Biology subjects

van der Meer, J. R.

Publications and source records attributed to van der Meer, J. R..

At least 19 recordsLinked to original sources

bioRxiv2026

Genome-scale metabolic models for a synthetic soil microbial community as a path for understanding community functioning

Microbial communities drive essential ecosystem processes, yet community-level behavior often deviates from predictions based on single-species studies. This mismatch reflects the context-dependent nature of nutrient dependencies, metabolic interactions, and resource availability in complex environments. Here, we present a mechanistic, species-resolved framework to dissect metabolism and nutrient exchange in a defined 21-member soil synthetic community spanning five bacterial phyla. For each isolate, we reconstructed and manually curated thermodynamically constrained genome-scale metabolic models, reconciling predictions with growth phenotypes across rich and minimal media. We mapped minimal nutrient requirements, cataloged environment-specific uptake and secretion profiles, and compared metabolic pathways to identify potential competitive and cooperative interactions. Using community-scale metabolomics, we assigned putative producers and consumers for detected metabolites and revealed medium-dependent shifts in niche overlap. This approach exposes metabolic strategies that govern community function and resilience, offering a predictive basis for understanding and manipulating microbiomes. Our findings highlight how species-level metabolic maps can clarify why microbial interventions succeed or fail and guide targeted manipulations in soil ecosystems.

systems biology↗

bioRxiv2026

Biphasic bacterial community assembly predicted from generalized first principles of monoculture growth and inferred species interactions

Microbial communities occur in all habitats, yet how individual growth on available nutrients scales to community assembly remains poorly understood. This gap stems largely from the unknown effects of species interactions. These interactions arise because individual populations both consume and transform primary substrates into metabolites exploitable by others, and because parasitic and predatory mechanisms can release cellular building blocks that enable nutrient reuse. Here, we present a mathematical framework that predicts community growth and compositional succession from monoculture growth kinetics, resource availability, and species interaction parameters. To parametrize species interactions, we use a simulated-annealing optimization algorithm to search parameter space for sets that minimize the difference between modeled community growth and experimental time series from soil microcosms inoculated with defined communities of 20 or 21 soil isolates, with or without an opportunistic bacteriovorous member. The optimized interaction parameter sets were then used to predict growth dynamics in an independent 21-member community and in species drop-out communities. We find that community development is biphasic: an initial phase dominated by competition for primary resources driven by inherent strain growth kinetics, followed by a phase governed by cross-feeding and biomass formation on released byproducts. Paired metatranscriptomic analysis corroborated predicted shifts in individual growth states and revealed metabolic repurposing associated with the sudden renewed availability of metabolites and cellular building blocks. Model simulations that excluded species interactions reproduced only one-fifth of the observed community biomass, highlighting the importance of cross-feeding for soil community growth. Overall, models that integrate monoculture growth kinetics with inferred species interactions can predict the dynamics of medium-complexity communities from starting inocula even when environmental nutrient composition is largely unknown.

microbiology↗

bioRxiv2026

Spatially mediated interactions shape founder-cell fitness and community assembly in multi-species soil bacteria

Microbial communities spontaneously colonize pristine environments, yet how species growth kinetics and individual cell variation shape community assembly remains poorly understood. Here, we use time-lapse microscopy imaging to track the division of individual founder cells in communities composed of up to seven soil bacterial isolates grown on nutrient surfaces. With cell lineage tracking, we quantify species-specific absolute biomass formation and growth kinetics from early growth through stationary phase. The reproductive success of individual founder cells depended on the timing of their first cell division, which determined their access to the primary substrate and their maximum growth rates. In mixed-species communities, founder cell success also depended on species-specific, substrate-dependent growth rates and yields. In addition, spatial factors - such as cells positioning, distances to non-kin neighbours, and identities of co-occurring species - further influenced outcomes. In spatially structured communities, interspecific interactions were globally governed by competition for primary substrates. We also observed cross-feeding of leaked metabolites, reflected in fluctuating paired interaction strengths and interaction signs. Species-pair interactions differed locally, with cells within distances of less than 15 {micro}m exhibiting opposite interaction behaviours. Global pairwise interactions predicted from monoculture growth kinetics were observed in approximately half of the measured pairs, whereas measured paired interactions generally weakened in combinations of three or more species. Using a spatially explicit agent-based Monod growth model that includes interspecific interactions, we accurately predicted the compositions of seven-member communities. Overall, our results indicate that emergent, spatially mediated interspecific interactions between cells of different bacterial species primarily drive local and temporal changes in individual cell growth rates, which in turn determine final biomass formation. Because most natural microbial habitats are spatially structured, stochastic founder-cell positioning and fitness differences are key determinants of locally formed interaction patterns and species coexistence.

microbiology↗

bioRxiv2026

Habitat fragmentation controls bacterial community composition outcomes

Natural habitats of bacteria are often highly structured in space, but how this affects their interactions and community composition outcomes is poorly understood. To address this gap, we studied the development of a synthetic soil community of 21 bacterial strains under a gradient of habitat fragmentation on single or mixed-substrate conditions. Fragmentation was produced by random microfluidic seeding of the mixed inoculum into culture medium droplets of variable volume (30-150 pL), targeting mean starting densities between 1 and 27 founder cells comprising 1-2, 7 or 14 taxa per droplet. Across all droplets for each of the fragmented states, globally different community compositions arose, suggesting variable individual taxa strategies and adaptation to differences in habitat fragmentation. In comparison to the same mixed inoculum growing under the same nutrient conditions in bulk culture, the more fragmented conditions allowed higher cell density and diversity, with less overgrowth by a few strains. Community evenness was highest when inocula were dispersed into individual taxon (1-2 taxa) or low-order combinations (7 taxa per droplet), but individual dispersion reduced the productivity of the meta-community across droplets. Monod-type simulations suggested that most community composition could be explained by the inherent individual kinetic properties and dispersal constraint effects of the fragmented habitat, with smaller effects from emerging interspecific interactions. Overall, our results show the strong effect of habitat structure on community outcomes, with higher fragmentation states favoring more even species coexistence. TEASERHabitat fragmentation results in the formation of locally isolated, smaller communities with varying richness and interactions, which altogether contribute positively to the maintenance of prokaryotic species diversity.

microbiology↗

bioRxiv2026

Horizontal transfer of ICEclc-like elements in Pseudomonas aeruginosa clinical isolates

Integrative and conjugative elements (ICEs) are widespread autonomous mobile DNA within bacterial chromosomes. ICEs contain the genes necessary for excision from the chromosome, conjugative transfer to a new recipient cell, and chromosomal reintegration. They can also carry accessory genes that, while not essential for transfer, confer adaptive phenotypes to the host, contributing to host survival under stressful or changing conditions. Genome studies have indicated that Pseudomonas aeruginosa clinical isolates carry a wide range of related ICEs with adaptive genes enriched for heavy metal resistance and efflux systems, however, their mobility has remained understudied. Here, we studied the activation and transfer mechanisms of a representative subset of ICEclc-type elements. We found that ICE excision could be induced in P. aeruginosa by ectopic expression of BisDC, the known master regulator of ICEclc activation, pointing to a similar regulatory cascade. A number of elements could be transferred to P. putida, where they conferred increased tolerance to specific heavy metals. We also assessed ICE excision rates in response to different classes of stressors using qPCR-based quantification. Sub-lethal copper exposure significantly increased ICE excision rates in several P. aeruginosa strains, although this response was strongly strain-dependent and absent in isolates with enhanced copper tolerance, highlighting the importance of host background. Despite elevated excision, copper did not stimulate ICE transfer or induce conjugation gene expression, indicating that ICE excision and conjugation can be uncoupled processes. Transcriptomic analyses revealed strain-specific regulatory responses to copper stress, including differential activation of metal-responsive regulators, oxidative stress pathways, and virulence-associated systems. IMPORTANCEIntegrative and conjugative elements (ICEs) play a major role in bacterial adaptation by mediating horizontal gene transfer, yet the environmental cues governing their activation remain poorly understood. Here, we demonstrate that ICEclc-type elements in Pseudomonas aeruginosa are transferable at low frequencies and that their excision can be selectively induced by specific stress conditions, notably copper exposure and hypoosmotic stress. Our findings reveal that ICE excision and conjugative transfer can be uncoupled and are strongly influenced by host genetic background, underscoring the complexity of ICE regulation. This work aimed to explore whether clinical conditions or antimicrobial treatment could inadvertently promote ICE-mediated gene transfer, with implications for understanding the evolution of antibiotic resistance and virulence.

microbiology↗

bioRxiv2025

A Modular Genetic Toolbox for Precise Gene Regulation and Multi-Color Imaging in Streptococci

Fluorescent labeling is a powerful tool in microbiology allowing live cell imaging and providing insights into dynamic cellular processes, quantification of gene expression and protein subcellular localization. Although multicolor imaging is widely used in Streptococcus pneumoniae and S. mutans, variants other than the green fluorescent protein (GFP) have rarely been applied in other streptococcal species. To address this gap in the streptococcal molecular toolbox, we benchmarked five different fluorescent proteins. The various fluorescent proteins were fused to the C-terminus of S. pneumoniae HlpA, a small non-specific DNA binding histone-like protein. These reporters, combined with four different antibiotic resistance genes, were engineered with various expression systems (inducible or constitutive) to form versatile cassettes. We provide methods to transfer these cassettes to different streptococcal species including S. salivarius and S. thermophilus. As a proof of concept, we generated a triple labeled S. salivarius strain in which HlpA, FtsZ and DivIVA were fused to three spectrally-distinct compatible fluorescent proteins. Multiple fluorescent labeling has broad applications for deciphering a wide range of scientific problems, from cellular processes to infectious disease mechanisms. The availability of these cassettes should allow for a wider use of single-cell labeling strategies in the Streptococcus clade and other closely related bacteria.

microbiology↗

bioRxiv2024

Habitat filtering but not microbiota origin controls microbiome transplant outcomes in soil

Human activities cause global losses of soil microbiome diversity and functionality. Microbiota transplants offer a potential solution, but the factors influencing transplant success remain unclear. We investigated how microbiota origin affects microbiome mergers, hypothesizing that native strains through niche preference are better adapted to their habitat and will outcompete non-native ones. To test this, we contrasted transplants between soil microcosm-cultured topsoil or lakewater communities with a community of 21 soil bacteria (SynCom). In both cases, SynCom transplant increased resident productivity but permanently shifted compositions, although its abundance dropped from an initial 50-80% to <1% within two months. Both merged and non-merged communities resembled natural soil microbiota in comparisons with over 81,000 soil, sediment and lake compositional data. Our results show that habitat filtering and niche competition, more than microbiota origin, determine transplant outcomes. Despite the limited proliferation of SynCom transplants, their capacity to instill lasting community trajectory changes opens new paths for microbiome engineering. TEASEREven transiently present microbiota transplants can alter resident microbiome composition through processes governed by habitat filtering.

microbiology↗

bioRxiv2024

Population-level control of two manganese oxidases expands the niche for bacterial manganese biomineralization

The enzymatic oxidation of aqueous divalent manganese (Mn) is a widespread microbial trait that produces reactive Mn(III, IV) oxide minerals. These biominerals drive carbon, nutrient, and trace metal cycles, thus playing important environmental and ecological roles. However, the regulatory mechanisms and physiological functions of Mn biomineralization are unknown. This challenge arises from the common occurrence of multiple Mn oxidases within the same organism and the use of Mn oxides as indicators of combined gene activity. Through detection of gene activation in individual cells, we discover that expression of mnxG and mcoA, two Mn oxidase-encoding genes in Pseudomonas putida GB-1, is confined to subsets of cells within the population, with each gene showing distinct spatiotemporal patterns that reflect local microenvironments. These coordinated intra-population dynamics control Mn biomineralization and illuminate the strategies used by microbial communities to dictate the extent, location and timing of biogeochemical transformations.

microbiology↗

bioRxiv2024

Orchestrated long-distance gene activation by a ParB-like BisD-CTP DNA clamp in low-frequency transfer competence development in Pseudomonas putida

Integrative conjugative elements (ICEs) are mobile DNA that remain integrated within the host bacterial genome until they activate their excision and transfer to recipient cells via conjugation. ICE transfer is initiated in a small subpopulation of cells that undergo a hierarchical gene expression cascade leading to transfer competence formation. In this study, we demonstrate that transfer competence formation of the ICEclc element in stationary phase Pseudomonas putida cells is regulated by the coordinated activity of a two-component transcriptional activator, BisC and BisD. Chromatin immunoprecipitation of tagged BisC or BisD followed by high throughput sequencing showed that both proteins accumulate at similar sites around ICEclc transfer competence promoters in P. putida cells. Genetic dissection and single cell microscopy showed that BisD is a dual domain protein, with a C-terminal gene activator domain and an N-terminal ParB-like domain, forming dimeric DNA clamps that self-load at distant sites and reach target promoters after extensive one-dimensional DNA sliding. Expressed mCherry-BisD in P. putida ICEclc cells form discrete fluorescent foci, dependent on parS-like sequences on the ICE. This focus formation is similar as what is seen with canonical ParB proteins accumulating on chromosomal DNA, but in case of BisD corresponds to both chromosomal and excised ICE-molecules. Sliding of BisD over [~]50 kb of ICE-DNA is asymmetric and follows the direction of ICE gene transcription. This may help to establish a temporal order of activation of transfer competence formation, optimizing ICE transfer. Given that ICEclc is activated in stationary phase cells, we hypothesize that BisD is not involved in segregating excised ICE-DNA among daughter cells, but rather in actively directing ICE-DNA molecules towards the (multiple) conjugative systems that are produced in transfer competent cells. BisD thus serves as a twin function protein, integrating gene activation and DNA segregation functions.

microbiology↗

bioRxiv2024

Inferring Bacterial Interspecific Interactions from Microcolony Growth Expansion

Interactions between species are thought to be crucial for modulating their growth and behaviour within communities, and determinant for the emergence of community functions. Several different interaction concepts exist, but there is no consensus on how interactions should be quantified and integrated in community growth theory. Here we expand on existing concepts of real-time measurements of pure culture microcolony growth to develop and benchmark coculture microcolony experiments, and show how these can both parametrize growth kinetic and interspecific interaction effects. We follow surface growth by time-lapse microscopy of fluorescently tagged Pseudomonas putida and Pseudomonas veronii under substrate competition with succinate, or under substrate indifference with D-mannitol and putrescine. Monoculture-grown microcolonies showed substrate concentration dependent expansion rates as expected from Monod relations, whereas individual microcolony yields were strongly dependent on densities and spatial positioning of founder cells. Maximum specific growth rates in cocultures under substrate competition were diminished by ca. 15%, which was seeding-density independent. The collective P. putida population dominated growth over that of P. veronii, but with 27% yield loss under competition compared to monoculture growth; and 90% for that of P. veronii. Incidental local reversal of competition was observed where P. veronii microcolonies profited at the detriment of P. putida, and between 9 and 43% of P. veronii microcolonies grew bigger than expected from bulk competition, depending on seeding density. Simulations with a cell-agent Monod surface growth model suggested that colony expansion rate decrease in competitive coculture is caused by metabolite cross-feeding, which was supported by exometabolite analysis during and after growth of the strains on their individual or swapped supernatant. Coculture microcolony growth experiments thus provide a flexible platform for analysis of kinetic and interspecific interactions, expanding from individual microcolony phenotypic effects to averaged behaviour across all microcolony pairs. The system in theory is scalable to follow real-time growth of multiple species simultaneously into communities.

microbiology↗

bioRxiv2024

Dimalis: A complete standalone pipeline to analyse prokaryotic cell growth from time-lapse imaging

Real-time imaging of bacterial cell division, population growth and behaviour is essential for our understanding of microbial-catalyzed processes at the microscale. However, despite the relative ease by which high resolution imaging data can be acquired, the extraction of relevant cell features from images remains cumbersome. Here we present a versatile pipeline for automated extraction of bacterial cell features from standalone or time-resolved image series, with standardized data output for easy downstream processing. The input consist of phase-contrast images with or without additional fluorescence details, which are denoised to account for potential out-of-focus regions, and segmented to outline the morphologies of individual cells. Cells are then tracked over subsequent time frame images to provide genealogy or microcolony spatial information. We test the pipeline with eight different bacterial strains, cultured in microfluidics systems with or without nutrient flow, or on agarose miniature surfaces to follow microcolony growth. Examples of downstream processing in form of extraction of growth kinetic parameters or bistable cell differentiation are provided. The pipeline is wrapped in a Docker to facilitate installation, consistent processing and avoiding constant software updates.

microbiology↗

bioRxiv2024

Bacttle: a microbiology educational board game for lay public and schools

1.Inspired by the positive impact of serious games on science understanding and motivated by personal interests in scienti[fi]c outreach, we developed Bacttle, an easy-to-play microbiology board game with adaptive difficulty, targeting any player from 7 years old onward. Bacttle addresses both the lay public and teachers for use in classrooms as a way of introducing microbiology concepts. The layout of the game and its mechanism are the result of multiple rounds of trial, feedback and re-design. The [fi]nal version consists of a deck of cards, a 3D-printed board and tokens (with a paper-based alternative), with all digital content open source. Players in Bacttle take on the character of a bacterial species. The aim for each species is to proliferate under the environmental conditions of the board and the interactions with the board and with other players, which vary as the play evolves. Players start with a given number of lives that will increase or decrease based on the traits they play for different environmental scenarios. Such bacterial traits come in the form of cards that can be deployed strategically. In order to assess the impact of the game on microbiological knowledge, we scored differences in the understanding of general concepts before and after playing the game. We assessed a total of 169 visitors at two different university open day science fairs. Players were asked to [fi]ll a brief survey before and after the game with questions targeting conceptual advances. Results show that Bacttle increases general microbiology knowledge on players as young as 5 years old, and with the highest impact on those who have no a priori microbiology comprehension.

scientific communication and education↗

bioRxiv2024

Fragmented micro-growth habitats present opportunities for alternative competitive outcomes

Bacteria in nature often proliferate in highly patchy environments, such as soil pores, particles, plant roots or leaves. The resulting spatial fragmentation leads to cells being constrained to smaller habitats, shared with potentially fewer other species. The effects of microhabitats on the emergence of bacterial interspecific interactions are poorly understood, but potentially important for the maintenance of diversity at a larger scale. To study this more in-depth, we contrasted paired species-growth in picoliter droplets at low population census with that in large (macro) population liquid suspended cultures. Four interaction scenarios were imposed by using different bacterial strain combinations and media: substrate competition, substrate independence, growth inhibition, and cell killing by tailocins. In contrast to macro-level culturing, we observed that fragmented growth in picoliter droplets in all cases yielded more variable outcomes, and even reversing the macro-level assumed interaction type in a small proportion of droplet habitats. Timelapse imaging and mathematical simulations indicated that the variable and alternative interaction outcomes are a consequence of founder cell phenotypic variation and small founder population sizes. Simulations further suggested that increased growth kinetic variation may be a crucial selectable property for slower-growing bacterial species to survive competition. Our results thus demonstrate how microhabitat fragmentation enables the proliferation of alternative interaction trajectories and contributes to the maintenance of higher species diversity under substrate competition.

microbiology↗

bioRxiv2023

Niche Availability and Competitive Facilitation Control Proliferation of Bacterial Strains Intended for Soil Microbiome Interventions

Microbiome engineering, the rational manipulation of microbial communities and their habitats, is considered a crucial strategy to revert dysbiosis. However, the concept is in its infancy and lacks experimental support. Here we study the ecological factors controlling the proliferation of focal bacterial inoculants into taxa-complex soil communities and their impact on resident microbiota. We demonstrate using standardized soil microbiomes with different growth phases that the proliferation of typical soil inoculants depends on niche competition. By adding an artificial, inoculant selective niche to soil we improve inoculant proliferation and show by metatranscriptomics to give rise to a conjoint metabolic network in the soil microbiome. Furthermore, using random paired growth assays we demonstrate that, in addition to direct competition, inoculants lose competitiveness with soil bacteria because of metabolite sharing. Thus, the fate of inoculants in soil is controlled by niche availability and competitive facilitation, which may be manipulated by selective niche generation. TeaserTypical bacterial inoculants for soil microbiome engineering suffer from facilitating growth of native resident microorganisms

ecology↗

bioRxiv2023

Diversity and Evolution of an Abundant ICEclc-Family of Integrative and Conjugative Elements in Pseudomonas aeruginosa

Integrative and conjugative elements (ICEs) are widespread autonomous mobile DNA, containing the genes necessary for their excision, conjugative transfer, and insertion into a new host cell. ICEs can carry additional genes that are non-essential for their transfer, but that can confer adaptive phenotypes to the host. Our aim here was to better characterize the presence, distribution and evolution of ICEs related to the well-described ICEclc among Pseudomonas aeruginosa clinical isolates, and to understand their potential role in spreading genes with adaptive benefit. We examined a total of 181 P. aeruginosa genome sequences obtained from patient or hospital environment isolates. More than 90% of the isolates carried one or more ICEclc-like elements, with different degrees of conservation to the known ICEclc-lifestyle and transfer genes. ICE clones closely matched their host clonal phylogeny, but not exclusively, indicating that both clonal evolution and ICE-horizontal transfer are occurring in the hospital environment. Variable gene regions among the clinical P. aeruginosa ICEclc-type elements were notably enriched for heavy metal resistance genes, toxin-antitoxin systems, potential efflux systems and multidrug resistance proteins, a metalloprotease and for a variety of regulatory systems, but not for specific recognizable antibiotic resistance cassettes. Clonal persistence suggests adaptive benefits of these functional categories; and micro-patterns of gene gain and loss indicate ongoing ICE evolution within the P. aeruginosa hosts.

microbiology↗

bioRxiv2023

Regulated bacterial interaction networks: A mathematical framework to describe competitive growth under inclusion of metabolite cross-feeding

When bacterial species with the same resource preferences share the same growth environment, it is commonly believed that direct competition will arise. A large variety of competition and more general interaction models have been formulated, but what is currently lacking are models that link mono-culture growth kinetics and community growth under inclusion of emerging biological interactions, such as metabolite cross-feeding. In order to understand and mathematically describe the nature of potential cross-feeding interactions, we design experiments where two bacterial species Pseudomonas putida and Pseudomonas veronii grow in liquid medium either in mono- or as co-culture in a resource-limited environment. We measure population growth under single substrate competition or with double species-specific substrates (substrate indifference), and starting from varying cell ratios of either species. Using experimental data as input, we first consider a mean-field model of resource-based competition, which captures well the empirically observed growth rates for mono-cultures, but fails to correctly predict growth rates in co-culture mixtures, in particular for skewed starting species ratios. Based on this, we extend the model by cross-feeding interactions where the consumption of substrate by one consumer produces metabolites that in turn are resources for the other consumer, thus leading to positive feedback loops in the species system. Two different cross-feeding options were considered, which either lead to constant metabolite cross-feeding, or to a regulated form, where metabolite utilization is activated with rates according to either a threshold or a Hill function, dependent on metabolite concentration. Both mathematical proof and experimental data indicate regulated cross-feeding to be the preferred model over constant metabolite utilization, with best co-culture growth predictions in case of high Hill coefficients, close to binary (on/off) activation states. This suggests that species use the appearing metabolite concentrations only when they are becoming high enough; possibly as a consequence of their lower energetic content than the primary substrate. Metabolite sharing was particularly relevant at unbalanced starting cell ratios, causing the minority partner to proliferate more than expected from the competitive substrate because of metabolite release from the majority partner. This effect thus likely quells immediate substrate competition and may be important in natural communities with typical very skewed relative taxa abundances and slower-growing taxa. In conclusion, the regulated bacterial interaction network correctly describes species substrate growth reactions in mixtures with few kinetic parameters that can be obtained from mono-culture growth experiments. 1 Author summaryCorrectly predicting growth of communities of diverse bacterial taxa remains a challenge, because of the very different growth properties of individual members and their myriads of interactions that can influence growth. Here we tried to improve and empirically validate mathematical models that combine theory of bacterial growth kinetics (i.e., Monod models) with mathematical definition of interaction parameters. We focused in particular on common cases of shared primary substrates (i.e., competition) and independent substrates (i.e., indifference) in an experimental system consisting of one fast-growing and one slower growing Pseudomonas species. Growth kinetic parameters derived from mono-culture experiments included in a Monod-type consumer-resource model explained some 75% of biomass formation of either species in co-culture, but underestimated the observed growth improvement when either of the species started as a minority compared to the other. This suggested an in important role of cross-feeding, whereby released metabolites from one of the partners is utilized by the other. Inclusion of cross-feeding feedback in the two-species Monod growth model largely explained empirical data at all species-starting ratios, in particular when cross-feeding is activated in almost binary manner as a function of metabolite concentration. Our results also indicate the importance of cross-feeding for minority taxa, which can explain their survival despite being poorly competitive.

microbiology↗

bioRxiv2022

STrack: A tool to Simply Track bacterial cells in microscopy time-lapse images

Bacterial growth can be studied at the single cell-level through time-lapse microscopy imaging. Technical advances in microscopy lead to increasing image quality, which in turn allows to visualize larger areas of growth, containing more and more cells. In this context, the use of automated computational tools becomes essential. In this paper, we present STrack, a tool that allows to track cells in time-lapse images in a fast and efficient way. We compared it to three recently published tracking tools on images ranging over six different bacterial strains, and STrack showed to be the most consistent tracking tool, returning more than 80% of correct cell lineages on average. The python implementation of STrack, a docker structure, and a tutorial on how to download and use the tool can be found on the following github page: https://github.com/Helena-todd/STrack

bioinformatics↗

bioRxiv2021

A bistable orthogonal prokaryotic differentiation system underlying development of conjugative transfer competence

The mechanisms and impact of horizontal gene transfer processes to distribute gene functions with potential adaptive benefit among prokaryotes have been well documented. In contrast, little is known about the life-style of mobile elements mediating horizontal gene transfer, whereas this is the ultimate determinant for their transfer fitness. Here, we investigate the life-style of an integrative and conjugative element (ICE) within the genus Pseudomonas that stands model for a widespread family transmitting genes for xenobiotic compound metabolism and antibiotic resistances. The ICE only transfers from a small fraction of cells in a population, which we uncover here, results from a dedicated transfer competence program imposed by the ICE. Transfer competence is orthogonally maintained in individual cells in which it is activated, making them the centerpiece of ICE conjugation. The components mediating transfer competence are widely conserved, underscoring their selected fitness for efficient transfer of this class of mobile elements.

microbiology↗