Photosynthetic organisms frequently experience abiotic stress that restricts their growth and development. Under such circumstances, most absorbed solar energy cannot be used for CO2 fixation and can cause the photoproduction of reactive oxygen species (ROS) that can damage the photosynthetic reaction centers of photosystem I and II (PSI and PSII), resulting in a decline in primary productivity. This work describes a biological 'switch' in the green alga Chlamydomonas reinhardtii that reversibly restricts photosynthetic electron transport (PET) at the cytochrome b6f (Cyt b6f) complex when the capacity for accepting electrons downstream of PSI is severely limited. We specifically show this restriction in STARCHLESS6 (sta6) mutant cells, which cannot synthesize starch when they are limited for nitrogen (growth inhibition) and subjected to a dark-to-light transition. This restriction represents a form of photosynthetic control that causes diminished electron flow to PSI and thereby prevents PSI photodamage but does not appear to rely on a DeltapH. Furthermore, when electron flow is restricted, the plastid alternative oxidase (PTOX) becomes active, functioning as an electron valve that dissipates some excitation energy absorbed by PSII and allows the formation of a proton motive force (PMF) that would drive some ATP production [potentially sustaining PSII repair and non-photochemical quenching (NPQ)]. The restriction at the Cyt b6f complex can be gradually relieved with continued illumination. This study provides insights into how photosynthetic electron transport responds to a marked reduction in availability of downstream electron acceptors and the protective mechanisms involved.

Modulation of photoassimilate export from the chloroplast is essential for controlling the distribution of fixed carbon in the cell and maintaining optimum photosynthetic rates. In this study we identified chloroplast TRIOSE PHOSPHATE/PHOSPHATE TRANSLOCATOR2 (CreTPT2) and CreTPT3 in the green alga Chlamydomonas (Chlamydomonas reinhardtii), which exhibit similar substrate specificities but whose encoding genes are differentially expressed over the diurnal cycle. We focused mostly on CreTPT3 because of its high level of expression and the severe phenotype exhibited by tpt3 relative to tpt2 mutants. Null mutants for CreTPT3 had a pleiotropic phenotype that affected growth, photosynthetic activities, metabolite profiles, carbon partitioning, and organelle-specific accumulation of H2O2. These analyses demonstrated that CreTPT3 is a dominant conduit on the chloroplast envelope for the transport of photoassimilates. In addition, CreTPT3 can serve as a safety valve that moves excess reductant out of the chloroplast and appears to be essential for preventing cells from experiencing oxidative stress and accumulating reactive oxygen species, even under low/moderate light intensities. Finally, our studies indicate subfunctionalization of the CreTPT transporters and suggest that there are differences in managing the export of photoassimilates from the chloroplasts of Chlamydomonas and vascular plants.

Controlling the transition from a multicellular motile state to a sessile biofilm is an important eco-physiological decision for most prokaryotes, including cyanobacteria. Photosynthetic and bio geochemically significant cyanobacterium Synechocystis sp. PCC6803 (Syn6803) uses Type IV pili (TFP) for surface-associated motility and light-directed phototaxis. We report the identification of a novel Chaperone-Usher (CU) system in Syn6803 that regulate secretion of minor pilins as a means of stabilizing TFP morphology. These secreted minor-pilins aid in modifying TFP morphology to suit the adhesion state by forming cell to surface contacts when motility is not required. This morphotype is structurally distinct from TFP assembled during motile phase. We further demonstrate by examining mutants lacking either the CU system or the minor-pilins, which produce aberrant TFP, that are morphologically and functionally distinct from wild-type (WT). Thus, here we report that in Syn6803, CU system work independent of TFP biogenesis machinery unlike reported for other pathogenic bacterial systems and contributes to provide multifunctional plasticity to TFP. cAMP levels play an important role in controlling this switch. This phenotypic plasticity exhibited by the TFP, in response to cAMP levels would allow cells and cellular communities to adapt to rapidly fluctuating environments by dynamically transitioning between motile and sessile states.Significance of this workHow cyanobacterial communities cope with fluctuating or extreme environments is crucial in understanding their role in global carbon and nitrogen cycles. This work addresses the key question: how do cyanobacteria modulate external appendages, called Type IV pili, to effectively switch between motile and sessile biofilm states? We demonstrate that cells transition between forming strong cell-surface interactions indispensable for biofilm formation to forming cell-cell interactions that allow for coordinated movement crucial for social motility by functional/ structural modification of same TFP appendage. The second messenger, cAMP and a Chaperone-Usher secretion are indispensible to achieve these structural modifications of TFP and control the complex phenotypic transition. We have uncovered a strategy that Syn6803 has evolved to deal with molecular decision-making under uncertainty, which we call phenotypic plasticity. Here we demonstrate how a single motility appendage can be structurally modified to attain two antagonistic functions in order to meet the fluctuating environmental demands.

High-throughput RNA sequencing offers unprecedented opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million RNA viral contigs. Via analysis of the 330k novel RNA-dependent RNA polymerases (RdRP), this expansion corresponds to a five-fold increase of RNA virus diversity. Extended RdRP phylogeny supports monophyly of the five established phyla, reveals two putative new bacteriophage phyla and numerous putative novel classes and orders. The dramatically expanded Lenarviricota phylum, consisting of bacterial and related eukaryotic viruses, now accounts for a third of the RNA virome diversity. Identification of CRISPR spacer matches and bacteriolytic proteins suggests that subsets of picobirnaviruses and partitiviruses, previously associated with eukaryotes, infect prokaryotic hosts. Gene content analysis revealed multiple domains previously not found in RNA viruses and implicated in virus-host interactions. This vast collection of new RNA virus genomes provides insights into RNA virus evolution and should become a major resource for RNA virology.

Anthropogenic habitat destruction and climate change are altering the geographic distributions of plant communities. Although mapping vegetation changes is now possible at high resolution using remote sensing data and deep convolutional neural networks, these approaches have not been applied to model the distributions of thousands of plant species to understand spatial changes in biodiversity. To address the current lack of scalable and automatic tools to map plant species distributions at a fine-grained scale, we created a dataset of over half a million citizen science observations of 2,221 plant species across California paired with satellite images at 1 meter resolution from solely free and public sources. With this we trained a deep convolutional neural network, deepbiosphere , that predicts presences of plant species within 256 × 256 meter satellite images and outperforms common low-resolution species distribution models . We showcase the novelty and potential applications of this framework by visualizing high-resolution predictions of keystone species such as coastal redwoods, identifying spatio-temporal ecosystem changes from wildfires and restoration management, and detecting urban biodiversity hotspots. Deep neural networks continuously trained on public remote sensing imagery and citizen science observations could enable cheap, automatic, and scalable monitoring of biodiversity and detect rapid anthropogenic impacts on ecosystems.

To describe a living organism it is often said that "the whole is greater than the sum of its parts". In genetics, we may also think that the effect of multiple mutations on an organism is greater than their additive individual effect, a phenomenon called epistasis or multiplicity. Despite the last decades discovery that many disease- and fitness-related traits are polygenic, or controlled by many genetic variants, it is still debated whether the effects of individual genes combine additively or not. Here we develop a flexible likelihood framework for genome-wide associations to fit complex traits such as fitness under both additive and non-additive polygenic architectures. Analyses of simulated datasets under different true additive, multiplicative, or other epistatic models, confirm that our method can identify global non-additive selection. Applying the model to experimental datasets of wild type lines of Arabidopsis thaliana, Drosophila melanogaster, and Saccharomyces cerevisiae, we find that fitness is often best explained with non-additive polygenic models. Instead, a multiplicative polygenic model appears to better explain fitness in some experimental environments. The statistical models presented here have the potential to improve prediction of phenotypes, such as disease susceptibility, over the standard methods for calculating polygenic scores which assume additivity.

The plant kingdom contains a stunning array of complex morphologies easily observed above ground, but largely unexplored below-ground. Understanding the magnitude of diversity in root distribution within the soil, termed root system architecture (RSA), is fundamental to determining how this trait contributes to species adaptation in local environments. Roots are the interface between the soil environment and the shoot system and therefore play a key role in anchorage, resource uptake, and stress resilience. Previously, we presented the GLO-Roots (Growth and Luminescence Observatory for Roots) system to study the RSA of soil-grown Arabidopsis thaliana plants from germination to maturity (Rellan-Alvarez et al. 2015). In this study, we present the automation of GLO-Roots using robotics and the development of image analysis pipelines in order to examine the natural variation of RSA in Arabidopsis over time. This dataset describes the developmental dynamics of 93 accessions and reveals highly complex and polygenic RSA traits that show significant correlation with climate variables.

The change in allele frequencies within a population over time represents a fundamental process of evolution. By monitoring allele frequencies, we can analyze the effects of natural selection and genetic drift on populations. To efficiently track time-resolved genetic change, large experimental or wild populations can be sequenced as pools of individuals sampled over time using high-throughput genome sequencing (called the Evolve & Resequence approach, E&R). Here, we present a set of experiments using hundreds of natural genotypes of the model plant Arabidopsis thaliana to showcase the power of this approach to study rapid evolution at large scale. First, we validate that sequencing DNA directly extracted from pools of flowers from multiple plants -- organs that are relatively consistent in size and easy to sample -- produces comparable results to other, more expensive state-of-the-art approaches such as sampling and sequencing of individual leaves. Sequencing pools of flowers from 25-50 individuals at [~]40X coverage recovers genome-wide frequencies in diverse populations with accuracy r > 0.95. Secondly, to enable analyses of evolutionary adaptation using E&R approaches of plants in highly replicated environments, we provide open source tools that streamline sequencing data curation and calculate various population genetic statistics two orders of magnitude faster than current software. To directly demonstrate the usefulness of our method, we conducted a two-year outdoor evolution experiment with A. thaliana to show signals of rapid evolution in multiple genomic regions. We demonstrate how these laboratory and computational Pool-seq-based methods can be scaled to study hundreds of populations across many climates.

The quantitative resistance gene ACCELERATED CELL DEATH 6 (ACD6), which encodes a transmembrane protein with intracellular ankyrin repeats, has been implicated in a trade-off between growth and defense among wild strains of Arabidopsis thaliana. Naturally hyperactive alleles of the ACD6-Est-1 type can lead to spontaneous activation of immune responses, although the extent of visible hyperimmunity in strains with this allele varies substantially. We have identified a natural suppressor locus, MODULATOR OF HYPERACTIVE ACD6 1 (MHA1), which codes for a small protein of ~7 kDa that attenuates activity of the ACD6-Est-1 allele. MHA1 and its paralog MHA1-LIKE (MHAL) differentially interact with specific ACD6 variants, and both MHA1 and MHAL peptides can bind to the ACD6 ankyrin repeats. MHAL also enhances accumulation of an ACD6 complex, thereby increasing activity of the ACD6 standard allele. The ACD6 ankyrin repeats are similar to those of transient receptor potential (TRP) ion channels, and several lines of evidence support that increased ACD6 activity is linked to enhanced calcium signaling. Our work highlights how the study of natural variation reveals new aspects of plant immunity.

How trade-offs between traits constrain adaptation to contrasted environments is critical to understand the distribution range of a given species. In Arabidopsis thaliana, genetic analyses recently revealed that a group of genotypes successfully recolonized Europe from its center after the last glaciation, outcompeting older lineages and leaving them only at the distribution margins, where environmental conditions are more stressing. However, whether trade-offs between traits related to dispersal, competition, and stress tolerance explain the success and persistence of different lineages across the species geographic range remains an open question. Here, we compared the genetic and phenotypic differentiation between 72 ecotypes originating from three geographical groups in Europe (North, South and Center). We measured key traits related to fecundity, dispersal ability, competition tolerance, and stress tolerance, and used genomic data to infer the effect of selection on these traits. We showed that a trade-off between plant fecundity and seed mass constrains the diversification of A. thaliana in Europe. In particular, the success of the cosmopolitan genotypes that recolonized Europe can be explained by their higher dispersal ability at the expense of their competitive ability and stress tolerance. Inversely, peripheral ecotypes exhibited the opposite trait syndrome: high competition and stress tolerance but low dispersal ability. Moreover, peripheral genotypes tend to differentiate from central ones at genes involved in dispersal and competitive traits such as seed mass. Combining ecological and genomic approaches, our study demonstrated the role of key ecological trade-offs as evolutionary drivers of the distribution of plant populations along a geographic gradient.