Biology subjects

Scarampi, A.

Publications and source records attributed to Scarampi, A..

7 recordsLinked to original sources

bioRxiv2026

Emergent particle collection by cyanobacteria through gliding motility and filament buckling

Cyanobacterial macrostructures such as mats, aggregates, and stromatolites are observed in diverse habitats. These structures incorporate organic and inorganic matter and form microenvironments enabling biochemical transformations. Macrostructures are found to be associated with motile, filamentous cyanobacteria, but to what extent, and how filament motility can drive macrostructure formation is unclear. To address this question, we study macrostructure formation in a well-characterised freshwater cyanobacterial community dominated by the filamentous cyanobacterium Fluctiforma draycotensis. We discover an emergent particle collection behaviour that results in aggregate macrostructures composed of a solid core surrounded by an outer layer dominated by entangled cyanobacterial filaments. We show that the particle collection and subsequent aggregate formation result from the gliding motility of the cyanobacteria. Developing a novel 3D model of active filament movement, we analyse how filament morphology and mechanical properties affect movement dynamics, particle collection, and filament entanglement. We predict that particle collection requires filaments above a certain length and flexibility. We confirm the resulting prediction of length dependence of particle collection behavior with shortened filaments of F. draycotensis and naturally short Pseudanabaena sp. filaments. Together, our results show that filamentous cyanobacteria can use gliding motility to actively engineer their environments through particle collection and macrostructure formation, and that this ability is confined to a part of the filament phase space in terms of length and flexibility. These insights will allow better prediction of macrostructure formation in natural habitats and specific cyanobacterial species, and the engineering of cyanobacterial macrostructures for biotechnological applications.

biophysics↗

bioRxiv2026

A conserved photosynthetic cytochrome enhances growth in fluctuating light

Having at least one of the small soluble electron carriers cytochrome c6 (c6) and plastocyanin is indispensable for photosynthesis. It was believed that c6 had been lost from plants until a ubiquitous and highly conserved homologue, now named cytochrome c6A (c6A), was found in Arabidopsis thaliana. In spite of an early suggestion that c6A functioned like c6 in the photosynthetic electron transport chain it was soon shown to be unable to do so despite the strong structural homology between the two proteins. The function of c6A, and why it is apparently universal in plants and green algae, therefore remained unknown. Here, we show that, in the green alga Chlamydomonas reinhardtii, c6A confers a growth advantage under fluctuating light and is crucial for maintaining the light harvesting balance between photosystems I and II in photomixotrophic conditions. We show that in the absence of c6A, the light harvesting balance shifts towards PSII, leading to a more reduced plastoquinone pool and increased photooxidative stress. This study provides insights into how photosynthetic organisms acclimatize to stressful light conditions, indicating that c6A is important for this adaptation. These findings provide a basis for further mechanistic studies on a hypothesized role for c6A in thiol-based redox regulation in the thylakoid lumen, with implications for photoprotection mechanisms such as state transitions.

plant biology↗

bioRxiv2026

Enrichment of convergent metabolic functions in microbial communities through imposed and emergent environmental niches

Microbial community composition is determined by numerous factors, including environmental filtering, biotic interactions, and stochasticity. Disentangling the relative contribution of these distinct processes is a fundamental problem for microbial ecology. Towards addressing it, here we used controlled experiments on replicate freshwater communities that vary individual factors, and used contig-based metagenomics methods to capture functional composition independently from uneven genome recovery across taxa. After repeated sub-culturing in minimal media lacking organic carbon but containing nitrate and vitamins, communities with distinct initial compositions consistently converged toward similar taxonomic structures and metabolic functions. These included oxygenic photosynthesis and nitrate metabolism, consistent with the imposed growth regime, and also showed reproducible enrichment of anoxygenic photosynthesis, vitamin biosynthesis and degradation pathways. These patterns indicate strong environmental filtering during assembly while also revealing a consistent role for emergent environments arising from microbial activity and metabolic interactions. To more directly test specific environmental drivers, we initiated replicate cultures from a single community and propagated them in the original medium and in variants lacking vitamins or both vitamins and nitrates. Only nitrate removal produced a distinct and statistically significant shift in both composition and function, with nitrate-free communities enriched for cyanobacterial nitrogen fixation and supporting metabolic functions in heterotrophs. Together, these results support a hierarchy of environmental filters determining community outcomes and provide a quantitative framework for predicting and steering community function through rational environmental design.

microbiology↗

bioRxiv2026

Using auxotrophic donor strains to explore pQBR57 plasmid host range among environmental soil bacterial isolates

Plasmid host range (PHR) plays a key role in the spread of ecologically important genes, alongside applications in microbiome engineering, and environmental biotechnology. PHR is a complex trait arising from the combination of plasmid, donor and recipient properties. Most studies of PHR use a single donor strain, leaving the role of the donor unexplored, and often require genetically tagged recipient strains for counter selection, which limits use of non-genetically tractable strains. Here we developed a PHR screening method using auxotrophic donors that bypasses the need to genetically tag recipients, thus allowing the screening of culturable environmental bacterial strains. Specifically, we used two auxotrophic donors (P. fluorescens and P. putida), and the plasmid pQBR57-tphKAB, an environmental plasmid engineered for terephthalic acid bioremediation. We screened a library of 101 soil isolates, as potential recipients, including common soil genera of soil bacteria, Pseudomonas, Bacillus and Xanthomonas. We only observed conjugation into other Pseudomonas, but donor identity affected PHR, with P. fluorescens conjugating the plasmid into more recipient strains than P. putida. Phylogenomic analysis revealed that transconjugants clustered with P. citronellosis and P. putida lineages. In strains that were close relatives of transconjugants but who were unable to acquire the plasmid, we observed 5 defence systems not present in transconjugants that may act as barriers to plasmid acquisition. Our method provides a rapid, tag-free framework for screening PHR in environmental isolates and for investigating the influence of donor identity on plasmid conjugation.

microbiology↗

bioRxiv2022

Establishment of a novel set of vectors for transformation of the dinoflagellate Amphidinium carterae

Peridinin-containing dinoflagellate algae have a chloroplast genome formed from plasmid-like minicircles. This fragmented genome has allowed us to develop a genetic modification methodology involving the use of biolistics to introduce artificial minicircles in Amphidinium carterae (Nimmo et al., 2019). The previously reported artificial minicircles were based on native minicircles containing either the psbA or atpB gene. Each artificial minicircle allowed expression of a single selectable marker instead of psbA or atpB. Here, we present two further artificial minicircles for use in transformation of A. carterae. One is based on the petD minicircle, allowing the expression of a single selectable marker. The second is based on the two-gene minicircle originally containing atpA and petB, and allows the dual expression of a selectable marker and a gene of interest. Our research suggest that all of the 20 or so minicircles in A. carterae are suitable for adaptation as artificial minicircles, allowing for the simultaneous introduction of multiple genes.

plant biology↗

bioRxiv2021

The Paradox of the Plankton: Coexistence of Structured Microbial Communities

In the framework of resource-competition models, it has been argued that the number of species stably coexisting in an ecosystem cannot exceed the number of shared resources. However, plankton seems to be an exception of this so-called "competitive-exclusion principle". In planktic ecosystems, a large number of different species stably coexist in an environment with limited resources. This contradiction between theoretical expectations and empirical observations is often referred to as "The Paradox of the Plankton". This project aims to investigate biophysical models that can account for the large biodiversity observed in real ecosystems in order to resolve this paradox. A model is proposed that combines classical resource competition models, metabolic trade-offs and stochastic ecosystem assembly. Simulations of the model match empirical observations, while relaxing some unrealistic assumptions from previous models. Paradox: from Greek para: "distinct from", and doxa: opinion. Sainsbury (1995) defines a paradox as "an apparently unacceptable conclusion derived by apparently acceptable reasoning from apparently acceptable premises". Paradoxes are useful research tools as they suggest logical inconsistencies. In order to spot the flaw, the validity of all the premises has to be carefully assessed. Plankton: refers to the collection of organisms that spend part or all of their lives in suspension in water (Reynolds 2006). Plankton, or plankters, are "organisms that have velocities significantly smaller than oceanic currents and thus are considered to travel with the water parcel they occupy" (Lombard et al. 2019). Phytoplankters refer to the members of the plankton that perform photosynthesis.

systems biology↗

bioRxiv2021

A modular toolset for electrogenetics

Synthetic biology research and its industrial applications rely on the deterministic spatiotemporal control of gene expression. Recently, electrochemical control of gene expression has been demonstrated in electrogenetic systems (redox-responsive promoters used alongside redox inducers and an electrode), allowing for the direct integration of electronics with complex biological processes for a variety of new applications. However, the use of electrogenetic systems is limited by poor activity, tunability and standardisation. Here, we have developed a variety of genetic and electrochemical tools that facilitate the design and vastly improve the performance of electrogenetic systems. We developed a strong, unidirectional, redox-responsive promoter before deriving a mutant promoter library with a spectrum of strengths. We then constructed genetic circuits with these parts and demonstrated their activation by multiple classes of redox molecules. Finally, we demonstrated electrochemical activation of gene expression in aerobic conditions utilising a novel, modular bioelectrochemical device. This toolset provides researchers with all the elements needed to design and build optimised electrogenetic systems for specific applications.

synthetic biology↗