Within-host genetic diversity of SARS-CoV-2 in the context of large-scale hospital-associated genomic surveillance.

The COVID-19 pandemic has resulted in extensive surveillance of the genomic diversity of SARS-CoV-2. Sequencing data generated as part of these efforts can also capture the diversity of the SARS-CoV-2 virus populations replicating within infected individuals. To assess this within-host diversity of SARS-CoV-2 we quantified low frequency (minor) variants from deep sequence data of thousands of clinical samples collected by a large urban hospital system over the course of a year. Using a robust analytical pipeline to control for technical artefacts, we observe that at comparable viral loads, specimens from patients hospitalized due to COVID-19 had a greater number of minor variants than samples from outpatients. Since individuals with highly diverse viral populations could be disproportionate drivers of new viral lineages in the patient population, these results suggest that transmission control should pay special attention to patients with severe or protracted disease to prevent the spread of novel variants.

Ecological mechanism of climate-mediated selection in a rapidly evolving invasive species.

Recurring seasonal changes can lead to the evolution of phenological cues. For example, many arthropods undergo photoperiodic diapause, a programmed developmental arrest induced by short autumnal day length. The selective mechanisms that determine the timing of autumnal diapause initiation have not been empirically identified. We quantified latitudinal clines in genetically determined diapause timing of an invasive mosquito, Aedes albopictus, on two continents. We show that variation in diapause timing within and between continents is explained by a novel application of a growing degree day (GDD) model that delineates a location-specific deadline after which it is not possible to complete an additional full life cycle. GDD models are widely used to predict spring phenology by modelling growth and development as physiological responses to ambient temperatures. Our results show that the energy accumulation dynamics represented by GDD models have also led to the evolution of an anticipatory life-history cue in autumn.

Animal-Microbe Interactions in the Context of Diapause.

Dormancy and diapause are key adaptations in many organisms, enabling survival of temporarily or seasonally unsuitable environmental conditions. In this review, we examine how our understanding of programmed developmental and metabolic arrest during diapause intersects with the increasing body of knowledge about animal co-development and co-evolution with microorganisms. Host-microbe interactions are increasingly understood to affect a number of metabolic, physiological, developmental, and behavioral traits and to mediate adaptations to various environments. Therefore, it is timely to consider how microbial factors might affect the expression and evolution of diapause in a changing world. We examine how a range of host-microbe interactions, from pathogenic to mutualistic, may have an impact on diapause phenotypes. Conversely, we examine how the discontinuities that diapause introduces into animal host generations can affect the ecology of microbial communities and the evolution of host-microbe interactions. We discuss these issues as they relate to physiology, evolution of development, local adaptation, disease ecology, and environmental change. Finally, we outline research questions that bridge the historically distinct fields of seasonal ecology and host-microbe interactions.

Environmental Sources of Bacteria and Genetic Variation in Behavior Influence Host-Associated Microbiota.

In many organisms, host-associated microbial communities are acquired horizontally after birth. This process is believed to be shaped by a combination of environmental and host genetic factors. We examined whether genetic variation in animal behavior could affect the composition of the animal's microbiota in different environments. The freshwater crustacean Daphnia magna is primarily planktonic but exhibits variation in the degree to which it browses in benthic sediments. We performed an experiment with clonal lines of D. magna showing different levels of sediment-browsing intensity exposed to either bacteria-rich or bacteria-poor sediment or whose access to sediments was prevented. We found that the bacterial composition of the environment and genotype-specific browsing intensity together influence the composition of the Daphnia-associated bacterial community. Exposure to more diverse bacteria did not lead to a more diverse microbiome, but greater abundances of environment-specific bacteria were found associated with host genotypes that exhibited greater browsing behavior. Our results indicate that, although there is a great deal of variation between individuals, behavior can mediate genotype-by-environment interaction effects on microbiome composition.IMPORTANCE An animal's behavior can affect its risk of infection, but it is not well understood how behavior affects microbiome composition. The aquatic crustacean Daphnia exhibits genetic variation in the extent to which it browses in the sediment at the bottoms of ponds. We show that this behavior affects the Daphnia microbiome, indicating that genetic variation among individuals may affect microbiome composition and the movement of bacteria in different environments.

The microbiota of diapause: How host-microbe associations are formed after dormancy in an aquatic crustacean.

A critical question in symbiosis research is where and how organisms obtain beneficial microbial symbionts in different ecological contexts. Microbiota of juveniles are often derived directly from their mother or from the immediate environment. The origin of beneficial symbionts, however, is less obvious in organisms with diapause and dispersal stages, such as plants with dormant seeds and animals in ephemeral or strongly seasonal habitats. In these cases, parents and offspring are separated in time and space, which may affect opportunities for both vertical and horizontal transmission of symbionts. The planktonic crustacean Daphnia produces long-lasting resting eggs to endure winter freezing and summer droughts and requires microbiota for growth and reproduction. It is unknown how hatchlings from resting stages form associations with microbial consorts after diapause. Using natural samples of D. magna resting eggs after several years of storage, we show that the total bacterial community derived from both the exterior and interior of the eggs' ephippial cases is sufficiently beneficial to ensure normal Daphnia functioning in otherwise bacteria-free conditions. We do not find direct evidence that the required bacteria are of maternal origin, though sequencing reveals that the resting stage is accompanied by bacterial taxa previously found in association with adult animals. These findings suggest that although Daphnia are strongly dependent on environmental bacteria for normal functioning, host-bacteria associations are somewhat general and availability of specific bacteria is not a strong constraint on host ecology. Nevertheless, animals and microbes may be ecologically linked through co-dispersal.

Presence of microbiota reverses the relative performance of Daphnia on two experimental diets.

The outcomes of host-symbiont interactions may differ according to environmental context, and symbioses may enable host adaptation to diverse environments. We find that the effects of two different experimental diets, algae and yeast, on the water flea Daphnia magna depend on whether the animals possess microbiota, suggesting that the presence of microbiota determines which diet is superior. Our study hints at both diet-dependent and diet-independent effects of microbiota on Daphnia fitness.

Impaired phagocytosis in fragile X.

Defects in phagocytosis underlie both neurological and immunological symptoms in a fly model of fragile X syndrome.

Stress signals in plants.

Selective autophagy mediates the cross-talk between plant growth and stress signaling pathways.

Blocking a signal to host cell histones.

A plant pathogen suppresses the host immune response by preventing histone acetylation.

NLS protects DNA damage protein.

A single motif targets a protein to the nucleus and directs its deubiquitylation, promoting high-fidelity DNA damage repair.

An insulin-like message from mother.

Nematodes experiencing osmotic stress signal to the germ-line to prepare their offspring.

Autophagy and vitamin D.

Vitamin D receptor represses basal autophagy in breast tissue, which is derepressed by vitamin D, slowing cancer progression.

UV radiation induces a gene's dual functionality.

A protein and noncoding RNA encoded by the same gene have opposing roles in the response to UV radiation-induced damage.

Polyglutamine makes the switch.

In worms, a regulator of noncoding RNA directly catalyzes formation of toxic protein aggregates in the presence of polyglutamine.

Ferroptosis-like cell death in plants.

Heat stress induces a form of cell death in plants that is morphologically and biochemically similar to ferroptosis in animal cells.

When silencing mRNA, position matters.

The mechanism of posttranscriptional silencing by an RNA-binding protein depends on the position of the protein-binding sequence in the mRNA.

Microbiome-dependent recombination shapes the host antibody repertoire.

Secreted IgD concentration depends on the presence of microbiota.

Sources of variation: Animal microbiota.

The diverse effects of microbiota on animal physiology contribute to experimental variability.

Guanidine throws the riboswitch.

A bacterial riboswitch responds to endogenously produced guanidine.

Recovering rRNA processing after heat shock.

NF-κB repressing factor controls localization and activation of an rRNA processing protein in heat stress response.