Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.01.07.698122

Host senescence and urbanized conditions drive bacterial communities of the freshwater sponge Spongilla lacustris

Lhomme, C.·PAIX, B.·de Voogd, N. J.
View original source ↗Export metadata ↓

Abstract

Freshwater sponge holobionts remain poorly characterized despite their ecological importance and exposure to strong anthropogenic pressures. Here, we investigated spatio-temporal dynamics of the bacterial microbiome within the freshwater sponge Spongilla lacustris across three sites with contrasting nutrient levels in the urban and peri-urban canal systems of Leiden (The Netherlands). Sponge and freshwater samples were collected every two weeks from October to December 2021, covering major stages of the adult sponge life cycle, including gemmulation, bleaching, and senescence. Using 16S rRNA gene metabarcoding, major differences in the sponge microbiome diversity were observed through a temporal dynamic, being associated with host physiological changes. Senescent and bleached sponges were characterized by an increased {beta}-diversity dispersion, consistent with a potential dysbiosis process following the Anna Karenina Principle. A wide range of biomarker taxa were associated with this bleached stage and may correspond to opportunistic microbial scavengers degrading organic matter released during host decomposition. To a lesser extent, spatial patterns were also observed: ammonium- and phosphate-enriched sites harbored a limited number of discriminant taxa, characterised primarily as denitrifiers and methanotrophs, suggesting nutrient-driven functional structuring. Together, these results indicate that S. lacustris microbiomes are primarily shaped by host senescence, while environmental eutrophication influences specific taxa, providing new insights into freshwater sponge holobiont ecology under urbanized conditions. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/698122v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1e361fdorg.highwire.dtl.DTLVardef@1363e87org.highwire.dtl.DTLVardef@4318deorg.highwire.dtl.DTLVardef@115b099_HPS_FORMAT_FIGEXP M_FIG C_FIG

Explore related subjects

microbiologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Lhomme, C., PAIX, B., de Voogd, N. J.. 2026-01-07. Host senescence and urbanized conditions drive bacterial communities of the freshwater sponge Spongilla lacustris. https://doi.org/10.64898/2026.01.07.698122

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

A population-scale landscape of the subgingival microbiome reveals divergent routes to periodontal dysbiosis

Periodontitis is an archetypical mucosal inflammatory disease in which microbiome dysbiosis at the tooth-epithelial interface interacts with host genetic and behavioral risk factors to drive immune-mediated tissue destruction. Although subgingival microbiome compositional shifts are thought to parallel disease severity, microbiome variation at the population-level and its relationship to periodontal clinical phenotypes and disease-modifying factors remain poorly defined. Here, we use unsupervised manifold learning to map the compositional landscape of the subgingival microbiome in 1,355 adults spanning periodontal health to severe periodontitis. We identified eight latent microbiome states organized along a branching continuum from eubiosis to dysbiosis. An intermediate microbial configuration marked ecological destabilization and bifurcation into two distinct periodontitis-associated dysbiotic trajectories, distinguished by links to gingival inflammation and smoking. Although the microbiome trajectories broadly tracked periodontal destruction, a minority of individuals showed discordant microbiome-clinical phenotypes, with some individuals with periodontitis retaining otherwise eubiotic microbiomes enriched for low-abundance pathobionts, while some cases of health or mild disease had highly dysbiotic communities, suggesting distinct host susceptibility. Together, these findings define a population-scale ecological landscape of the subgingival microbiome, reveal divergent trajectories to periodontal dysbiosis, and highlight heterogeneity in the relationship between microbial community structure and clinical disease expression.

microbiology↗
bioRxiv2026

The iron-binding siderophore enterobactin is required for the response of multi-drug resistant Klebsiella pneumoniae to zinc limitation

To persist during infection Klebsiella pneumoniae must overcome nutrient iron and zinc limitation imposed by the host immune system through a process called nutritional immunity. Secreted small molecule siderophores are a major virulence determinant of Klebsiella pneumoniae pathogenesis and are presumed to overcome nutritional immunity by binding iron for bacterial acquisition. In this work, we set out to identify how a multi-drug resistant K. pneumoniae grows in zinc limited environments. Using unbiased transcriptomics, proteomics, and an arrayed transposon screen, we identified that synthesis and uptake of the siderophore enterobactin is required to allow for growth in low zinc conditions. Iron-specific chelators did not replicate this phenotype and addition of supplemental iron through heme in growth media could not complement severe growth defects of enterobactin mutant K. pneumoniae experiencing zinc limitation. Finally, zinc starvation induced enterobactin production independent of the canonical zinc uptake regulator (Zur) transcription factor suggesting an unidentified regulatory mechanism by which Gram-negative pathogens may respond to zinc stress. Together, these studies expand the role of enterobactin beyond iron regulation and highlight a previously unreported link between iron and zinc homeostasis in Klebsiella pneumoniae.

microbiology↗
bioRxiv2026

A microbiota-derived protease links phage susceptibility to host epithelial responses

Bacteriophages are major ecological drivers of gut microbial ecology, yet whether bacterial mechanisms that determine phage susceptibility have consequences for the mammalian host remains poorly understood. Here, we identify dipeptidyl peptidase 11 (Dpp11a), the predominant active serine protease of the prevalent gut commensal Phocaeicola vulgatus, as an unexpected bacterial defence factor. Dpp11a protects against environmental proteases and confers resistance to bacteriophage infection. Metatranscriptomic analyses further reveal increased expression of both dpp11a and P. vulgatus-associated phage transcripts in ulcerative colitis stool samples, indicating that both components of this interaction are transcriptionally active in disease-associated human microbiomes. Using the microfluidic gut-on-a-chip co-culture model HuMiX, we show that the absence of Dpp11 is accompanied by altered epithelial tight-junction remodelling during phage-bacterial infection. Together, our findings reveal that the consequences of bacterial phage defence can extend beyond phage-bacterium interactions to the mammalian epithelium.

microbiology↗