Biology subjects

Bouderka, F.

Publications and source records attributed to Bouderka, F..

3 recordsLinked to original sources

bioRxiv2026

Phagocytosis without mitochondria is a lineage trait of planctomycetal bacteria of prey

Phagocytosis is considered energetically out of reach for prokaryotes. Mitochondria-first models of eukaryogenesis therefore suggest a non-phagocytic archaeal host. Yet two recently described planctomycetes lack mitochondria and engulf entire bacteria. Whether this mode of predation is an oddity of two isolates or the hallmark of a bacterial lineage remained unresolved. Here, we report eight additional predatory Planctomycetota from three aquatic habitats. The ten cultured strains now span two classes of the phylum Planctomycetota,"Candidatus Uabimicrobiia" and one newly proposed class. Using engineered fluorescent prey, we show that nine strains internalize prey into fully sealed compartments whereas one digests its prey externally, a non-engulfing predator for comparison. The strains additionally divide by two distinct modes, however, not correlating with their feeding behavior. Sequence- and structure-based searches detect no eukaryotic phagocytosis protein conserved across the engulfing strains. The actin homologue previously proposed to mediate uptake occurs only in three engulfing strains. Routine engulfment by aerobic bacteria without mitochondria thus unsettles a premise of mitochondria-first models and reopens the question of which cell plans could have hosted the mitochondrial endosymbiont.

microbiology↗

bioRxiv2026

Novel Extended Tetraether Lipids Found in a High-CO2 Geyser

The growing research into the archaeal lipidome has uncovered a remarkable structural diversity in glycerol dialkyl glycerol tetraethers (GDGTs) and revealed complex membrane adaptations, especially in extreme environments. We performed a comprehensive analysis of the lipidome from the subsurface water of a CO2-rich, cold-water Geyser Andernach (Germany), using ultra-high-resolution mass spectrometry methods. We detected GDGT-0, presumably derived from the dominant community member Candidatus Altiarchaeum, providing evidence for its ability to synthesize tetraethers as previously predicted from metagenomic data. Beyond the typical GDGT-0 and acyclic glycerol trialkyl glycerol tetraether (GTGT-0), we discovered novel structural analogues, here referred to as extended GDGTs and GTGTs, characterized by the asymmetrical addition of up to two isoprenoid units to only one of their hydrocarbon side chains, analogous to those found in extended archaeols. The lack of GDGT ring synthase A (GrsA) and GrsB homologs in the corresponding metagenome-assembled genome, suggests that the producing archaeon may utilize extended GDGTs as a membrane adaptation to cope with the energy-depleted conditions of the geyser environment, highlighting the adaptive flexibility of archaea to extreme physicochemical conditions.

biochemistry↗

bioRxiv2025

A uniform stress response of stream microbiomes in the hyporheic zone across North America

BackgroundStream hyporheic zones represent a unique ecosystem at the interface of stream water and surrounding sediments, characterized by high heterogeneity and accelerated biogeochemical activity. These zones are increasingly impacted by anthropogenic stressors and environmental changes at a global scale, directly altering their microbiomes. Despite their importance, the current body of literature lacks a systematic understanding of active nitrogen and sulfur cycling across stream sediment and surface water microbiomes, particularly across geographic locations and in response to environmental stressors. ResultsBased on previously published and unpublished datasets, 363 stream metagenomes were combined to build a comprehensive MAG and gene database from stream sediments and surface water including a full-factorial mesocosm experiment which had been deployed to unravel microbial stress response. Metatranscriptomic data from 23 hyporheic sediment samples collected across North America revealed that microbial activity in sediments was distinct from the activity in surface water, contrasting similarly encoded metabolic potential across the two compartments. The expressed energy metabolism of the hyporheic zone was characterized by increased cycling of sulfur and nitrogen compounds, governed by Nitrospirota and Desulfobacterota lineages. While core metabolic functions like energy conservation were conserved across sediments, temperature and stream order change resulted in differential expression of stress response genes previously observed in mesocosm studies. ConclusionsThe hyporheic zone is a microbial hotspot in stream ecosystems, surpassing the activity of overlaying riverine surface waters. Metabolic activity in the form of sulfur and nitrogen cycling in hyporheic sediments is governed by multiple taxa interacting through metabolic handoffs. Despite the spatial heterogeneity of streams, the hyporheic sediment microbiome encodes and expresses conserved stress responses to anthropogenic stressors, e.g., temperature, in streams of separate continents. The high number of uncharacterized differentially expressed genes as a response to tested stressors is a call-to-action to deepen the study of stream systems.

microbiology↗