Biology subjects

Marshall, I. P. G.

Publications and source records attributed to Marshall, I. P. G..

8 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

Extracellular electron transfer in cable bacteria enables growth rates comparable to aerobic respiration

Cable bacteria are filamentous sulphide-oxidisers performing long-distance electron transfer in redox-stratified sediments by transporting electrons over centimetre-scale distances to reduce oxygen. Here, we show that the freshwater cable bacterium Electronema aureum GS can respire insoluble electron acceptors under anoxic conditions via a versatile extracellular electron transfer (EET) system, supporting growth rates comparable to those under aerobic conditions. Using electrochemical and molecular biology analyses, we demonstrate that E. aureum GS engages in both direct and mediated electron transfer to electrodes, including at +600 mV vs. Ag/AgCl--an unusually high redox potential typically not accessed by electroactive bacteria. Two distinct cell-surface redox components were identified, which are metal-dependent, pH-sensitive, and heat-labile, consistent with outer-membrane-localised cytochromes. Moreover, the redox shuttle riboflavin accumulated extracellularly and enhanced current production in bioelectrochemical systems, indicating a role for soluble mediators in cable bacteria. Together, these findings reveal a previously unrecognised respiratory flexibility in E. aureum GS and highlight EET as a key alternative strategy for energy conservation in fluctuating redox environments.

microbiology↗

bioRxiv2025

Let-them-stick: Increasing biofilm formation by the acetogen Sporomusa ovata through adaptive laboratory evolution

Acetogenic bacteria are attractive biocatalysts for the conversion of CO2 with H2 into acetate, as in gas fermentation. Gas fermentation reactors may benefit from biofilm formation, but cell attachment by acetogens is often limited. This study indeed found that the acetogen Sporomusa ovata 2663 was mainly planktonic and aimed to increase its biofilm formation through adaptive laboratory evolution. The adaptation strategy consisted of growing S. ovata on plastic carriers in bottles with a H2:CO2 headspace and transferring few carriers to bottles with fresh carriers over eight serial transfers. This procedure resulted in the evolved S. ovata 2663-BF, which had a consistent increased propensity to attach. In heterotrophic growth conditions, four times more cells attached to the bottom of well plates in comparison to the wild type. Moreover, twice as many cells adhered to carriers when grown on H2:CO2. This improved attachment, however, did not lead to higher acetate production rates in simple trickle bed reactors, as the used experimental setup likely stimulated planktonic growth due to a low trickling frequency. Only after some medium replacements to remove planktonic cells, higher gas consumption rates were recorded for the evolved culture. Interestingly, the evolved S. ovata had a relevant point mutation in the gene galU, encoding UDP-glucose pyrophosphorylase, an enzyme involved in the synthesis of extracellular polysaccharides. Overall, this study demonstrates that cell attachment by S. ovata was increased through adaptive laboratory evolution, offering the prospect of investigating the importance of biofilm formation in biofilm-based gas fermentation reactors. IMPORTANCEAcetogenic bacteria are attractive biocatalysts for the conversion of CO2 with H2 into acetate, as in gas fermentation and microbial electrosynthesis. Both biotechnologies could benefit from biofilm formation, since biofilm formation retains the catalytic activity inside continuously operated reactors. In addition, biofilm-based gas fermentation reactor systems are advantageous to improve the gas to liquid mass transfer of H2 and CO2. Moreover, microbial electrosynthesis benefits from biofilms on cathodes to consume H2 as soon as it gets generated. Acetogenic bacteria are however often found to only form thin or sparse biofilms. In the current study, we demonstrated that adaptive laboratory evolution is a useful strategy to increase the biofilm formation capabilities of the acetogen, Sporomusa ovata. The obtained biofilm improved S. ovata is of interest to deepen our fundamental understanding of biofilm formation by acetogens, as well as to assess the importance of biofilm formation for the performance of biofilm-based bioreactors.

microbiology↗

bioRxiv2024

Adaptation to high pressure; insights from the genome of an evolved Escherichia coli strain with increased piezotolerance

Pressure is a key environmental parameter that influences the activity and distribution of microbial life on our planet. Despite its key role there is still not a definitive list of essential genes for microbial adaptation to life under increasing pressure. In this study we used a previously characterized Escherichia coli strain (AN62) evolved to grow at pressure (60 MPa) non-permissive to the parental strain and performed comparative genomics in order to identify the genome-level adaptations that might allowed the observed pressure-adapted phenotype. We identified 18 mutations in total of which 3 mutations were present in both the parental and evolved strain, 3 mutations were only present in the parental strain, and 12 mutations were observed only in the evolved AN62 strain. Among the characterized mutations we observed a point mutation in the acyl carrier protein (acpPV43G). Complementation experiments revealed that the observed V43G mutation in AcpP is responsible for increased levels of cis-vaccenic acid but is not alone responsible for the pressure adapted phenotype. Further molecular dynamics and docking simulations suggested that the V43G mutation promoted stronger binding of the AcpP protein to partner enzymes of the fatty acid biosynthesis pathway involved in fatty acid unsaturation. Data SummaryEscherichia coli reads from the parental and evolved strain have been deposited in the Sequence Read Archive (SRA) under accession number RJNA600359. All software used in the bioinformatic analysis is publicly available. Impact StatementPressure is a key environmental parameter. Two-thirds of our planet is covered by oceans with an average depth of 3800m, which means that the majority of the marine life experiences deep sea conditions. Our results offer a list of gene mutations that could contribute to an improved pressure growth phenotype in Escherichia coli, offering a unique insight on the genome level adaptations that might contribute to high pressure adaptation.

microbiology↗

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↗

bioRxiv2022

Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria

Cable bacteria of the Desulfobulbaceae family are centimeter-long filamentous bacteria, which are capable of conducting long-distance electron transfer. Currently, all cable bacteria are classified into two candidate genera: Candidatus Electronema, typically found in freshwater environments, and Candidatus Electrothrix, typically found in saltwater environments. This taxonomic framework is based on both 16S rRNA gene sequences and metagenome-assembled genome (MAG) phylogenies. However, most of the currently available MAGs are highly fragmented, incomplete, and thus likely miss key genes essential for deciphering the physiology of cable bacteria. To address this, we performed Nanopore long read (total 162.4 Gbp) and Illumina short read (total 148.3 Gbp) shotgun sequencing of selected environmental samples and a single-strain enrichment of Ca. Electronema aureum. We recovered multiple cable bacteria MAGs, including two circular and one single-contig. Phylogenomic analysis, also confirmed by 16S rRNA gene-based phylogeny, classified one circular MAG and the single-contig MAG as novel species of cable bacteria, which we propose to name Ca. Electronema halotolerans and Ca. Electrothrix laxa, respectively. The Ca. Electronema halotolerans, despite belonging to the previously recognized freshwater genus of cable bacteria, was retrieved from brackish-water sediment. Metabolic predictions showed several adaptations to a high salinity environment, similar to the "saltwater" Ca. Electrothrix species, indicating how Ca. Electronema halotolerans may be the evolutionary link between marine and freshwater cable bacteria lineages.

microbiology↗

bioRxiv2020

Cutting out the middle clam: lucinid endosymbiotic bacteria are also associated with seagrass roots worldwide

Seagrasses and lucinid bivalves inhabit highly reduced sediments with elevated sulphide concentrations. Lucinids house symbiotic bacteria (Ca. Thiodiazotropha) capable of oxidising sediment sulphide, and their presence in sediments has been proposed to promote seagrass growth by decreasing otherwise phytotoxic sulphide levels. However, vast and productive seagrass meadows are present in ecosystems where lucinids do not occur. Hence, we hypothesised that seagrasses themselves host sulphur-oxidising bacteria that could secure their survival when lucinids are absent. We analysed newly generated and publicly available 16S rRNA gene sequences from seagrass roots and sediments across 14 seagrass species and 10 countries and found that persistent and colonising seagrasses across the world harbour sulphur-oxidising Ca. Thiodiazotropha, regardless of the presence of lucinids. We used fluorescence in situ hybridisation to visually confirm the presence of Ca. Thiodiazotropha on roots of Halophila ovalis, a colonising seagrass species with wide geographical, water depth range, and sedimentary sulphide concentrations. We provide the first evidence that Ca. Thiodiazotropha are commonly present on seagrass roots, providing a mechanism for seagrasses to alleviate sulphide stress globally.

plant biology↗