This paper illustrates the potential for seasonal prediction of wind and solar energy resources through a case study in the Yangtze River estuary. Sea surface temperature and geopotential height-based climate predictors, each with high correlation to ensuing seasonal wind speed and solar radiation at the Baoshan weather observing station, are identified and used to build statistical models to predict seasonal wind speed and solar radiation. Leave-one-out-cross-validation is applied to verify the predictive skill of the best performing candidate model for each season. We find that predictive skill is highest for both wind speed and solar radiation during winter, and lowest during summer. Specifically, we find the most skill when using climate information from the July-September season to predict wind speed or solar radiation during the subsequent November-January season. The ability to predict wind and solar energy availability in the upcoming season can help energy system planners and operators anticipate seasonal surpluses or shortfalls and take precautionary actions.

Estuaries at the global scale are significant but highly uncertain sources of atmospheric nitrous oxide (N2O), which is an intense greenhouse gas and ozone depletion agent. As the largest estuary in the United States, the Chesapeake Bay is suggested to be a spatially and temporally variable source and sink of N2O. However, limited observations of N2O cycling preclude us from estimating and predicting its net N2O flux. To improve our mechanistic understanding of the processes that control the N2O flux at the point of production, we applied multiple N-15 tracers (NH4+15$$ {}<^>{15}{\mathrm{NH}}_4<^>{+} $$, N-15-urea, NO2-15,$$ {}<^>{15}{\mathrm{NO}}_2<^>{-}, $$ and NO3-15$$ {}<^>{15}{\mathrm{NO}}_3<^>{-} $$) to separately track N2O production from nitrification and denitrification under in situ and manipulated O-2 concentrations in the Chesapeake Bay. Nitrification was the major N2O production pathway in oxic waters (up to 7.5 nmol N2O L-1 d(-1)). In contrast, denitrification dominated N2O production from hypoxic/anoxic waters (up to 20 nmol N2O L-1 d(-1)). N2O production from urea was observed for the first time in estuarine waters. The contribution from urea was small, but interestingly, showed a depth pattern distinct from other N2O precursors. Experimentally lowering the O-2 concentration substantially enhanced N2O production. Therefore, the expansion of hypoxic and anoxic zones in the Chesapeake Bay under climate change as suggested by some climate models may favor the production of N2O, potentially providing positive feedback on warming. Overall, our study provides mechanistic constraints on N2O dynamics that could benefit modeling studies to better estimate the N2O flux in the Chesapeake Bay and other coastal environments.

Estuaries emit a large but highly uncertain amount of Nitrous oxide (N2O) into the atmosphere. To better understand N2O cycling processes in estuaries, we provide the first direct observations of N2O consumption in the seasonally anoxic Chesapeake Bay, the largest estuary in the United States. N2O consumption rates in anoxic waters reached up to 3.3 nmol L-1 d(-1) but were generally undetectable in oxygenated waters. However, N2O consumption rates were substantially enhanced when the oxygen concentration was experimentally decreased in initially oxygenated samples, indicating the potential of N2O consumption in oxygenated environments, for example, surface waters. These potential N2O consumption rates followed Michaelis-Menten kinetics as a function of increasing N2O substrate concentration. N2O-consuming microbes that predominantly contained the clade II nitrous oxide reductase gene were detected throughout the water column. These new observations of environmental controls on N2O consumption will benefit the modeling of N2O cycling and help to constrain the estuarine N2O flux.

The Plant Ontology (PO; ext-link-type="uri" xlink:href="http://www.plantontology.org/" xmlns:xlink="http://www.w3.org/1999/xlink">http://www.plantontology.org/) is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary ('ontology') of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded to include all green plants. The PO was the first multispecies anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. As of Release #18 (July 2012), there are about 2.2 million annotations linking PO terms to > 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and quantitative trait loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs.

The disjunct temperate rainforests of the Pacific Northwest of North America (PNW) are characterized by late-successional dominant tree species Thuja plicata (western redcedar) and Tsuga heterophylia (western hemlock). The demographic histories of these species, along with the PNW rainforest ecosystem in its entirety, have been heavily impacted by geological and climatic changes the PNW has experienced over the last 5 million years, including mountain orogeny and repeated Pleistocene glaciations. These environmental events have ultimately shaped the history of these species, with inland populations potentially being extirpated during the Pleistocene glaciations. Here, we collect genomic data for both species across their ranges to test multiple demographic models, each reflecting a different phylogeographical hypothesis on how the ecosystem-dominating species may have responded to dramatic climatic change. Our results indicate that inland and coastal populations in both species diverged similar to 2.5 million years ago in the early Pleistocene and experienced decreases in population size during glacial cycles, with subsequent population expansion. Importantly, we found evidence for gene flow between coastal and inland populations during the mid-Holocene. It is likely that intermittent migration in these species during this time has prevented allopatric speciation via genetic drift alone. In conclusion, our results from combining genomic data and demographic inference procedures establish that populations of the ecosystem dominants Thuja plicata and Tsuga hetero-phyla persisted in refugia located in both the coastal and inland regions of the PNW throughout the Pleistocene, with populations expanding and contracting in response to glacial cycles with occasional gene flow.

We sought to assess effects of fragmentation and quantify the contribution of ecological processes to community assembly by measuring species richness, phylogenetic, and phenotypic diversity of species found in local and regional plant communities. Specifically, our fragmented system is Craters of the Moon National Monument and Preserve, Idaho, USA. CRMO is characterized by vegetated islands, kipukas, that are isolated in a matrix of lava. We used floristic surveys of vascular plants in 19 kipukas to create a local species list to compare traditional dispersion metrics, mean pairwise distance, and mean nearest taxon distance (MPD and MNTD), to a regional species list with phenotypic and phylogenetic data. We combined phylogenetic and functional trait data in a novel machine-learning model selection approach, Community Assembly Model Inference (CAMI), to infer probability associated with different models of community assembly given the data. Finally, we used linear regression to explore whether the geography of kipukas explained estimated support for community assembly models. Using traditional metrics of MPD and MNTD neutral processes received the most support when comparing kipuka species to regional species. Individually no kipukas showed significant support for overdispersion. Rather, five kipukas showed significant support for phylogenetic clustering using MPD and two kipukas using MNTD. Using CAMI, we inferred neutral and filtering models structured the kipuka plant community for our trait of interest. Finally, we found as species richness in kipukas increases, model support for competition decreases and lower elevation kipukas show more support for habitat filtering models. While traditional phylogenetic community approaches suggest neutral assembly dynamics, recently developed approaches utilizing machine learning and model choice revealed joint influences of assembly processes to form the kipuka plant communities. Understanding ecological processes at play in naturally fragmented systems will aid in guiding our understanding of how fragmentation impacts future changes in landscapes.

Photosynthetic organisms are frequently exposed to excess light conditions and hence to photo-oxidative stress. To counteract photo-oxidative damage, land plants and most algae make use of non- photochemical quenching (NPQ) of excess light energy, in particular the rapidly inducible and relaxing qE-mechanism. In vascular plants, the constitutively active PsbS protein is the key regulator of qE. In the green algae C. reinhardtii, however, qE activation is only possible after initial high-light (HL) acclimation for several hours and requires the synthesis of LHCSR proteins which act as qE regulators. The precise function of PsbS, which is transiently expressed during HL acclimation in C. reinhardtii, is still unclear. Here, we investigated the impact of different PsbS amounts on HL acclimation characteristics of C. reinhardtii cells. We demonstrate that lower PsbS amounts negatively affect HL acclimation at different levels, including NPQ capacity, electron transport characteristics, antenna organization and morphological changes, resulting in an overall increased HL sensitivity and lower vitality of cells. Contrarily, higher PsbS amounts do not result in a higher NPQ capacity, but nevertheless provide higher fitness and tolerance towards HL stress. Strikingly, constitutively expressed PsbS protein was found to be degraded during HL acclimation. We propose that PsbS is transiently required during HL acclimation for the reorganization of thylakoid membranes and/or antenna proteins along with the activation of NPQ and adjustment of electron transfer characteristics, and that degradation of PsbS is essential in the fully HL acclimated state.

The circadian clock regulates plant tissue hydraulics to synchronize water supply with environmental cycles and thereby optimize growth. The circadian fluctuations in aquaporin transcript abundance suggest that aquaporin water channels play a role in these processes. Here, we show that hydraulic conductivity (K-ros) of Arabidopsis (Arabidopsis thaliana) rosettes displays a genuine circadian rhythmicity with a peak around midday. Combined immunological and proteomic approaches revealed that phosphorylation at two C-terminal sites (Ser280, Ser283) of PLASMA MEMBRANE INTRINSIC PROTEIN 2;1 (AtPIP2;1), a major plasma membrane aquaporin in rosettes, shows circadian oscillations and is correlated with K-ros. Transgenic expression of phosphodeficient and phosphomimetic forms of this aquaporin indicated that AtPIP2;1 phosphorylation is necessary but not sufficient for K-ros regulation. We investigated the supporting role of 14-3-3 proteins, which are known to interact with and regulate phosphorylated proteins. Individual knockout plants for five 14-3-3 protein isoforms expressed in rosettes lacked circadian activation of K-ros. Two of these [GRF4 (14-3-3Phi); GRF10 (14-3-3Epsilon)] showed direct interactions with AtPIP2;1 in the plant and upon coexpression in Xenopus laevis oocytes and activated AtPIP2;1, preferentially when the latter was phosphorylated at its two C-terminal sites. We propose that this regulatory mechanism assists in the activation of phosphorylated AtPIP2;1 during circadian regulation of K-ros.

To promote photomorphogenesis, including plastid development and metabolism, the phytochrome (phy) and the cryptochrome (cry) photoreceptors orchestrate genome-wide changes in gene expression in response to Red (R)- and Blue (B)-light cues. While phys and crys have a clear role in modulating photosynthesis, their role in the coordination of the nuclear genome and the plastome, essential for functional chloroplasts, remains underexplored. Using publicly available genome datasets for WT andphyABCDEorcry1cry2Arabidopsis seedlings, grown, respectively, under R- or B-light, we bioinformatically analyzed the influence of light inputs and photoreceptors in the control of nuclear genes with a function in the chloroplast, and evaluated the role of phyB in the modulation of plastome-encoded genes. We show gene co-induction by R-phys and B-crys for genes with a chloroplastic function, and also apparent photoreceptor-driven preferential responses. Evidence from phyB in Arabidopsis together with published evidence from CRY2 in tomato also supports the participation of both photoreceptor families in the global modulation of the plastome genes. To begin addressing how these light-sensors orchestrate changes in an organellar genome, we evaluated their effect over genes with potential functions in plastid gene-expression regulation based on their TAIR annotation. Results indicate that both crys and phys modulate 'plastome-regulatory genes' with enrichment in the contribution of crys to all processes and of phys to post-transcription and transcription. Furthermore, we identified a new role for HY5 as a relevant light-signaling component in photoreceptor-based anterograde signaling leading to plastome gene regulation.

Plant morphogenesis requires differential and often asymmetric growth. A key role in controlling anisotropic expansion of individual cells is played by the cortical microtubule array. Although highly organized, the array can nevertheless rapidly change in response to internal and external cues. Experiments have identified the microtubule-severing enzyme katanin as a central player in controlling the organizational state of the array. Katanin action is required both for normal alignment and the adaptation of array orientation to mechanical, environmental, and developmental stimuli. How katanin fulfills its controlling role, however, remains poorly understood. On the one hand, from a theoretical perspective, array ordering depends on the "weeding out" of discordant microtubules through frequent catastrophe-inducing collisions among microtubules. Severing would reduce average microtubule length and lifetime, and consequently weaken the driving force for alignment. On the other hand, it has been suggested that selective severing at microtubule crossovers could facilitate the removal of discordant microtubules. Here we show that this apparent conflict can be resolved by systematically dissecting the role of all of the relevant interactions in silico. This procedure allows the identification of the sufficient and necessary conditions for katanin to promote array alignment, stresses the critical importance of the experimentally observed selective severing of the "crossing" microtubule at crossovers, and reveals a hitherto not appreciated role for microtubule bundling. We show how understanding the underlying mechanism can aid with interpreting experimental results and designing future experiments.