Biology subjects

Bonne, R.

Publications and source records attributed to Bonne, R..

5 recordsLinked to original sources

bioRxiv2026

Artificial sediments enable reproducible cultivation and recapitulate ecological interactions of cable bacteria

Cable bacteria are filamentous microbes that couple sulfide oxidation to oxygen reduction over centimeter distances via long-distance electron transport. While their activity creates characteristic biogeochemical gradients that shape sediment ecology, the study of cable bacteria has been constrained by the chemical and physical heterogeneity of the natural sediments they inhabit. To date, laboratory cultivation efforts have relied on these undefined environmental matrices. Here, we established a reproducible enrichment and cultivation platform using an artificial sediment matrix coupled with chemically defined media. This matrix successfully supported the growth of both freshwater and marine cable bacteria and enabled serial propagation over multiple transfers. Microsensor profiling confirmed that the incubations recapitulated hallmark geochemical signatures, including the sulfide, oxygen and pH gradients associated with electrogenic sulfur oxidation. Scanning electron microscopy confirmed the presence of cable bacteria, while 16S rRNA sequencing confirmed enrichment of the cable bacteria together with a stable co-enriched community that included taxa associated with sulfur and iron cycling as well as cellulose decomposition. This defined cultivation system eliminates the variability inherent to natural samples, providing a controlled platform for dissecting the physiology, genetics, and microbial interactions of cable bacteria.

microbiology↗

bioRxiv2025

Opportunistic diver-assisted eDNA sampling unpicks fine-scale ecological and conservation signals in tropical reef fishes

Coral reefs are emblematic ecosystems of astonishing biological diversity and significant economic value for many countries, yet they are increasingly vulnerable to direct and indirect human-related threats, such as heavy tourism and global warming. To assess the biodiversity status, track assemblage changes and forecast future trends of these megadiverse ecosystems, there is pressing need for accurate, rapid and comprehensive assessments of fish communities. Here, we employed a versatile low-tech passive environmental DNA collector, the metaprobe, in association with the recreational activity of scuba divers to collect eDNA data from reefs in the Seychelles archipelago and assess both the taxonomic and functional fish diversity of the area. Using a fish-specific 12S marker on eDNA metaprobe samples collected during 18 dives, we detected 174 fish taxa, eight elasmobranchs and 166 teleosts, corresponding to 112 unique functional entities and including iconic tropical reef taxa, endangered elasmobranchs and commercially valuable species. Despite the geographic proximity of dive sites, we identified ecological patterns of fish composition and community structure influenced by both the presence of marine protected areas (MPAs) and the type of predominant substrate (i.e., coral vs rocky). Ecological differences between MPA/non-MPA and coral/rocky habitats involved both taxonomic and functional community elements, which returned very similar patterns of significantly higher fish diversity in protected and coral areas. We argue that simple, inexpensive eDNA-based collection tools in association with recreational activities, such as scuba diving, provide a promising approach for upscaling ecological data collection and expanding biodiversity monitoring, while engaging and empowering the public.

ecology↗

bioRxiv2023

Electrically controlled interaction between cable bacteria and carbon electrodes

Cable bacteria couple the oxidation of sulphide in sediments to the reduction of oxygen via long-distance electron transfer through periplasmic wires. While direct electron transfer between cable bacteria cells belonging to the same filament is a well-known phenomenon, electron transfer from the filament to electrodes has remained elusive. In this study, we demonstrate that living cable bacteria are attracted to electrodes in different bioelectrochemical systems. Carbon felt and carbon fibre electrodes poised at +200 mV against an Ag/AgCl reference attracted live cable bacteria from the sediment. When the applied potential was switched off, cable bacteria retracted from the electrode. qPCR and scanning electron microscopy corroborated this finding and revealed cable bacteria adhered onto the electrode surface. These experiments raise new possibilities to cultivate cable bacteria and utilise them for important applications in bioelectrochemical systems.

microbiology↗

bioRxiv2023

Comparative electric and ultrastructural studies of cable bacteria reveal new components of conduction machinery

Cable bacteria encompass at least two genera, and they are known to vary greatly in habitat preferences and filament thickness. We systematically investigated variations and similarities in cellular structures and electrical properties of different cable bacteria strains. Using SEM, TEM, STEM-EDX and ToF-SIMS, we characterized shared features of cable bacteria, such as inner and outer membranes, surface layer and cell junction architecture, as well as strain specific features, like the number and size of periplasmic conductive fibers (PCFs). Our data indicates that the PCFs are organized as loose stranded rope-like structures. With spatially resolved elemental analysis we detected nickel-containing co-factors within the PCF of cable bacteria strains in both genera suggesting a conserved conduction mechanism. Electrical conductivity of different cable bacteria strains showed a range of values covering three orders of magnitude indicating an unknown metabolic adaptation. Using cryogenic electron tomography we discovered multiple polar chemosensory arrays, abundant cytoplasmic inner membrane-attached vesicles (IMVs), polysomes and inner membrane invaginations that shed light on cable bacteria metabolism including complex motility control mechanisms, localized protein synthesis, and membrane remodeling. We propose that the IMVs discovered in this work are novel metabolic hubs closely connected to the unique conductive fiber structure of cable bacteria.

microbiology↗

bioRxiv2019

A Highly-ordered and Fail-safe Electrical Network in Cable Bacteria

Cable Bacteria are an emerging class of electroactive organisms that sustain unprecedented long-range electron transport across centimeter-scale distances. The pathways of the electrical currents in these filamentous microorganisms remain unresolved. Here, the electrical circuitry in a single cable bacterium is visualized with nanoscopic resolution using Conductive Atomic Force Microscopy. Combined with perturbation experiments, it is demonstrated that electrical currents are conveyed through a parallel network of conductive fibers embedded in the cell envelope which are electrically interconnected between adjacent cells. This redundant structural organization of electrical pathways likely forms a crucial adaptive trait for organisms capable of long-distance electron transport. The observed electrical circuit architecture is unique in biology and could inspire future technological applications in bioelectronics.

biophysics↗