Biology subjects

Duxbury, S. J. N.

Publications and source records attributed to Duxbury, S. J. N..

4 recordsLinked to original sources

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↗

bioRxiv2024

Cellular (de)coordination in gliding motility and plectoneme formation

2Cyanobacteria are key contributors to biogeochemical cycles through photosynthesis and carbon fixation. In filamentous, multicellular cyanobacteria these functions can be influenced through gliding motility, which enables filaments to localise in response to light and also form aggregates. Here, we use the aggregate forming species Fluctiforma draycotensis to study gliding motility dynamics in detail. We find that filaments move in curved and straight trajectories interspersed with re-orientation or reversal of direction. Most reversals take few seconds but some take substantially longer, resulting in a long-tailed distribution of stoppage times. Mean filament speeds range around a micron per second with a relatively uniform distribution against filament length, implying that all or fixed proportion of cells in a filament contribute to movement. We implement a biophysical model that can recapitulate these findings. Model simulations show that for filaments to reverse quickly, cells in a filament must achieve high coordination of the direction of the forces that they generate. To seek experimental support of this prediction, we track individual cells in a filament. This reveals that cells translational movement is fully coupled with their rotation along the long-axis of the filament, and that cellular movement remains coordinated throughout a reversal. For some filaments, especially longer ones, however, we also find that cellular coordination can be lost, and filaments can form buckles that can twist around themselves, resulting in plectonemes. The experimental findings and the biophysical model presented here will inform future studies of individual and collective filament movement. 1 Significance StatementCyanobacteria contribute to global oxygen production and carbon capture. Some cyanobacteria exist as multicellular filaments and display gliding motility that allows them to respond to light and to form aggregates, which influences their biological functions. Here, we study the dynamics of gliding motility. We find that filaments movement is interspersed with re-orientation or reversal of direction and that mean filament speed is mostly independent of filament length. We implement a biophysical model that predicts these features to relate to cells in a filament having high coordination of the direction of the forces that they generate. We find experimental support for this predicted cellular coordination, but also discover instances of longer filaments loosing coordination, resulting in buckling and entangling with other filaments.

biophysics↗

bioRxiv2022

Reproducible spatial structure formation and stable community composition in the cyanosphere predicts metabolic interactions

Understanding how microbial communities maintain stable compositional diversity is key for predicting community function. Studies from species pairwise interactions and synthetic communities indicate that metabolic interactions and spatial organisation can influence coexistence, but the relevance of these factors in more complex communities is unclear. Model systems often lack multi-species complexity, thereby making it difficult to study community diversity temporally. Here we used a spatially-organised cyanobacterial enrichment community to investigate compositional diversity and its stability. Over a year of passaging in media without significant carbon source, we found that the community maintains relatively high diversity, with 17 co-existing bacterial species. Using short and long read shotgun metagenomics sequencing from different time point samples, we have reconstructed complete genomes. Genomic annotation of these species revealed complementary metabolic functions involving carbon breakdown and vitamin biosynthesis suggesting interactions amongst community members. Using isolated species, we provide experimental support for carbon provision through cyanobacterial slime and growth on the component substrates by representative members of the Proteobacteria and Actinobacteriota phyla. Additionally, we experimentally show vitamin provision and uptake between prototrophic and auxotrophic members. We also found genomic capability for (an)oxygenic photosynthesis and sulfur cycling in several species. We show consistent formation of oxygen gradients across photogranule structures, supporting niches that can sustain these specific metabolic functions. These findings indicate that spatial niche formation and metabolic interactions enable maintenance of community compositional stability and diversity. SIGNIFICANCE STATEMENTMicrobes exist as species-diverse communities in nature and understanding their stability is an open challenge in microbial ecology. We established and maintained a spatially-organised, photosynthetic microbial community from a freshwater reservoir through long-term culturing in laboratory medium. We found that this community maintained a taxonomically-diverse set of 17 bacterial species. Combining genomic and physiological assays, we characterised a novel filamentous cyanobacterium capable of carbohydrate-rich slime secretion supporting growth of other microbes. We predict inter-species vitamin exchanges and identify sulfur cycling and alternative types of photosynthesis that are likely to be favoured in oxygen-free zones identified within the spatial structures. Our findings indicate that metabolic interactions and spatial structures can enable stable microbial coexistence in natural ecosystems.

microbiology↗

bioRxiv2020

Estimating the rate of plasmid transfer in liquid mating cultures

Plasmids are important vectors for the spread of genes among diverse populations of bacteria. However, there is no standard method to determine the rate at which they spread horizontally via conjugation. Here, we compare commonly used methods on simulated and experimental data, and show that the resulting conjugation rate estimates often depend strongly on the time of measurement, the initial population densities, or the initial ratio of donor to recipient populations. Differences in growth rate, e.g. induced by sub-lethal antibiotic concentrations or temperature, can also significantly bias conjugation rate estimates. We derive a new end-point measure to estimate conjugation rates, which extends the well-known Simonsen method to include the effects of differences in population growth and conjugation rates from donors and transconjugants. We further derive analytical expressions for the parameter range in which these approximations remain valid. We present an easy to use R package and web interface which implement both new and previously existing methods to estimate conjugation rates. The result is a set of tools and guidelines for accurate and comparable measurement of plasmid conjugation rates. HighlightsO_LIWe present an R package and Shiny app to estimate conjugation rates from experimental data C_LIO_LIWe highlight the diversity of existing measures used to estimate conjugation rates C_LIO_LIWe show these measures are biased for populations with differing growth and conjugation rates from donors or transconjugants C_LIO_LIWe develop a new end-point measure which accounts for such differences in growth and conjugation rates C_LI

microbiology↗