. Their sulfur-oxidizing (SOX) symbionts were recently shown to encode abundant toxin-related genes (TRGs) in their genomes, which may play a role in beneficial host-microbe interactions. Here, we compared TRGs in the genomes of SOX symbionts from 10 bathymodioline mussel and two sponge species to better understand their potential functions and evolutionary origins. Despite the close phylogenetic relatedness of these symbionts, the number and classes of encoded toxins varied greatly between host species. One of the TRG classes, YDs, has experienced gene expansions multiple times, suggesting that these genes are under adaptive selection. Some symbiont genomes contained secretion systems, which can play a role in host-microbe interactions. Both TRGs and secretion systems had a heterogeneous distribution, suggesting that these closely related bacteria have acquired different molecular mechanisms for interacting with the same family of animal hosts, possibly through convergent evolution.

microbiology↗

bioRxiv2018

Genetic evidence for two carbon fixation pathways in symbiotic and free-living bacteria: The Calvin-Bassham cycle and the reverse tricarboxylic acid cycle

Very few bacteria are able to fix carbon via both the reverse tricarboxylic acid (rTCA) and the Calvin-Benson-Bassham (CBB) cycles, such as symbiotic, sulfur-oxidizing bacteria that are the sole carbon source for the marine tubeworm Riftia pachyptila, the fastest growing invertebrate. To date, this co-existence of two carbon fixation pathways had not been found in a cultured bacterium and could thus not be studied in detail. Moreover, it was not clear if these two pathways were encoded in the same symbiont individual, or if two symbiont populations, each with one of the pathways, co-existed within tubeworms. With comparative genomics, we show that Thioflavicoccus mobilis, a cultured, free-living gammaproteobacterial sulfur oxidizer, possesses the genes for both carbon fixation pathways. Here, we also show that both the CBB and rTCA pathways are likely encoded in the genome of the sulfur-oxidizing symbiont of the tubeworm Escarpia laminata from deep-sea asphalt volcanoes in the Gulf of Mexico. Finally, we provide genomic and transcriptomic data suggesting a potential electron flow towards the rTCA cycle carboxylase 2-oxoglutarate:ferredoxin oxidoreductase, via a rare variant of NADH dehydrogenase/heterodisulfide reductase. This electron bifurcating complex, together with NAD(P)+ transhydrogenase and Na+ translocating Rnf membrane complexes may improve the efficiency of the rTCA cycle in both the symbiotic and the free-living sulfur oxidizer.\n\nImportancePrimary production on Earth is dependent on autotrophic carbon fixation, which leads to the incorporation of carbon dioxide into biomass. Multiple metabolic pathways have been described for autotrophic carbon fixation, but most autotrophic organisms were assumed to have the genes for only one of these pathways. Our finding of a cultivable bacterium with two carbon fixation pathways in its genome opens the possibility to study the potential benefits of having two pathways and the interplay between these pathways. Additionally, this will allow the investigation of the unusual, and potentially very efficient mechanism of electron flow that could drive the rTCA cycle in these autotrophs. Such studies will deepen our understanding of carbon fixation pathways and could provide new avenues for optimizing carbon fixation in biotechnological applications.

microbiology↗