Biology subjects

Richards, T.

Publications and source records attributed to Richards, T..

10 recordsLinked to original sources

bioRxiv2025

Intracellular niche specialisation drives evolutionary entrapment of endosymbiotic algae

Endosymbiosis underpins the evolution of complex life and the function of diverse ecosystems, but the mechanisms driving the origin and stability of endosymbiosis remain unclear. Fitness trade-offs between intracellular and extracellular niches could drive the emergence of stable endosymbiosis if adaptation to the intracellular niche reduces fitness in the extracellular niche, reinforcing endosymbiosis through niche specialisation by the endosymbiont. We tested this hypothesis by quantifying phenotypic divergence between endosymbiotic and free-living populations of a facultative algal endosymbiont along trait axes predicted to contrast between its intracellular and extracellular lifestyles. Consistent with endosymbiont specialisation, we observed strong divergence involving multiple traits between endosymbiotic and free-living populations. Specifically, endosymbionts showed convergent losses of multiple nitrogen metabolism pathways, increased export of maltose and glucose, increased sensitivity to acidification, higher and less variable photosynthetic efficiency, and reduced free-living growth rate. Intracellular environments are stable, safe from natural enemies, and come with a reliable supply of specific nutrients, but are acidic and place demands upon endosymbionts to provision their hosts; our data suggest that adapting to this niche is likely to reduce free-living growth and survival of endosymbionts. Our findings support fitness trade-offs between contrasting intracellular and extracellular environments as a mechanism stabilising endosymbiosis by driving evolutionary entrapment of niche-specialist endosymbionts.

evolutionary biology↗

bioRxiv2025

Single-cell sequencing reveals unexpected genetic diversity among Bodo spp. flagellates and their bacterial endosymbionts

Bodo is a cosmopolitan genus of free living bacterivorous single-celled flagellates in the class Kinetoplastea. Members of genus Bodo are considered the closest free-living relatives to the parasitic lineages Trypanosoma and Leishmania, the causative agents of the human diseases sleeping sickness, Chagas disease, and leishmaniasis. Currently, a single genome exists for the one formally described species in the genus, Bodo saltans. Previous studies on B. saltans have shown that it is dependent on an endosymbiotic bacterium from the order Holosporales, "Candidatus Bodocaedibacter vickermanii". Using single cell-sequencing, we isolated, sequenced, and assembled genomes for seven uncultured Bodo spp. cells from a single freshwater sample from Royal Leamington Spa, UK. By using comparative genomics, we show that these seven cells represent three potentially novel Bodo species and exhibit unexpected levels of diversity at the genome level. Our results indicate that Small Subunit (SSU) rDNA sequencing, often used to classify Bodo flagellates, is insufficient for determining species delimitation in this genus. In addition, we recovered a Holosporales bacterium genome from all seven Bodo spp. cells. Surprisingly, these seven bacterial endosymbionts also represent three potentially novel species and one novel genus of Holosporales bacteria. This diversity would be indistinguishable in routinely-used SSU ribosomal DNA (rDNA) metabarcoding or bulk sequencing pipelines, thus demonstrating the utility of using single-cell sequencing to reveal the level of genomic diversity within lineages of microbial eukaryotes and their cobionts.

microbiology↗

bioRxiv2025

Phagocytosis repurposed: infection strategies in a globalmarine diatom-parasite interaction

Microbial host-parasite interactions shape global biogeochemical cycles, yet their cellular and evolutionary mechanisms remain poorly understood. Here, we developed a novel model pathosystem to explore the interaction between the globally distributed eukaryotic microparasite, Pirsonia, and its host, the bloom-forming diatom, Coscinodiscus. Culture conditions recapitulated Pirsonias rapid life cycle in vitro and live-cell imaging enabled quantitative assessments of infection dynamics and host mortality. To investigate the genetic basis of this interaction, we assembled the Pirsonia genome and identified unique genetic innovations relative to their oomycete relatives. Time-resolved dual RNA-Seq enabled tracking of parasite gene expression through the infection cycle and revealed an upregulation of an expanded multi-gene family of integrin-like proteins in Pirsonia zoospores, analogous to the variable surface proteins in other parasitic lineages. Genes upregulated during infection were associated with cytoskeletal dynamics and drug inhibition assays confirmed that actin is required for host infection, consistent with the presence of parasitic pseudopodia on infected hosts. The dependence on both actin-based phagocytic mechanisms and parasitic-like surface proteins highlights Pirsonias intermediate state between predator and parasite, providing new insights into the evolution of parasite strategies and the complex cellular interactions controlling parasitic shunts in marine trophic networks.

evolutionary biology↗

bioRxiv2024

Discordance between biomarkers of iron status in plasma and myocardium across iron replete, iron deficiency, and iron replacement states.

It is unclear whether plasma measures of iron status reflect iron status in tissues. This study compared the effects of iron deficiency or treatment with intravenous iron on plasma versus myocardial measures of iron metabolism and mitochondrial dysfunction in mice and humans. The human study included 31 people undergoing cardiac surgery. Twenty-two (71%) were iron deficient. The mouse study included 88 mice randomly allocated to iron replete diet group (Controls, n=29), an Iron Deficient diet (n=31) or an iron deficient diet followed by IV Iron administration (n=28). Outcomes included plasma iron and ferritin concentrations, and myocardial total iron, ferritin, IRP1 binding, and mitochondrial complex activity and DNA damage. In the human study, plasma ferritin positively correlated with myocardial ferritin (r2=0.155, p=0.012). People with iron deficiency had significantly lower myocardial ferritin levels than those without iron deficiency. There were no differences or significant correlations for other outcomes. In the mouse study, plasma ferritin negatively correlated with myocardial ferritin (r2=0.113, p=0.004), and iron deficiency reduced myocardial ferritin levels (p=0.018) as well as the binding affinity of myocardial IRP1 to the Ferritin heavy chain mRNA (p=0.033). Intravenous iron had divergent effects on plasma (increased) and myocardial (decreased) ferritin levels, and increased IRP1 binding affinity and mitochondrial respiratory complex activity (p=0.049). These finding suggest that measures of iron metabolism and iron deficiency in plasma do not consistently reflect myocardial iron status across iron replete, iron deficient, and iron replacement states.

molecular biology↗

bioRxiv2024

Membrane permeability selection drove the stereochemistry of life

Early in the evolution of life a proto-metabolic network was encapsulated within a membrane compartment. The permeability characteristics of the membrane determined several key functions of this network by determining which compounds could enter the compartment and which compounds could not. One key feature of known life is the utilisation of right-handed D- ribose and deoxyribose sugars and left-handed L- amino acid stereochemical isomers (enantiomers), however, it is not clear why life adopted this specific chirality. We previously demonstrated that an archaeal and an intermediate membrane mimic, bearing a mixture of bacterial and archaeal lipid characteristics (a hybrid membrane), display increased permeability compared to bacterial-like membranes. Here, we investigate if these membranes can drive stereochemical selection on pentose sugars, hexose sugars and amino acids. Using permeability assays of homogenous unilamellar vesicles, we demonstrate that both membranes select for D- ribose and deoxyribose sugars while the hybrid membrane uniquely selects for a reduced alphabet of L- facing amino acids. This repertoire includes alanine, the plausible first L- amino acid utilised. We conclude such compartments could provide stereochemical compound selection thereby demonstrating a solution to the chirality problem during the evolution of life.

evolutionary biology↗

bioRxiv2022

Positive indirect effects more than balance negative direct effects of ungulate grazers on population growth of a grassland herb

O_LIHerbivores can affect plant population dynamics both directly because of the damage they inflict, and indirectly by moderating conditions for plant recruitment, competition and other biotic interactions. Still, the relative importance of indirect effects of herbivores on plant population dynamics is poorly known. C_LIO_LIWe quantified direct and indirect effects of ungulate grazers on population growth rate of the short-lived perennial herb Primula farinosa, using integral projection models based on demographic data collected over 7 years in exclosures and open control plots at nine grassland sites in southern Sweden. In addition, we explored the mechanisms behind indirect effects with simulations. C_LIO_LIGrazers had negative direct effects on P. farinosa population growth rate, but these were more than balanced by positive indirect effects. The positive indirect effects were mainly linked to improved conditions for plant recruitment. Simulations indicated that indirect effects of ungulate grazers on population growth rate via interactions with pollinators, seed predators, and small herbivores were weak in this system. C_LIO_LISynthesis. The results demonstrate that a full understanding of the effects of grazing on plant population dynamics requires that both direct and indirect effects are identified and quantified. Plant species vary considerably in their response to shifts in grazing regime. Our study sets an example for how the causes of such variation can be assessed, and thus providing a better understanding of the variable effects of herbivores on plant fitness, abundance and distribution. C_LI

ecology↗

bioRxiv2022

Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells

The interaction between a cell and its environment shapes fundamental intracellular processes such as cellular metabolism. In most cases growth rate is treated as a proximal metric for understanding the cellular metabolic status. However, changes in growth rate might not reflect metabolic variations in individuals responding to environmental fluctuations. Here we use single-cell microfluidics-microscopy combined with transcriptomics, proteomics and mathematical modelling to quantify the accumulation of glucose within Escherichia coli cells. In contrast to the current consensus, we reveal that environmental conditions which are comparatively unfavourable for growth, where both nutrients and salinity are depleted, increase glucose accumulation rates in individual bacteria and population subsets. We find that these changes in metabolic function are underpinned by variations at the translational and posttranslational level but not at the transcriptional level and are not dictated by changes in cell size. The metabolic response-characteristics identified greatly advance our fundamental understanding of the interactions between bacteria and their environment and have important ramifications when investigating cellular processes where salinity plays an important role.

microbiology↗

bioRxiv2020

The genetic basis of adaptation in phenology in an introduced population of Black Cottonwood (Populus trichocarpa, Torr. & Gray)

O_LIEntering and exiting winter dormancy presents important trade-offs between growth and survival at northern latitudes and many forest trees display local adaptation across latitude. Transfers of a species outside its native range introduce the species to novel combinations of environmental conditions potentially requiring different combinations of alleles to optimize growth. C_LIO_LIWe performed genome wide association analyses and a selection scan in a P. trichocarpa mapping population derived from crossings between clones collected across the native range and introduced into Sweden. GWAS analyses were performed using phenotypic data collected across two field seasons and in a controlled phytotron experiment. C_LIO_LIWe uncovered 629 putative candidate genes associated with spring and autumn phenology traits as well as with growth. Many regions harboring variation significantly associated with the initiation of leaf shed and leaf autumn coloring appeared to have been evolving under positive selection in the native environments of P. trichocarpa. C_LIO_LIA comparison between the candidate genes identified with results from earlier GWAS analyses performed in the native environment found a smaller overlap for spring phenology traits than for autumn phenology traits, aligning well with earlier observations that spring phenology transitions have a more complex genetic basis that autumn phenology transitions. C_LI

evolutionary biology↗

bioRxiv2020

Quantitative genetic architecture of adaptive phenology traits in the deciduous tree, Populus trichocarpa (Torr. & Gray).

In a warming climate, the ability to accurately predict and track shifting environmental conditions will be fundamental for plant survival. Environmental cues define the transitions between growth and dormancy as plants synchronise development with favourable environmental conditions, however these cues are predicted to change under future climate projections which may have profound impacts on tree survival and growth. Here, we use a quantitative genetic approach to estimate the genetic basis of spring and autumn phenology in Populus trichocarpa to determine this species capacity for climate adaptation. We measured bud burst, leaf coloration, and leaf senescence traits across two years (2017-2018) and combine these observations with measures of lifetime growth to determine how genetic correlations between phenology and growth may facilitate or constrain adaptation. Timing of transitions differed between years, although we found strong cross year genetic correlations in all traits, suggesting that genotypes respond in consistent ways to seasonal cues. Spring and autumn phenology were correlated with lifetime growth, where genotypes that burst leaves early and shed them late had the highest lifetime growth. We also identified substantial heritable variation in the timing of all phenological transitions (h2 = 0.5-0.8) and in lifetime growth (h2 = 0.8). The combination of abundant additive variation and favourable genetic correlations in phenology traits suggests that cultivated varieties of P. trichocarpa have the capability to create populations which may adapt their phenology to climatic changes without negative impacts on growth.

genetics↗

bioRxiv2018

Chronic, Low-Level Oral Exposure to Marine Toxin, Domoic Acid, Alters Whole Brain Morphometry in Nonhuman Primates

Domoic acid (DA) is an excitatory neurotoxin produced by marine algae and responsible for Amnesiac Shellfish Poisoning in humans. Current regulatory limits (~0.075-0.1 mg/kg/day) protect against acute toxicity, but recent studies suggest that the chronic consumption of DA below the regulatory limit may produce subtle neurotoxicity in adults, including decrements in memory. As DA-algal blooms are increasing in both severity and frequency, we sought to better understand the effects of chronic DA exposure on reproductive and neurobehavioral endpoints in a preclinical nonhuman primate model. To this end, we initiated a long-term study using adult, female Macaca fascicularis monkeys exposed to daily, oral doses of 0.075 or 0.15 mg/kg of DA for a range of 321-381, and 346-554 days, respectively. This time period included a pre-pregnancy, pregnancy, and postpartum period. Throughout these times, trained data collectors observed intentional tremors in some exposed animals during biweekly clinical examinations. The present study explores the basis of this neurobehavioral finding with in vivo imaging techniques, including diffusion tensor magnetic resonance imaging and spectroscopy. Diffusion tensor analyses revealed that, while DA exposed macaques did not significantly differ from controls, increases in DA-related tremors were negatively correlated with fractional anisotropy, a measure of structural integrity, in the internal capsule, fornix, pons, and corpus callosum. Brain concentrations of lactate, a neurochemical closely linked with astrocytes, were also weakly, but positively associated with tremors. These findings are the first documented results suggesting that chronic oral exposure to DA at concentrations near the current human regulatory limit are related to structural and chemical changes in the adult primate brain.

pharmacology and toxicology↗