Biology subjects

Witting, L.

Publications and source records attributed to Witting, L..

18 recordsLinked to original sources

bioRxiv2026

Systematic evaluation of Cyanidioschyzon merolae across photobioreactor systems: Linking reactor design to biomass production and biochemical composition

Extremophilic red microalgae are promising platforms for sustainable biotechnology, combining robust growth under selective thermoacidophilic conditions with production of thermostable phycobiliproteins and carbon-rich biomass. However, reactor-dependent effects on growth, product formation and biomass composition remain insufficiently resolved. Here, we systematically evaluated the extremophilic red microalga Cyanidioschyzon merolae across cultivation scales and reactor formats and benchmarked its performance against the well-established Galdieria javensis and Limnospira platensis. In small-scale multi-cultivator photobioreactors and microfluidic growth chambers, C. merolae showed superior growth, reaching a maximum growth rate of 0.034 {+/-} 0.001 h-1 and 8.3 {+/-} 0.3 g l-1 cell dry weight. Microfluidic cultivation enabled growth analysis at single-cell resolution and matched growth rates obtained in photobioreactors. To identify scalable production strategies, C. merolae was further cultivated in a flat-panel photobioreactor and a custom-designed internally illuminated photobioreactor. The custom-designed photobioreactor delivered the highest biomass concentration and productivity, yielding 11.5 {+/-} 0.6 g l-1 cell dry weight and 1.07 {+/-} 0.06 g l-1 d-1, and comparable yields with regard to R-phycocyanin and R-allophycocyanin. Biomass analysis revealed substantial carbon and nitrogen contents, starch accumulation up to > 20 % of cell dry weight, and fatty acids dominated by palmitic, linoleic and oleic acids. Despite its reduced cell wall fraction, C. merolae contained structurally diverse, cultivation-dependent polysaccharides. These results establish C. merolae as a versatile chassis for thermostable pigment production and renewable feedstock generation, highlighting photobioreactor design as a key determinant of productivity and biomass quality.

microbiology↗

bioRxiv2026

A multichromatic UV-RGB optogenetic toolbox for control of gene expression in Pseudomonas putida

Optogenetics uses light to provide precise, reversible, and non-invasive control over bacterial functions including gene expression with high spatiotemporal resolution. Although many optogenetic systems have been developed for Escherichia coli, only a limited number is available for other prokaryotes, such as pseudomonads. Here, we establish a toolbox of genomically integrated optogenetic gene cassettes for light-responsive regulation of target gene expression in Pseudomonas putida with UV-A, blue, green, and red light. Using transposon Tn7-mediated chromosomal integration, we implemented four optogenetic systems: the photocaged IPTG/Ptac-LacI system, the LOV-based Dusk switch, the cyanobacteriochrome system CcaS/R, and different bacteriophytochrome-based REDusk variants. Benchmarking with the mCherry reporter demonstrated high dynamic ranges of up to [~]270-fold, low basal expression, and largely homogeneous population responses in P. putida. Spatial illumination further enabled patterned single- and dual-color gene expression. As a proof of concept, we applied the toolbox for light-controlled regulation of pyoverdine (PVD) biosynthesis in P. putida. The expression of the alternative sigma factor PfrI, which upregulates the production of the siderophore during iron-limitation, was placed under optogenetic control in a {Delta}pfrI background. The red-light responsive switches resulted in the strongest induction of PVD synthesis and enabled spatial control of siderophore-mediated microbial interactions. To demonstrate transferability, light-dependent pyoverdine production was further established in the human pathogen Pseudomonas aeruginosa PAO1. Together, this optogenetic plug-and-play toolbox enables non-invasive, spatiotemporal reprogramming of gene expression and cellular processes in pseudomonads and expands the available optogenetic repertoire beyond established model organisms.

synthetic biology↗

bioRxiv2026

Glycogen deficiency impairs diurnal energy metabolism and cell division in Synechocystis

Diurnal changes in light availability are a defining feature of life on Earth. Photoautotrophic organisms therefore store reduced carbon during the day to sustain energy metabolism at night. In cyanobacteria, glycogen is the primary carbon storage compound and supports both energy homeostasis and stress responses. Although glycogen-deficient Synechocystis strains have been studied previously, how these mutants cope with the loss of the major daytime carbon sink and can sustain themselves during the night remains unclear. Using single-cell microfluidics, transcriptomics, and metabolomics, we show that {Delta}glgC mutants exhibit pronounced light sensitivity. At sub-lethal light intensities, daytime transcriptional responses are dominated by downregulation of photosynthesis-related genes, likely preventing NADPH overaccumulation in the absence of a carbon sink. During the night, mutants display severe energy limitation, characterized by reduced ATP levels, altered redox balance, and depletion of central carbon intermediates. In contrast, fumarate and malate accumulate, indicating enhanced respiratory flux through succinate dehydrogenase. These metabolic constraints lead to extended lag phases and delayed cell divisions after the onset of light, demonstrating that glycogen-deficient cells fail to efficiently reinitiate growth after dawn. Overall, our results as a snapshot of the initial response to diurnal regimes highlight glycogen as a central integrator of diurnal physiology in Synechocystis, coordinating energy metabolism, redox balance, and cell division, with implications for metabolic robustness and the evolutionary constraints shaping (endo)symbiosis. Short summaryGlycogen deficiency disrupts day-night energy and redox homeostasis in Synechocystis, revealing constraints on growth, division, and symbiotic potential.

plant biology↗

bioRxiv2026

On the stock structure bias of the space-time fidelity of mark-recapture studies

Mark-recapture analyses on the delineation of natural populations between areas often assume random sampling, with a between/within (B/W) area resighting ratio that declines towards zero as the population components of two areas become more-and-more isolated from one another, with fewer-and-fewer individuals mixing between areas. I use an individual based population model split in two areas to simulate this result, analysing also for the potential effects of the space-time fidelity of the mark-recapture sampling in the areas. I find that small B/W resighting ratios--that traditionally is taken as evidence of population isolation--can easily be observed within a completely mixing population if a random sampling scheme is restricted in space and/or time. Random sampling within restricted areas and time windows is not sufficient to estimate mixing rates and population isolation between areas, unless the resighting rates are analysed by a method that accounts both for the space-time fidelity of the scientific sampling scheme and the space-time fidelity of the distributional behaviour of the individuals in the population.

ecology↗

bioRxiv2026

Live-cell imaging enables reporter-free monitoring of the circadian rhythm in individual Synechocystis cells

In vivo monitoring of circadian rhythms depends on reliable and non-invasive detection methods. This is often achieved by expressing reporter genes heterologously under the control of a circadian promoter. The activity or fluorescence of the gene product is then used as a readout. To avoid the need for generation of such reporter strains, we recently established a reporter-free detection method for cyanobacterial batch cultures. To determine whether these rhythms are driven at the level of individual cells or result from population-based effects, such as gating of cell division, we analyzed individual Synechocystis sp. PCC 6803 cells by combining a microfluidic cultivation technique with multipoint time-lapse microscopy imaging at the single-cell resolution. Hundreds of time-lapse image sequences, acquired over a period of up to ten days, were processed using our deep learning cell segmentation workflow. Although the cells had been entrained by a 12-hour light-dark cycle, neither cell size nor cell division displayed circadian rhythms. This indicates the absence of circadian gating of cell division in Synechocystis. Instead, we observed circadian oscillation in the average brightness of the phase contrast of individual Synechocystis cells. To demonstrate how phase-contrast analysis of single cells can be complemented by backscatter analysis of batch cultures, we investigated the wildtype, a deletion mutant known to affect circadian rhythms ({Delta}kaiC3) and complementation strains at both, the single-cell and batch levels. We concluded that phase contrast and backscatter likely measured the same rhythmic changes in the refractive index of the cells. The method presented here will advance circadian research by enabling the analysis of circadian rhythms in individual cells without the need for expression of reporter molecules.

microbiology↗

bioRxiv2024

Environmental and molecular noise buffering by the cyanobacterial clock in individual cells

Circadian clocks enable organisms to anticipate daily cycles, while being robust to molecular and environmental noise. Here, we show how the cyanobacterial clock buffers genetic and environmental perturbations through its core phosphorylation loop. We first characterise single-cell clock dynamics in clock mutants using a microfluidics device that allows precise control of the microenvironment. We find known clock regulators are dispensable for clock robustness, whilst perturbations of the core clock reveal that the wild-type operates at a noise optimum that we can reproduce in a stochastic model of just the core phosphorylation loop. We then examine how the clock responds to noisy environments, including natural light conditions. The model accurately predicts how the clock filters out environmental noise, including fast light fluctuations, to keep time while remaining responsive to environmental shifts. Our findings illustrate how a simple clock network can exhibit complex noise filtering properties, advancing our understanding of how biological circuits can perform accurately in natural environments.

systems biology↗

bioRxiv2024

Cause and effect in the natural selection of the population ecological life histories of mammals

The inter-specific life history and ecological variation of mammals is often explained as allometric consequences of physiological adaptations to unexplained body mass variation. But these hypotheses are unnecessary because the allometric scaling is explained already by the natural selection that explains the variation in mass. I decompose the population ecological life histories of 4,936 species of mammals to show how the selection of mass accounts for the life history and population ecological variation in mammals. This shows that 55% of the within order variance, and 91% of the between order differences, in the body mass, demography, and population ecological traits are reconciled by the response of population dynamic feedback selection to variation in net energy, mortality, and intra-specific interactive competition.

evolutionary biology↗

bioRxiv2024

Causality in the natural selection of the population ecological life histories of birds

Contingent life history theory explains evolution backwards by analysing the fitness consequences of tradeoffs and constraints in the evolved species of today, bypassing the essential challenge of predicting evolution forwardly by the cause and effect of natural selection. I do the latter to decompose the population ecological life histories of 11,187 species of birds. This shows how the selection of mass accounts for inter-specific variation, with 76% of the within order variance, and 72% of the between order differences, in the body mass, demography, and population ecological traits being reconciled by the response of population dynamic feedback selection to variation in net energy, mortality, and intra-specific interactive competition.

evolutionary biology↗

bioRxiv2023

Population dynamic population delineation in North American birds

Andrewartha and Birch (1954) envisioned that natural populations are surrounded by ecological barriers, yet statistical estimates of population structure are almost completely driven by genetic analyses void of ecological information. I develop an ecological clustering routine that delineates natural populations from the synchronisation and desynchronisation in the population dynamics of continuously distributed species. The method is applied to the North American Breeding Bird Survey (Sauer et al. 2017), where it identifies two to five populations per species for 160 species, and leaves the population differentiation unresolved for 139 species. This provides one of the first statistical methods for population dynamics delineated population structure.

ecology↗

bioRxiv2023

Huge narwhal displacement following shipping of iron ore in the Canadian Arctic Archipelago

With 100,000 narwhals inhabiting populations in the Canadian Arctic Archipelago, the Northwest Passage runs through the largest aggregation of narwhals in the world. I use a metapopulation analysis that covers eight of the narwhal populations in the area to estimate that about 25,000 narwhals have emigrated from Eclipse Sound to Admiralty Inlet since 2007, causing almost total population collapse in Eclipse Sound following shipping of iron ore through Milne Inlet and Eclipse Sound. It is estimated that up to about 30,000 narwhals may vanish in the long run, unless shipping is increasingly regulated, or narwhals adapt to the disturbance and reinhabits the abandoned areas. Reflecting only a local disturbance, these population effects warn against intense shipping in other fjords with narwhals, and against a potentially much larger impact from increased shipping through the Northwest Passage in the future.

ecology↗

bioRxiv2022

Behind the scene of body mass allometries

I use data based life history models for 9,488 species of birds and 4,865 species of mammals to illustrate natural selection causes for the evolution of inter-specific body mass allometries. Each model integrates the growth and demography of individuals with the life history energetics and population ecology of the species. I show i) how the primary selection of resource handling and mass-specific metabolism generates the net energy of individuals, ii) how the selected net energy generates a population dynamic feedback selection where intra-specific interactive competition selects body masses that scale in proportion with net energy on the timescale of natural selection, iii) how the primary selection of metabolism selects an allometric curvature where the residual mass-specific metabolism--relative to the expectation of the mass-rescaling allometry--is an initially declining function of mass in terrestrial placentals and birds, but not in marsupials and bats, iv) how the selection of body mass buffers ecological variation in survival, and v) how the joint selection of mass and optimal foraging selects the exponents of body mass allometries from the dominant spatial dimensionality of the foraging ecology.

evolutionary biology↗

bioRxiv2021

Life histories of 9,488 bird and 4,865 mammal species

With life history traits determining the natural selection fitnesses of individuals and growth of populations, estimates of their variation are essential to advance evolutionary theory and ecological management during times of global change. As quantitative predictions improve with the completeness of models, and as data are usually incomplete or missing for most species, I use published data and inter-specific allometric extrapolations to estimate complete population dynamic life history models for birds and mammals with known body masses. This constructs models for 11,188 species of birds and 4,937 species of mammals, covering 27 life history and ecological traits per species. The estimates are used to illustrate natural selection mechanisms and explain a diverse range of population dynamic trajectories by the inclusion of population dynamic regulation. This provides a first step towards the construction of freely accessible and ready-to-use online population dynamic simulations covering all species of birds and mammals.

evolutionary biology↗

bioRxiv2021

On selection-regulated population dynamics in birds and mammals

I fit species-specific age-structured population dynamic models to 3,369 and 483 abundance timeseries for 900 and 208 bird and mammal species, using AIC model-selection to differentiate dynamics with and without natural selection. The AIC includes natural selection in 79% to 92% of the accepted models, explaining 80% of the population dynamics variance, with median selection regulation estimated 1.2 (se:0.11) times stronger than density regulation. The estimated regulation is naturally selected by the population dynamic feedback selection of the density-frequency-dependent interactive competition among the individuals in the population, and it accelerates and decelerates population growth around the naturally selected population dynamic equilibrium, generating damped to stable population cycles with median periods around seven and eight generations given stable cycles. These results resolve several population cycle enigmas, highlighting the population dynamic implications of a feedback selection that predicts also the life history and abundance body mass allometries of animals. The selection regulated models are available for online simulations at https://mrLife.org.

ecology↗

bioRxiv2018

Saving killer whale populations from a global collapse: rebuttal against Desforges et al. (2018)

In their Science paper, Desforges et al. (2018) address PCB pollution in killer whales, predicting a decline in calf survival and an associated collapse of killer whale populations worldwide. I refute the collapse, showing that it follows from a flawed model parametrisation. The result is not questioning contamination problems in killer whales, but only the bold prediction of global collapse.

ecology↗

bioRxiv2016

The natural selection of metabolism explains curvature in allometric scaling

I simulate the evolution of metabolism and mass to explain the curvature in the metabolic allometry for placental and marsupial mammals. I assume that the release of inter-specific competition by the extinction of dinosaurs 65 million years ago made it possible for each clade to diversity into a multitude of species across a wide range of niches. The natural selection of metabolism and mass was then fitted to explain the maximum observed body masses over time, as well as the current inter-specific allometry for metabolism. The estimated selection of mass specific metabolism was found to bend the metabolic allometry over time, with the strongest curvature in the placental clade. The rate of exponential increase in mass specific metabolism for placentals was estimated to 9.3 x 10-9 (95% CI:7.3 x 10-9 - 1.1 x 10-8) on the per generation time-scale. This is an order of magnitude larger than the estimate for marsupials, in agreement with an average metabolism that is 30% larger in placentals relative to marsupials of similar size.

evolutionary biology↗

bioRxiv2016

The natural selection of metabolism bends body mass evolution in time

The natural selection of metabolism and mass can explain inter-specific allometries from prokaryotes to mammals (Witting 2017a), with exponents that depend on the selected metabolism and the spatial dimensionality (2D/3D) of intra-specific behaviour. The predicted 2D-exponent for total metabolism increases from 3/4 to 7/4 when the fraction of the inter-specific body mass variation that follows from primary variation in metabolism increases from zero to one.\n\nA 7/4 exponent for mammals has not been reported from inter-specific comparisons, but I detect the full range of allometries for evolution in the fossil record. There are no fossil data for allometric correlations between metabolism and mass, but I estimate life history allometries from the allometry [Formula] for the rate of evolution [Formula] in mass (w) in physical time (t).\n\nThe [Formula] exponent describes the curvature of body mass evolution, with predicted values being: 3/2 (2D) for within niche evolution in small horses over 54 million years. 5/4 (2D) and 9/8 (3D) for across niche evolution of maximum mass in four mammalian clades. 3/4 (2D) for fast evolution in large horses, and maximum mass in trunked and terrestrial mammals. 1 for maximum mass across major life-forms during 3.5 billion years of evolution along a metabolic bound.

evolutionary biology↗

bioRxiv2016

The natural selection of metabolism and mass selects lifeforms from viruses to multicellular animals

I show that the natural selection of metabolism and mass is selecting for the major life history and allometric transitions that define lifeforms from viruses, over prokaryotes and larger unicells, to multicellular animals with sexual reproduction.\n\nThe proposed selection is driven by a mass specific metabolism that is selected as the pace of the resource handling that generates net energy for self-replication. This implies that an initial selection of mass is given by a dependence of mass specific metabolism on mass in replicators that are close to a lower size limit. A maximum dependence that is sublinear is shown to select for virus-like replicators with no intrinsic metabolism, no cell, and practically no mass. A maximum superlinear dependence is instead selecting for prokaryote-like self-replicating cells with asexual reproduction and incomplete metabolic pathways. These self-replicating cells have selection for increased net energy, and this generates a gradual unfolding of a population dynamic feed-back selection from interactive competition. The incomplete feed-back is shown to select for larger unicells with more developed metabolic pathways, and the completely developed feed-back to select for multicellular animals with sexual reproduction.\n\nThis model unifies natural selection from viruses to multicellular animals, and it provides a parsimonious explanation where allometries and major life history transitions evolve from the natural selection of metabolism and mass.

evolutionary biology↗

bioRxiv2016

The natural selection of metabolism and mass selects allometric transitions from prokaryotes to mammals

Inter-specific body mass allometries can evolve from the natural selection of mass, with {+/-}1/4 and {+/-}3/4 exponents following from the geometry of intra-specific interactions when density dependent foraging occurs in two spatial dimensions (2D, Witting, 1995). The corresponding values for three dimensional interactions (3D) are {+/-}1/6 and {+/-}5/6.\n\nBut the allometric exponents in mobile organisms are more diverse than the prediction. The exponent for mass specific metabolism tends to cluster around -1/4 and -1/6 in terrestrial and pelagic vertebrates, but it is strongly positive in prokaryotes with an apparent value around 5/6 (DeLong et al., 2010). And a value around zero has been reported in protozoa, and on the macro evolutionary scale from prokaryotes over larger unicells to multicellular vertebrates (Makarieva et al., 2005, 2008).\n\nI show that mass specific metabolism can be selected as the pace of the resource handling that generates net energy for self-replication and the selection of mass, and that this selection of metabolism and mass is sufficient to explain metabolic exponents that decline from 5/6 over zero to -1/6 in 3D, and from 3/4 over zero to -1/4 in 2D. The decline follows from a decline in the importance of mass specific metabolism for the selection of mass, and it suggests i) that the body mass variation in prokaryotes is selected from primary variation in mass specific metabolism, ii) that the variation in multicellular animals are selected from primary variation in the handling and/or densities of the underlying resources, iii) that protozoa are selected as an intermediate lifeform between prokaryotes and multicellular animals, and iv) that macro evolution proceeds along an upper bound on mass specific metabolism.

evolutionary biology↗