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Abstract Arabidopsis root is a classic model system in plant cell and molecular biology. The sensitivity of plant roots to local environmental perturbation challenges data reproducibility and incentivizes further optimization of imaging and phenotyping tools. Here we present RoPod, an easy-to-use toolkit for low-stress live time-lapse imaging of Arabidopsis roots. RoPod comprises a dedicated protocol for plant cultivation and a customizable 3D-printed vessel with integrated microscopy-grade glass that serves simultaneously as a growth and imaging chamber. RoPod reduces impact of sample handling, preserves live samples for prolonged imaging sessions, and facilitates application of treatments during image acquisition. We describe a protocol for RoPods fabrication and provide illustrative application pipelines for monitoring root hair growth and autophagic activity. Furthermore, we showcase how the use of RoPods advanced our understanding of plant autophagy, a major catabolic pathway and a key player in plant fitness. Specifically, we obtained fine time resolution for autophagy response to commonly used chemical modulators of the pathway and revealed previously overlooked cell type-specific changes in the autophagy response. These results will aid a deeper understanding of the physiological role of autophagy and provide valuable guidelines for choosing sampling time during end-point assays currently employed in plant autophagy research.

Summary: The endomembrane system consists of various membrane‐bound organelles including the endoplasmic reticulum (ER), Golgi apparatus, trans‐Golgi network (TGN), endosomes, and the lysosome/vacuole. Membrane trafficking between distinct compartments is mainly achieved by vesicular transport. As the endomembrane compartments and the machineries regulating the membrane trafficking are largely conserved across all eukaryotes, our current knowledge on organelle biogenesis and endomembrane trafficking in plants has mainly been shaped by corresponding studies in mammals and yeast. However, unique perspectives have emerged from plant cell biology research through the characterization of plant‐specific regulators as well as the development and application of the state‐of‐the‐art microscopical techniques. In this review, we summarize our current knowledge on the plant endomembrane system, with a focus on several distinct pathways: ER‐to‐Golgi transport, protein sorting at the TGN, endosomal sorting on multivesicular bodies, vacuolar trafficking/vacuole biogenesis, and the autophagy pathway. We also give an update on advanced imaging techniques for the plant cell biology research. [ABSTRACT FROM AUTHOR]

Summary: Phosphatidylinositol 4‐phosphate (PI4P) is an anionic phospholipid which has been described as a master regulator of the Golgi apparatus in eukaryotic cells. However, recent evidence suggests that PI4P mainly accumulates at the plasma membrane in all plant cells analyzed so far. In addition, many functions that are typically attributed to phosphatidylinositol 4,5‐bisphosphate (PI(4,5)P2) in animal and yeast cells are also supported by PI4P in plants. For example, PI4P is the key anionic lipid that powers the strong electrostatic properties of the plasma membrane. Phosphatidylinositol 4‐phosphate is also required for the establishment of stable membrane contacts between the endoplasmic reticulum and the plasma membrane, for exocytosis and to support signaling pathways. Thus, we propose that PI4P has a prominent role in specifying the identity of the plasma membrane and in supporting some of its key functions and should be considered a hallmark lipid of this compartment. [ABSTRACT FROM AUTHOR]

We have recently described 'Cytobacts' as abundant intracellular endophytic bacteria inhabiting live plant cells based on the observations with callus and cell suspension cultures of grapevine and other plant species with the origin ascribable to field explants. In this study, we investigated the prevalence of such cytoplasmic bacterial associations in field plants across different taxa, their cultivability, and the extent of taxonomic diversity and explored the possibility of their embryo-mediated vertical transmission. Over 100 genera of field plants were surveyed for 'Cytobacts' through bright-field live-cell imaging as per our previous experience using fresh tissue sections from surface-sterilized shoot-tissues with parallel cultivation-based assessments. This revealed widespread cellular bacterial associations visualized as copious motile micro-particles in the cytoplasm with no or sparse colony forming units (CFU) from the tissue-homogenates indicating their general non-cultivability. Based on the ease of detection and the abundance of 'Cytobacts' in fresh tissue sections, the surveyed plants were empirically classified into three groups: (i) motile bacteria detected instantly in most cells; (ii) motility not so widely observed, but seen in some cells; and (iii) only occasional motile units observed, but abundant non-motile bacterial cells present. Microscopy versus 16S-rRNA V3–V4 amplicon profiling on shoot-tip tissues of four representative plants—tomato, watermelon, periwinkle, and maize—showed high bacterial abundance and taxonomic diversity (11–15 phyla) with the dominance of Proteobacteria followed by Firmicutes/Actinobacteria, and several other phyla in minor shares. The low CFU/absence of bacterial CFU from the tissue homogenates on standard bacteriological media endorsed their cultivation-recalcitrance. Intracellular bacterial colonization implied that the associated organisms are able to transmit vertically to the next generation through the seed-embryos. Microscopy and 16S-rRNA V3–V4 amplicon/metagenome profiling of mature embryos excised from fresh watermelon seeds revealed heavy embryo colonization by diverse bacteria with sparse or no CFU. Observations with grapevine fresh fruit-derived seeds and seed-embryos endorsed the vertical transmission by diverse cultivation-recalcitrant endophytic bacteria (CREB). By and large, Proteobacteria formed the major phylum in fresh seed-embryos with varying shares of diverse phyla. Thus, we document 'Cytobacts' comprising diverse and vertically transmissible CREBs as a ubiquitous phenomenon in vascular plants. [ABSTRACT FROM AUTHOR]

We have recently described ‘Cytobacts’ as abundant intracellular endophytic bacteria inhabiting live plant cells based on the observations with callus and cell suspension cultures of grapevine and other plant species with the origin ascribable to field explants. In this study, we investigated the prevalence of such cytoplasmic bacterial associations in field plants across different taxa, their cultivability, and the extent of taxonomic diversity and explored the possibility of their embryo-mediated vertical transmission. Over 100 genera of field plants were surveyed for ‘Cytobacts’ through bright-field live-cell imaging as per our previous experience using fresh tissue sections from surface-sterilized shoot-tissues with parallel cultivation-based assessments. This revealed widespread cellular bacterial associations visualized as copious motile micro-particles in the cytoplasm with no or sparse colony forming units (CFU) from the tissue-homogenates indicating their general non-cultivability. Based on the ease of detection and the abundance of ‘Cytobacts’ in fresh tissue sections, the surveyed plants were empirically classified into three groups: (i) motile bacteria detected instantly in most cells; (ii) motility not so widely observed, but seen in some cells; and (iii) only occasional motile units observed, but abundant non-motile bacterial cells present. Microscopy versus 16S-rRNA V3–V4 amplicon profiling on shoot-tip tissues of four representative plants—tomato, watermelon, periwinkle, and maize—showed high bacterial abundance and taxonomic diversity (11–15 phyla) with the dominance of Proteobacteria followed by Firmicutes/Actinobacteria, and several other phyla in minor shares. The low CFU/absence of bacterial CFU from the tissue homogenates on standard bacteriological media endorsed their cultivation-recalcitrance. Intracellular bacterial colonization implied that the associated organisms are able to transmit vertically to the next generation through the seed-embryos. Microscopy and 16S-rRNA V3–V4 amplicon/metagenome profiling of mature embryos excised from fresh watermelon seeds revealed heavy embryo colonization by diverse bacteria with sparse or no CFU. Observations with grapevine fresh fruit-derived seeds and seed-embryos endorsed the vertical transmission by diverse cultivation-recalcitrant endophytic bacteria (CREB). By and large, Proteobacteria formed the major phylum in fresh seed-embryos with varying shares of diverse phyla. Thus, we document ‘Cytobacts’ comprising diverse and vertically transmissible CREBs as a ubiquitous phenomenon in vascular plants.

Stromules, or "stroma-filled tubules", are narrow, tubular extensions from the surface of the chloroplast that are universally observed in plant cells but whose functions remain mysterious. Alongside growing attention on the role of chloroplasts in coordinating plant responses to stress, interest in stromules and their relationship to chloroplast signaling dynamics has increased in recent years, aided by advances in fluorescence microscopy and protein fluorophores that allow for rapid, accurate visualization of stromule dynamics. Here, we provide detailed protocols to assay stromule frequency in the epidermal chloroplasts of Nicotiana benthamiana, an excellent model system for investigating chloroplast stromule biology. We also provide methods for visualizing chloroplast stromules in vitro by extracting chloroplasts from leaves. Finally, we outline sampling strategies and statistical approaches to analyze differences in stromule frequencies in response to stimuli, such as environmental stress, chemical treatments, or gene silencing. Researchers can use these protocols as a starting point to develop new methods for innovative experiments to explore how and why chloroplasts make stromules.

Organelles of the plant cell cooperate to synthesize and secrete a strong yet flexible polysaccharide-based extracellular matrix: the cell wall. Cell wall composition varies among plant species, across cell types within a plant, within different regions of a single cell wall, and in response to intrinsic or extrinsic signals. This diversity in cell wall makeup is underpinned by common cellular mechanisms for cell wall production. Cellulose synthase complexes function at the plasma membrane and deposit their product into the cell wall. Matrix polysaccharides are synthesized by a multitude of glycosyltransferases in hundreds of mobile Golgi stacks, and an extensive set of vesicle trafficking proteins govern secretion to the cell wall. In this review, we discuss the different subcellular locations at which cell wall synthesis occurs, review the molecular mechanisms that control cell wall biosynthesis, and examine how these are regulated in response to different perturbations to maintain cell wall homeostasis. Organelles of the plant cell cooperate to synthesize and secrete a strong yet flexible cell wall. Hoffmann et al. describe the subcellular locations at which cell wall synthesis occurs and review the mechanisms underlying biosynthesis. They also examine how synthesis is regulated in response to different perturbations to maintain cell wall homeostasis. [ABSTRACT FROM AUTHOR]

Summary: Chris Hawes had a lively fascination for the immensely complex organisation of the endomembrane system, including the process of endocytosis. This is the method by which eukaryotic cells internalise membrane proteins, lipids, carbohydrates, and cell wall enzymes from the cell surface through membrane bound vesicles. Endocytosis occurs progressively, starting with early membrane deformation, scission, and finally the release of the vesicle into the cytoplasm. Next to secretion, endocytosis allows the cell to control the proteome composition of its inner and outer surface membrane and as such, its communication with the outside world. Whereas endocytosis was initially considered theoretically impossible in plants due to their high turgor pressure, it is now established as essential for plant life. Furthermore, endocytosis remains a highly active field of research, both in yeast, animal, and plant model systems. Over the past three decades, the tools and techniques used to visualise, quantify, and characterise endocytosis have resulted in an increasingly higher spatiotemporal understanding of this process. Here we provide a brief history of plant endocytosis research from the time when Chris Hawes was investigating the process, to the current state‐of‐the‐art in the field. We will end this chapter with a discussion on some promising future developments for plant endocytosis research. Lay Description: Endocytosis is a key process whereby eukaryotic cells can selectively take up membrane proteins, extracellular material and lipids. As this process controls the abundance and protein composition of the plasma membrane, it also controls the communication of the cell with the outside world. Whereas endocytosis was initially considered theoretically impossible in plants due to their high turgor pressure, it is now established as essential for plant life. Today, endocytosis remains a highly active field of research, both in yeast, animal, and plant model systems. Endocytosis was one of the favourite research topics of Chris Hawes, which is why this mini‐review is part of the Festschrift issue in his honour. We provide here a brief history of plant endocytosis research from the time when Chris Hawes was investigating the process, to the current state‐of‐the‐art in the field. Over the past three decades, the tools and techniques that were developed to visualise, quantify, and characterise endocytosis have allowed to achieve an increasingly higher spatiotemporal understanding of this process. We end this chapter with a discussion on some promising future developments for plant endocytosis research. [ABSTRACT FROM AUTHOR]

Regime shifts involving critical transitions are a type of rapid ecological change that are difficult to predict, but may be preceded by decreases in resilience. Time series statistics like lag-1 autocorrelation may be useful for anticipating resilience declines; however, more study is needed to determine whether the dynamics of autocorrelation depend on the resolution of the time series being analyzed, i.e., whether they are time-scale dependent. Here, we examined timeseries simulated from a lake eutrophication model and gathered from field measurements. The field study involved collecting high frequency chlorophyll fluorescence data from an unmanipulated reference lake and a second lake undergoing experimental fertilization to induce a critical transition in the form of an algal bloom. As part of the experiment, the fertilization was halted in response to detected early warnings of the algal bloom identified by increased autocorrelation. We tested these datasets for time-scale dependence in the dynamics of lag-1 autocorrelation and found that in both the simulation and field experiment, the dynamics of autocorrelation were similar across time scales. In the simulated time series, autocorrelation increased exponentially approaching algal bloom development, and in the field experiment, the difference in autocorrelation between the manipulated and reference lakes increased sharply. These results suggest that, as an early warning indicator, autocorrelation may be robust to the time scale of the analysis. Given that a time scale can be shortened by increasing sampling frequency, or lengthened by aggregating data during analysis, these results have important implications for management as they demonstrate the potential for detecting early warning signals over a wide range of monitoring frequencies and without requiring analysts to make situation-specific decisions regarding aggregation. Such an outcome provides promise that data collection procedures, especially by automated sensors, may be used to monitor and manage ecosystem resilience without the need for strict attention to time scale. [ABSTRACT FROM AUTHOR]

Achieving global food security for the estimated 9 billion people by 2050 is a major scientific challenge. Crop productivity is fundamentally restricted by the rate of fixation of atmospheric carbon. The dedicated enzyme, RubisCO, has a low turnover and poor specificity for CO2. This limitation of C3 photosynthesis (the basic carbon-assimilation pathway present in all plants) is alleviated in some lineages by use of carbon-concentrating-mechanisms, such as the C4 cycle—a biochemical pump that concentrates CO2 near RubisCO increasing assimilation efficacy. Most crops use only C3 photosynthesis, so one promising research strategy to boost their productivity focuses on introducing a C4 cycle. The simplest proposal is to use the cycle to concentrate CO2 inside individual chloroplasts. The photosynthetic efficiency would then depend on the leakage of CO2 out of a chloroplast. We examine this proposal with a 3D spatial model of carbon and oxygen diffusion and C4 photosynthetic biochemistry inside a typical C3-plant mesophyll cell geometry. We find that the cost-efficiency of C4 photosynthesis depends on the gas permeability of the chloroplast envelope, the C4 pathway having higher quantum efficiency than C3 for permeabilities below 300 μm/s. However, at higher permeabilities the C4 pathway still provides a substantial boost to carbon assimilation with only a moderate decrease in efficiency. The gains would be capped by the ability of chloroplasts to harvest light, but even under realistic light regimes a 100% boost to carbon assimilation is possible. This could be achieved in conjunction with lower investment in chloroplasts if their cell surface coverage is also reduced. Incorporation of this C4 cycle into C3 crops could thus promote higher growth rates and better drought resistance in dry, high-sunlight climates. [ABSTRACT FROM AUTHOR]

Research purpose and findings: Coralline algae are key biological substrates of many carbonate systems globally. Their capacity to build enduring crusts that underpin the formation of tropical reefs, rhodolith beds and other benthic substrate is dependent on the formation of a calcified thallus. However, this important process of skeletal carbonate formation is not well understood. We undertook a study of cellular carbonate features to develop a model for calcification. We describe two types of cell wall calcification; 1) calcified primary cell wall (PCW) in the thin-walled elongate cells such as central medullary cells in articulated corallines and hypothallial cells in crustose coralline algae (CCA), 2) calcified secondary cell wall (SCW) with radial Mg-calcite crystals in thicker-walled rounded cortical cells of articulated corallines and perithallial cells of CCA. The distinctive banding found in many rhodoliths is the regular transition from PCW-only cells to SCW cells. Within the cell walls there can be bands of elevated Mg with Mg content of a few mol% higher than radial Mg-calcite (M-type), ranging up to dolomite composition (D-type). Model for calcification: We propose the following three-step model for calcification. 1) A thin (< 0.5 μm) PCW forms and is filled with a mineralising fluid of organic compounds and seawater. Nanometer-scale Mg-calcite grains precipitate on the organic structures within the PCW. 2) Crystalline cellulose microfibrils (CMF) are extruded perpendicularly from the cellulose synthase complexes (CSC) in the plasmalemma to form the SCW. 3) The CMF soaks in the mineralising fluid as it extrudes and becomes calcified, retaining the perpendicular form, thus building the radial calcite. In Clathromorphum, SCW formation lags PCW creating a zone of weakness resulting in a split in the sub-surface crust. All calcification seems likely to be a bioinduced rather than controlled process. These findings are a substantial step forward in understanding how corallines calcify. [ABSTRACT FROM AUTHOR]

Chloroplast plays an important role in the plant life cycle. However, the details of its development remain elusive in rice. In this study, we report the fine-mapping of a novel rice gene wpb1 (white panicle branch 1), which affects chloroplast biogenesis, from a tropical japonica variety that results in an albino panicle branches at and after the heading stage. The wpb1 variety was crossed with Nipponbare to generate the F2 and BC1F2 populations. Green and white panicle branch phenotypes with a 3:1 segregation ratio was observed in the F2 population. Bulked segregant analysis (BSA) based on whole genome resequencing was conducted to determine the wpb1 locus. A candidate interval spanning from 11.35 to 23.79M (physical position) on chromosome 1 was identified. The results of BSA analysis were verified by a 40K rice SNP-array using the BC1F2 population. A large-scale F2 population was used to pinpoint wpb1, and the locus was further narrowed down to a 95-kb interval. Furthermore, our results showed that the expression levels of the majority of the genes involved in Chl biosynthesis, photosynthesis and chloroplast development were remarkably affected in wpb1 variety and in F2 plants with a white panicle branch phenotype. In line with the results mentioned above, anatomical structural examination and chlorophyll (Chl) content measurement suggested that wpb1 might play an important role in the regulation of chloroplast development. Further cloning and functional characterization of the wpb1 gene will shed light on the molecular mechanism underlying chloroplast development in rice. [ABSTRACT FROM AUTHOR]

Water deficiency up to a certain level and duration leads to a stress condition called drought. It is a multi-dimensional stress causing alteration in the physiological, morphological, biochemical, and molecular traits in plants resulting in improper plant growth and development. Drought is one of the major abiotic stresses responsible for loss of crops including muskmelon (Cucumis melo. L). Muskmelon genotype SC-15, which exhibits high drought resistance as reported in our earlier reports, was exposed to deficient water condition and studied for alteration in physiological, molecular and proteomic profile changes in the leaves. Drought stress results in reduced net photosynthetic rate (Pn), stomatal conductance (Gs) and transpiration (E) rate. With expanded severity of drought, declination recorded in content of total chlorophyll and carotenoid while enhancement observed in phenol content indicating generation of oxidative stress. In contrary, activities of catalase (CAT), superoxide dismutase (SOD), ascorbate peroxidase (APX), and guaiacol (POD) were increased under drought stress. Peptide mass fingerprinting (PMF) showed that drought increased the relative abundance of 38 spots while decreases10 spots of protein. The identified proteins belong to protein synthesis, photosynthesis, nucleotide biosynthesis, stress response, transcription regulation, metabolism, energy and DNA binding. A drought-induced MADS-box transcription factor was identified. The present findings indicate that under drought muskmelon elevates the abundance of defense proteins and suppresses catabolic proteins. The data obtained exhibits possible mechanisms adopted by muskmelon to counter the impacts of drought induced stress. [ABSTRACT FROM AUTHOR]

Bioactive herbicidal compounds produced by soil microorganisms might be used to creating a bioherbicide for biological weed control. A total of 1,300 bacterial strains were isolated and screened for herbicidal activity against grass and broadleaf weeds. Among primarily selected 102 strains, the herbicidal activity of bacterial fermentation broths from the following three isolates strain-101, strain-128, and strain-329 reduced the growth of D. sanguinalis by 66.7%, 78.3%, and 100%, respectively as compared with control. Phylogenetic analysis of 16S rRNA gene sequencing determined that the strain-329 has 99% similarity to Streptomyces anulatus (HBUM 174206). The potential bioherbicidal efficacy of Streptomyces strain-329 was tested on grass and broadleaf weeds for phytotoxic activity through pre- and post-emergence applications. At pre-emergence application, the phytotoxic efficacy to D. sanguinalis and S. bicolor on seed germination were 90.4% and 81.3%, respectively at the 2x concentration, whereas in the case of Solanum nigrum, 85.2% phytotoxic efficacy was observed at the 4x concentration. The efficacy of Streptomyces strain-329 was substantially higher at post-emergence application, presenting 100% control of grass and broadleaf weeds at the 1x concentration. Two herbicidal compounds coded as 329-C1 and 329-C3 were extracted and purified by column chromatography and high-performance liquid chromatography methods. The active compound 329-C3 slightly increased leaf electrolytic leakage and MDA production as concentration-dependent manner. These results suggest that new Streptomyces sp. strain-329 produced bioherbicidal metabolites and may provide a new lead molecule for production an efficient bioherbicide to regulate grass and broadleaf weeds. [ABSTRACT FROM AUTHOR]

Many microbes exhibit quorum sensing (QS) to cooperate, share and perform a social task in unison. Recent studies have shown the emergence of reversible phenotypic heterogeneity in the QS-responding pathogenic microbial population under laboratory conditions as a possible bet-hedging survival strategy. However, very little is known about the dynamics of QS-response and the nature of phenotypic heterogeneity in an actual host-pathogen interaction environment. Here, we investigated the dynamics of QS-response of a Gram-negative phytopathogen Xanthomonas pv. campestris (Xcc) inside its natural host cabbage, that communicate through a fatty acid signal molecule called DSF (diffusible signal factor) for coordination of several social traits including virulence functions. In this study, we engineered a novel DSF responsive whole-cell QS dual-bioreporter to measure the DSF mediated QS-response in Xcc at the single cell level inside its natural host plant in vivo. Employing the dual-bioreporter strain of Xcc, we show that QS non-responsive cells coexist with responsive cells in microcolonies at the early stage of the disease; whereas in the late stages, the QS-response is more homogeneous as the QS non-responders exhibit reduced fitness and are out competed by the wild-type. Furthermore, using the wild-type Xcc and its QS mutants in single and mixed infection studies, we show that QS mutants get benefit to some extend at the early stage of disease and contribute to localized colonization. However, the QS-responding cells contribute to spread along xylem vessel. These results contrast with the earlier studies describing that expected cross-induction and cooperative sharing at high cell density in vivo may lead to synchronize QS-response. Our findings suggest that the transition from heterogeneity to homogeneity in QS-response within a bacterial population contributes to its overall virulence efficiency to cause disease in the host plant under natural environment. [ABSTRACT FROM AUTHOR]

In some parts of the Southern Ocean (SO), even though low surface concentrations of iron (Fe) and manganese (Mn) indicate FeMn co-limitation, we still lack an understanding on how Mn and Fe availability influences SO phytoplankton ecophysiology. Therefore, this study investigated the effects of Fe and Mn limitation alone as well as their combination on growth, photophysiology and particulate organic carbon production of the bloom-forming Antarctic diatom Chaetoceros debilis. Our results clearly show that growth, photochemical efficiency and carbon production of C. debilis were co-limited by Fe and Mn as highest values were only reached when both nutrients were provided. Even though Mn-deficient cells had higher photochemical efficiencies than Fe-limited ones, they, however, displayed similar low growth and POC production rates, indicating that Mn limitation alone drastically impeded the cell’s performance. These results demonstrate that similar to low Fe concentrations, low Mn availability inhibits growth and carbon production of C. debilis. As a result from different species-specific trace metal requirements, SO phytoplankton species distribution and productivity may therefore not solely depend on the input of Fe alone, but also critically on Mn acting together as important drivers of SO phytoplankton ecology and biogeochemistry. [ABSTRACT FROM AUTHOR]

The demand for agricultural crops continues to escalate with an increasing population. To meet this demand, marginal land can be used as a sustainable source for increased plant productivity. However, moisture stress not only affects crop growth and productivity but also induces plants’ susceptibility to various diseases. The positive role of plant growth hormone, salicylic acid (SA), on the defence systems of plants has been well documented. With this in mind, a combination of plant growth promoting rhizobacteria (PGPR) and SA was used to evaluate its performance on wheat grown under rainfed conditions (average moisture 10–14%). The selected bacterial strains were characterized for proline production, indole-3-acetic acid (IAA), hydrogen cyanide (HCN), ammonia (NH3), and exopolysaccharides (EPS). Wheat seeds of two genotypes, Inqilab-91 (drought tolerant) and Shahkar-2013 (drought sensitive), which differed in terms of their sensitivity to drought stress, were soaked for three hours prior to sowing in 24-hour old cultures of the bacterial strains Planomicrobium chinense strain P1 (accession no. MF616408) and Bacillus cereus strain P2 (accession no. MF616406). SA was applied (150 mg/L), as a foliar spray on one-month-old wheat seedlings. A significant reduction in the physiological parameters was noted in the plants grown in rainfed conditions but the PGPR and SA treatment effectively ameliorated the adverse effects of moisture stress. The wheat plants treated with PGPR and SA showed significant increases in leaf protein and sugar contents and maintained higher chlorophyll content, chlorophyll fluorescence (fv/fm) and performance index (PI) under rainfed conditions. Leaf proline content, lipid peroxidation, and antioxidant enzyme activity were higher in the non-inoculated plants grown in rainfed conditions but significantly reduced in the inoculated plants of both genotypes. Integrative use of a combination of PGPR strains and SA appears to be a promising and eco-friendly strategy for reducing moisture stress in plants. [ABSTRACT FROM AUTHOR]

The genetics and responses to biotic stressors of tetraploid switchgrass (Panicum virgatum L.) lowland cultivar ‘Kanlow’ and upland cultivar Summer are distinct and can be exploited for trait improvement. In general, there is a paucity of data on the basal differences in transcription across tissue developmental times for switchgrass cultivars. Here, the changes in basal and temporal expression of genes related to leaf functions were evaluated for greenhouse grown ‘Kanlow’, and ‘Summer’ plants. Three biological replicates of the 4th leaf pooled from 15 plants per replicate were harvested at regular intervals beginning from leaf emergence through senescence. Increases and decreases in leaf chlorophyll and N content were similar for both cultivars. Likewise, multidimensional scaling (MDS) analysis indicated both cultivar-independent and cultivar-specific gene expression. Cultivar-independent genes and gene-networks included those associated with leaf function, such as growth/senescence, carbon/nitrogen assimilation, photosynthesis, chlorophyll biosynthesis, and chlorophyll degradation. However, many genes encoding nucleotide-binding leucine rich repeat (NB-LRRs) proteins and wall-bound kinases associated with detecting and responding to environmental signals were differentially expressed. Several of these belonged to unique cultivar-specific gene co-expression networks. Analysis of genomic resequencing data provided several examples of NB-LRRs genes that were not expressed and/or apparently absent in the genomes of Summer plants. It is plausible that cultivar (ecotype)-specific genes and gene-networks could be one of the drivers for the documented differences in responses to leaf-borne pathogens between these two cultivars. Incorporating broad resistance to plant pathogens in elite switchgrass germplasm could improve sustainability of biomass production under low-input conditions. [ABSTRACT FROM AUTHOR]

Impact of barge movement on phytoplankton abundance and biomass was assessed in the lower stretch of river Ganga, popularly known as Bhagirathi-Hooghly river, during April 2016 to March, 2017. Based on the magnitude of tide, intensity of shipping and boating activities, the stretch from Baranagar to Lalbag (278 km), located at latitude (22°38'33.41"N to 24°10'59.75"N) and longitude (88°21'21.29"E to 88°16'5.65"E) was divided into three zones viz. zone—I (Baranagar to Barrackpore), zone II (Triveni to Balagarh) and zone III (Nabadweep to Lalbag). Water samples were collected randomly from six stations covering 22 barge movements at their passage at three different time intervals viz., 30 minutes before ‘barge movement’, during ‘barge movement’ and 30 minutes after ‘barge movement’. Analysis revealed the presence of 52 phytoplankton taxa belonged to 5 phylum during the study period. The abundance of phytoplankton was highest in zone—I followed by zone III and the zone II. A 44% decrease (1,997 ±1,510 ul-1) in phytoplankton abundance was observed during ‘barge movement’ with respect to normal condition (3,513 ± 2,239 ul-1) which could be due to propeller turbulence in the passage. Cell damage study revealed 21% damage in phytoplankton cell structure in ‘during barge’ followed by ‘after barge’ (10%) condition compared to natural state (6%). Study revealed that phytoplankton biomass (Chlorophyll a) was influenced by ‘barge movement’ in the sampling stretches and the impact was assessed by one way ANOVA. The effect was found significant at Barrackpore (p <0.01), Triveni (p <0.01), Balagarh (p <0.01) and Lalbag (p <0.01) where as it was insignificant at Baranagar and Nabadweep, which may be due to continuous and existing boat trafficking at Baranagar and Nabadweep. Two way ANOVA computed using ‘barge movement’ and sampling stations showed significant (p<0.01) effect on magnitude of Chl a concentrations in the sampling locations. Thus, the ‘barge movement’ influenced phytoplankton abundance and biomass, it had a detrimental effect on phytoplankton cell architecture also. The data set of this work serves as foundation information to understand the ecological implications augmented barge induced environmental disturbances in waterways. This is the first such study which depicts the impact of ‘barge movement’ on aquatic food chain linkages in Bhagirathi- Hooghly river. [ABSTRACT FROM AUTHOR]

Leaf senescence plays an important role in the improvement of maize kernel yields. However, the underlying regulatory mechanisms of leaf senescence in maize are largely unknown. We isolated ZmVQ52 and studied the function of ZmVQ52 which encoded, a VQ family transcription factor. ZmVQ52 is constitutively expressed in maize tissues, and mainly expressed in the leaf; it is located in the nucleus of maize protoplasts. Four WRKY family proteins—ZmWRKY20, ZmWRKY36, ZmWRKY50, and ZmWRKY71—were identified as interacting with ZmVQ52. The overexpression of ZmVQ52 in Arabidopsis accelerated premature leaf senescence. The leaf of the ZmVQ52-overexpression line showed a lower chlorophyll content and higher senescence rate than the WT. A number of leaf senescence regulating genes were up-regulated in the ZmVQ52-overexpression line. Additionally, hormone treatments revealed that the leaf of the ZmVQ52-overexpressed line was more sensitive to salicylic acid (SA) and jasmonic acid (JA), and had an enhanced tolerance to abscisic acid (ABA). Moreover, a transcriptome analysis of the ZmVQ52-overexpression line revealed that ZmVQ52 is mainly involved in the circadian pathway and photosynthetic pathways. [ABSTRACT FROM AUTHOR]

Risks associated with drought are increasing and are a global problem. Therefore, there is a need for new solutions for the safe production of food, while maintaining respect for the environment. Fungicides are designed to protect maize plants against disease, but some of the active substances used in preparations can also promote plant growth, which is known as the 'physiological effect'. However, there is a paucity of information as to how some of the 'new generation' fungicides act in stimulating grain yield in plants under abiotic stress, especially drought. Therefore, the effects of these products on conventional and stay-green maize varieties need to be better understood in order to reduce losses caused by droughts and to maximize production. In this study, the effect of a pyraclostrobin + epoxiconazole fungicide preparation on maize plants was evaluated at different times after spraying; during induced drought conditions and again during the regeneration process of the plants. The preparation was applied to 'KWS 1325' (conventional) and 'Ambrosini' (stay-green) varieties at the recommended dose, three times in greenhouse conditions. Plant gas exchange, plant water use efficiency, chlorophyll fluorescence and fresh and dry plant biomass were evaluated. The pyraclostrobin + epoxiconazole preparation increased stomatal conductance and photosynthesis intensity in the 'Ambrosini' plants. When maintained under a high light intensity, the variety used increased efficiency and exchanged excessive energy in the form of thermal energy to protect the maize leaf from light-induced damage under drought stress. Plant photosynthetic efficiency (ETR and Yield parameters) during drought stress and after regeneration was significantly higher in treated plants than in the controls. Thus, the beneficial effects on the physiology of the maize varieties grown under drought stress from the fungicide application are significant for farmers and growers. [ABSTRACT FROM AUTHOR]

The internal phenotypes of netted muskmelon (Cucumis melo L. var. eticulates Naud.) are always associated with its external phenotypes. In this study, the parameters of external phenotypic traits were extracted from muskmelon images captured by machine vision, and the internal phenotypes of interest to us were measured. Pearson analysis showed that most external phenotypic traits were highly correlated with these internal phenotypes in muskmelon fruit. In this study, we used the random forest algorithm to predict muskmelon fruit internal phenotypes based on the significantly associated external parameters. Carotenoids, sucrose, and total soluble solid (TSS) were the three most accurately monitored internal phenotypes with prediction R-squared (R2) values of 0.947 (root-mean-square error (RMSE) = 0.019 mg/100 g), 0.918 (RMSE = 3.233 mg/g), and 0.916 (RMSE = 1.089%), respectively. Further, a simplified model was constructed and validated based on the top 10 external phenotypic parameters associated with each internal phenotype, and these parameters were filtered with the varImp function from the random forest package. The top 10 external phenotypic parameters correlated with each internal phenotype used in the simplified model were not identical. The results showed that the simplified models also accurately monitored the melon internal phenotypes, despite that the predicted R2 values decreased 0.3% to 7.9% compared with the original models. This study improved the efficiency and accuracy of real-time fruit quality monitoring for greenhouse muskmelon. [ABSTRACT FROM AUTHOR]

Ceratopteris thalictroides, a model fern, has two kinds of gametophytes with different sex expression: male and hermaphrodite. Hermaphroditic gametophytes have one or several archegonia beneath the growing point and a few antheridia at the base or margin. Male gametophytes show a spoon-like shape with much longer than the width and produce many antheridia at the margin and surface. The results of chlorophyll fluorescence detection showed that the photochemical efficiency of hermaphrodites was higher than that of males. By using two-dimensional electrophoresis and mass spectrometry, the differentially abundant proteins in hermaphroditic and male gametophytes were identified. A total of 1136 ± 55 protein spots were detected in Coomassie-stained gels of proteins from hermaphroditic gametophytes, and 1130 ± 65 spots were detected in gels of proteins from male gametophytes. After annotation, 33 spots representing differentially abundant proteins were identified. Among these, proteins involved in photosynthesis and chaperone proteins were over-represented in hermaphrodites, whereas several proteins involved in metabolism were increased in male gametophytes in order to maintain their development under relatively nutritionally deficient conditions. Furthermore, the differentially abundant cytoskeletal proteins detected in this study, such as centrin and actin, may be involved in the formation of sexual organs and are directly related to sex expression. These differentially abundant proteins are important for maintaining the development of gametophytes of different sexes in C. thalictroides. [ABSTRACT FROM AUTHOR]

We present a discrete mechanical model to study plant development. The method is built up of mass points, springs and hinges mimicking the plant cell wall’s microstructure. To model plastic growth the resting lengths of springs are adjusted; when springs exceed a threshold length, new mass points, springs and hinges, are added. We formulate a stiffness tensor for the springs and hinges as a function of the fourth rank tensor of elasticity and the geometry of the mesh. This allows us to approximate the material law as a generalized orthotropic Hooke’s law, and control material properties during growth. The material properties of the model are illustrated in numerical simulations for finite strain and plastic growth. To solve the equations of motion of mass points we assume elastostatics and use Verlet integration. The method is demonstrated in simulations when anisotropic growth causes emergent residual strain fields in cell walls and a bending of tissue. The method can be used in multilevel models to study plant development, for example by coupling it to models for cytoskeletal, hormonal and gene regulatory processes. [ABSTRACT FROM AUTHOR]

In the eastern Pacific Ocean, the tropical tuna purse-seine fishery incidentally captures high numbers of five mobulid bycatch species; all of which are classified as mortalities by the Inter-American Tropical Tuna Commission due to uncertainties in post-release mortality rates. To date, the factors (operational or environmental) leading to the capture of these species by the fishery have not been well studied. Here, we developed Generalized Additive Models for fisheries observer data to analyze the relationships between the presence/absence of Mobula mobular bycatch and oceanographic conditions, the spatial and temporal variability in fishing location, and the set type (associated with dolphins, free-swimming tuna schools or floating objects). Our results suggest that chlorophyll concentration and sea surface height are the most important variables to describe the presence of M. mobular in conjunction with geographic location (latitude and longitude) and set type. Presence of the species was predicted in waters with chlorophyll concentrations between 0.5–1 mg·m-3 and with sea surface height values close to 0; which indicates direct relationships with productive upwelling systems. Seasonally, M. mobular was observed more frequently during December-January and August-September. We also found the highest probability of presence observed in School sets, followed by Dolphin sets. Three areas were observed as important hotspots: the area close to the coastal upwelling of northern Peru, the area west to Islands Colon Archipelago (Galapagos) and the area close to the Costa Rica Dome. This information is crucial to identify the mobulids habitat and hotspots that could be managed and protected under dynamic spatial management measures to reduce the mortality of mobulid rays in the eastern Pacific purse-seine fishery and, hence, ensure the sustainability of the populations of these iconic species. [ABSTRACT FROM AUTHOR]

Dinoflagellates from the Symbiodiniaceae family and corals have an ecologically important endosymbiotic relationship. Scleractinian corals cannot survive for long periods without their symbionts. These algae, also known as zooxanthellae, on the other hand, thrives outside the coral cells. The free-living populations of zooxanthellae are essential for the resilience of the coral to environmental stressors such as temperature anomalies and ocean acidification. Yet, little is known about how ocean acidification may affect the free-living zooxanthellae. In this study we aimed to test morphological, physiological and biochemical responses of zooxanthellae from the Symbiodinium genus isolated from the coral Mussismilia braziliensis, endemic to the Brazilian coast, to acidification led by increased atmospheric CO2. We tested whether photosynthetic yield, cell ultrastructure, cell density and lipid profile would change after up to 16 days of exposure to pH 7.5 in an atmospheric pCO2 of 1633 μatm. Photosynthetic yield and cell density were negatively affected and chloroplasts showed vesiculated thylakoids, indicating morphological damage. Moreover, Symbiodinium fatty acid profile drastically changed in acidified condition, showing lower polyunsaturated fatty acids and higher saturated fatty acids contents, when compared to the control, non-acidified condition. These results show that seawater acidification as an only stressor causes significant changes in the physiology, biochemistry and ultrastructure of free-living Symbiodinium. [ABSTRACT FROM AUTHOR]

Resolving the phylogenetic relationships of closely related species using a small set of loci is challenging as sufficient information may not be captured from a limited sample of the genome. Relying on few loci can also be problematic when conflict between gene-trees arises from incomplete lineage sorting and/or ongoing hybridization, problems especially likely in recently diverged lineages. Here, we developed a method using limited genomic resources that allows identification of many low copy candidate loci from across the nuclear and chloroplast genomes, design probes for target capture and sequence the captured loci. To validate our method we present data from Eucalyptus and Melaleuca, two large and phylogenetically problematic genera within the Myrtaceae family. With one annotated genome, one transcriptome and two whole-genome shotgun sequences of one Eucalyptus and four Melaleuca species, respectively, we identified 212 loci representing 263 kbp for targeted sequence capture and sequencing. Of these, 209 were successfully tested from 47 samples across five related genera of Myrtaceae. The average percentage of reads mapped back to the reference was 57.6% with coverage of more than 20 reads per position across 83.5% of the data. The methods developed here should be applicable across a large range of taxa across all kingdoms. The core methods are very flexible, providing a platform for various genomic resource availabilities and are useful from shallow to deep phylogenies. [ABSTRACT FROM AUTHOR]

Soil salinization is a serious problem that affects the seedling growth in many regions. A greenhouse experiment was carried to investigate the adaptation ability of seedlings (Sorghum bicolor (L.) Moench.) in coastal saline alkaline environment. Seedlings of sorghum were treated by different salt and alkali stress (NaCl: Na2SO4: NaHCO3 were 2:1:0, 2:1:1, 2:1:2). The treatments consisted of three levels of salinity (100, 200 and 300 mmol/L) and pH values were 7.08, 8.78 and 9.04. The results showed that the seedlings of sorghum have good adaptability to salt stress under low pH (pH ≤7.08). The plant height, the maximum leave areas of seedlings all dropped and root length first ascended and then descended with the increasing of salt and alkali stress. The contents of Chlorophyll b degraded significantly under salt and alkali stress. Salt and alkali stress stimulated the accumulation of organic solutes (proline and protein) and inorganic ions (Na+, Cl-, SO42-). Our results showed that salt and alkali stress have significant effect on growth indexes except root length and the interaction effect has significantly on physiology. [ABSTRACT FROM AUTHOR]

Direct protein delivery into intact plants remains a challenge for the agricultural and plant science fields. Cell-penetrating peptide (CPP)-mediated protein delivery requires the binding of CPPs to a protein to carry the protein into the cell through the cell wall and lipid bilayer. Thus, we prepared ionic complexes of a CPP-containing carrier peptide and a cargo protein, namely, Citrine yellow fluorescent protein, and subsequently studied their physicochemical properties. Two types of carrier peptides, BP100(KH)9 and BP100CH7, were investigated for delivery efficiency into rice callus. Both BP100(KH)9 and BP100CH7 successfully introduced Citrine protein into rice callus cells under pressure and vacuum treatment. Moreover, delivery efficiency varied at different growth stages of rice callus; 5-day rice callus was a more efficient recipient for Citrine than 21-day callus. [ABSTRACT FROM AUTHOR]

Plant cell walls development is an integrated process during which several components are deposited successively. In the cell walls in grass, the accessibility of structural polysaccharides is limited by the cell walls structure and composition mainly as a result of phenolic compounds. Here, we studied the patterns of cell walls establishment in the internode supporting the ear in three distinct maize genotypes. The developmental patterns observed in the internode cell walls in terms of its composition are reported with an emphasis on lignification, p-coumaroylation and feruloylation. We combined biochemical and histological approaches and revealed that internode cell walls development in maize before flowering is characterized by the rapid deposition of secondary cell walls components and robust lignification in both the pith and the rind. After flowering and until silage maturity, the slow deposition of secondary walls components occurs in the cortical region, and the deposited lignins are rich in β-O-4 bonds and are highly p-coumaroylated. We conclude the paper by proposing a revised spatiotemporal model based on that proposed by Terashima et al. (1993) for cell walls development in grass. [ABSTRACT FROM AUTHOR]

Knowing what animals eat is fundamental to our ability to understand and manage biodiversity and ecosystems, but researchers often must rely on indirect methods to infer trophic position and food intake. Using an approach that combines evidence from stable isotope analysis and DNA metabarcoding, we assessed the diet and trophic position of Anthene usamba butterflies, for which there are no known direct observations of larval feeding. An earlier study that analyzed adults rather than caterpillars of A. usamba inferred that this butterfly was aphytophagous, but we found that the larval guts of A. usamba and two known herbivorous lycaenid species contain chloroplast 16S sequences. Moreover, chloroplast barcoding revealed high sequence similarity between chloroplasts found in A. usamba guts and the chloroplasts of the Vachellia drepanolobium trees on which the caterpillars live. Stable isotope analysis provided further evidence that A. usamba caterpillars feed on V. drepanolobium, and the possibilities of strict herbivory versus limited omnivory in this species are discussed. These results highlight the importance of combining multiple approaches and considering ontogeny when using stable isotopes to infer trophic ecology where direct observations are difficult or impossible. [ABSTRACT FROM AUTHOR]

Superoxide dismutases (SODs) protect against reactive oxygen species (ROS) by detoxifying superoxide. Three types of SOD are present in plants: FeSOD, CuSOD, and MnSOD. The Arabidopsis thaliana genome contains three FeSOD genes, in which two (FSD2, and FSD3) are targeted to chloroplast thylakoids. Loss of FSD2 or FSD3 expression impairs growth and causes leaf bleaching. FSD2 and FSD3 form heterocomplexes present in chloroplast nucleoids, raising the question of whether FSD2 and FSD3 are functionally interchangeable. In this study, we examined how loss of FSD2 or FSD3 expression affects photosynthetic processes and whether overexpression of one compensates for loss of the other. Whereas loss of the cytosolic FSD1 had little effect, an fsd2 mutant exhibited increased superoxide production, reduced chlorophyll levels, lower PSII efficiency, a lower rate of CO2 assimilation, but elevated non-photochemical quenching (NPQ). In contrast, fsd3 mutants failed to survive beyond the seedling stage and overexpression of FSD2 could not rescue the seedlings. Overexpression of FSD3 in an fsd2 mutant, however, partially reversed the fsd2 mutant phenotype resulting in improved growth characteristics. Overexpression of FSD2 or FSD3, either individually or together, had little effect. These results indicate that, despite functioning as FeSODs, FSD2 and FSD3 are functionally distinct. [ABSTRACT FROM AUTHOR]

Translucent flash disorder (TFD) is one of the important physiological disorders in mangosteen (Garcinia mangostana L.). TFD has symptoms such as flesh arils that become firm and appear transparent similar to watercore in apple or pear. Information on the changes of gene expression in TFD-affected tissues remain limited, and investigations into the effects of different water regimes still need to be undertaken. Through an RNA sequencing approach using the Ion Proton, 183,274 contigs with length ranging from 173–13,035 bp were constructed by de novo assembly. Functional annotation was analyzed using various public databases such as non-redundant protein NCBI, SwissProt, and Gene Ontology, and KEGG pathway. Our studies compared different water regimes to incidence and differentially expressed genes of TFD-like physiological disorders. From the differentially expressed gene (DEG) between normal air and TFD-affected aril, we identified DEG-related TFD events, which 6228 DEGs in the control condition and 3327 DEGs in under water stress treatment condition remained, and confirmed these with RT-qPCR, including sucrose synthase (SUSY), endoglucanase (GUN), xyloglucan endotransglucosylase/hydrolase (XTH), and polygalacturonase (PG) showed statistically significant. In addition, transcription factors also indicated changes in MYB, NAC and WRKY between tissues and different water regimes. [ABSTRACT FROM AUTHOR]

Expansin is a type of cell wall elongation and stress relaxation protein involved in various developmental processes and stress resistances in plant. In this study, we identified 36 potato (Solanum tuberosum L.) genes belonging to the expansin (StEXP) gene family from the genome reference. These genes included 24 α-expansins (StEXPAs), five β-expansins (StEXPBs), one expansin-like A (StEXLA) and six expansin-like B (StEXLBs). The RNA-Seq analysis conducted from a variety of tissue types showed 34 expansins differentially expressed among tissues, some of which only expressed in specific tissues. Most of the StEXPAs and StEXPB2 transcripts were more abundant in young tuber compared with other tissues, suggesting they likely play a role in tuber development. There were 31 genes, especially StEXLB6, showed differential expression under the treatments of ABA, IAA and GA3, as well as under the drought and heat stresses, indicating they were likely involved in potato stress resistance. In addition, the gene co-expression analysis indicated the StEXLBs likely contribute to a wider range of stress resistances compared with other genes. We found the StEXLA and six StEXLBs expressed differently under a range of abiotic stresses (salt, alkaline, heavy metals, drought, heat, and cold stresses), which likely participated in the associated signaling pathways. Comparing with the control group, potato growing under the drought or heat stresses exhibited up-regulation of the all six StEXLB genes in leaves, whereas, the StEXLB3, StEXLB4, StEXLB5 and StEXLB6 showed relatively higher expression levels in roots. This suggested these genes likely played a role in the drought and heat tolerance. Overall, this study has shown the potential role of the StEXP genes in potato growth and stress tolerance, and provided fundamental resources for the future studies in potato breeding. [ABSTRACT FROM AUTHOR]

Phototrophic cyanobacteria are limited in growth locations by their need for visible light and must also cope with intermittent ultraviolet radiation (UVR), especially in extreme environments such as deserts and on early Earth. One survival method for cyanobacteria is growing endolithically within minerals such as micas, gypsum, and quartz minerals. However, the capability of different mica minerals to protect cyanobacteria from UVR, while at the same time allowing transmission of photosynthetically active radiation (PAR), has only been minimally examined. In this study, we performed laboratory incubation experiments to demonstrate that a model filamentous cyanobacterium, Leptolyngbya sp., can colonize micas, such as muscovite, phlogopite, and biotite. After inoculation experiments confirmed that these cyanobacteria grew between the sheets of mica, Leptolyngbya sp. colonies were exposed to UVB and UVC for up to 24 hrs, and the level of survival was determined using chlorophyll a and carotenoid assays. Of the three micas investigated, muscovite, being an Fe-poor and Al-rich mica, provided the least attenuation of UVR, however it transmitted the most visible light. Fe-rich biotite provided the best UVR shielding. Phlogopite, apparently because of its intermediate amount of Fe, showed the greatest ability to shield UVR while still transmitting an adequate amount of visible light, making it the ideal habitat for the cyanobacterium. Upon exposure to UVR, significant shifts in several important fatty acids of the cyanobacterium were detected such as linolenic acid and oleic acid, 18:3ω3 and 18:1ω9c, respectively. These cellular changes are interpreted to be a consequence of UVR and other accessory stress (such as O3). [ABSTRACT FROM AUTHOR]

Larix populations at the tundra-taiga ecotone in northern Siberia are highly under-represented in population genetic studies, possibly due to the remoteness of these regions that can only be accessed at extraordinary expense. The genetic signatures of populations in these boundary regions are therefore largely unknown. We aim to generate organelle reference genomes for the detection of single nucleotide polymorphisms (SNPs) that can be used for paleogenetic studies. We present 19 complete chloroplast genomes and mitochondrial genomic sequences of larches from the southern lowlands of the Taymyr Peninsula (northernmost range of Larix gmelinii (Rupr.) Kuzen.), the lower Omoloy River, and the lower Kolyma River (both in the range of Larix cajanderi Mayr). The genomic data reveal 84 chloroplast SNPs and 213 putatively mitochondrial SNPs. Parsimony-based chloroplast haplotype networks show no spatial structure of individuals from different geographic origins, while the mitochondrial haplotype network shows at least a slight spatial structure with haplotypes from the Omoloy and Kolyma populations being more closely related to each other than to most of the haplotypes from the Taymyr populations. Whole genome alignments with publicly available complete chloroplast genomes of different Larix species show that among official plant barcodes only the rcbL gene contains sufficient polymorphisms, but has to be sequenced completely to distinguish the different provenances. We provide 8 novel mitochondrial SNPs that are putatively diagnostic for the separation of L. gmelinii and L. cajanderi, while 4 chloroplast SNPs have the potential to distinguish the L. gmelinii/L. cajanderi group from other Larix species. Our organelle references can be used for a targeted primer and probe design allowing the generation of short amplicons. This is particularly important with regard to future investigations of, for example, the biogeographic history of Larix by screening ancient sedimentary DNA of Larix. [ABSTRACT FROM AUTHOR]

Leaf traits are often strongly correlated with yield, which poses a major challenge in rice breeding. In the present study, using a panel of Vietnamese rice landraces genotyped with 21,623 single-nucleotide polymorphism markers, a genome-wide association study (GWAS) was conducted for several leaf traits during the vegetative stage. Vietnamese landraces are often poorly represented in panels used for GWAS, even though they are adapted to contrasting agrosystems and can contain original, valuable genetic determinants. A panel of 180 rice varieties was grown in pots for four weeks with three replicates under nethouse conditions. Different leaf traits were measured on the second fully expanded leaf of the main tiller, which often plays a major role in determining the photosynthetic capacity of the plant. The leaf fresh weight, turgid weight and dry weight were measured; then, from these measurements, the relative tissue weight and leaf dry matter percentage were computed. The leaf dry matter percentage can be considered a proxy for the photosynthetic efficiency per unit leaf area, which contributes to yield. By a GWAS, thirteen QTLs associated with these leaf traits were identified. Eleven QTLs were identified for fresh weight, eleven for turgid weight, one for dry weight, one for relative tissue weight and one for leaf dry matter percentage. Eleven QTLs presented associations with several traits, suggesting that these traits share common genetic determinants, while one QTL was specific to leaf dry matter percentage and one QTL was specific to relative tissue weight. Interestingly, some of these QTLs colocalize with leaf- or yield-related QTLs previously identified using other material. Several genes within these QTLs with a known function in leaf development or physiology are reviewed. [ABSTRACT FROM AUTHOR]

Diatoms are the most diverse lineage of algae, but the diversity of their chloroplast genomes, particularly within a genus, has not been well documented. Herein, we present three chloroplast genomes from the genus Halamphora (H. americana, H. calidilacuna, and H. coffeaeformis), the first pennate diatom genus to be represented by more than one species. Halamphora chloroplast genomes ranged in size from ~120 to 150 kb, representing a 24% size difference within the genus. Differences in genome size were due to changes in the length of the inverted repeat region, length of intergenic regions, and the variable presence of ORFs that appear to encode as-yet-undescribed proteins. All three species shared a set of 161 core features but differed in the presence of two genes, serC and tyrC of foreign and unknown origin, respectively. A comparison of these data to three previously published chloroplast genomes in the non-pennate genus Cyclotella (Thalassiosirales) revealed that Halamphora has undergone extensive chloroplast genome rearrangement compared to other genera, as well as containing variation within the genus. Finally, a comparison of Halamphora chloroplast genomes to those of land plants indicates diatom chloroplast genomes within this genus may be evolving at least ~4–7 times faster than those of land plants. Studies such as these provide deeper insights into diatom chloroplast evolution and important genetic resources for future analyses. [ABSTRACT FROM AUTHOR]

Biotic stresses in plants have a significant impact on agricultural productivity. In the present study, in vivo experiments were conducted to determine the physiological responses of tomato (Solanum lycopersicum L.) seedlings by inoculation with an endophytic actinobacterium, Streptomyces thermocarboxydus isolate BPSAC147 under greenhouse conditions. Further, photochemical quantum yield of photosystem II (PSII) (Fv/Fm), photochemical quenching (qP) and non-photochemical (NPQ) were calculated in seedlings inoculated with S. thermocarboxydus (T1) and were compared with control (T0) plants. Furthermore, the electron transport rate (ETR) of PSII exhibited a significant increase in T1 plants, relative to T0 plants. These results indicate that inoculation of tomato seedlings with S. thermocarboxydus had a positive effect on the process of photosynthesis, resulting in enhanced chlorophyll fluorescence parameters due to increased ETR in the thylakoid membrane. GC-MS analysis showed significant differences in the volatile compounds in the different treatments performed under greenhouse conditions. The present study suggests that S. thermocarboxydus can be used as new biocontrol agent to control Fusarium wilt in tomato crops and enhance productivity by enhancing photosynthesis. [ABSTRACT FROM AUTHOR]

The Symbiodinaceae are paradoxical in that they play a fundamental role in the success of scleractinian corals, but also in their dismissal when under stress. In the past decades, the discovery of the endosymbiont’s genetic and functional diversity has led people to hope that some coral species can survive bleaching events by associating with a stress-resistant symbiont that can become dominant when seawater temperatures increase. The variety of individual responses encouraged us to scrutinize each species individually to gauge its resilience to future changes. Here, we analyse the temporal variation in the Symbiodinaceae community associated with Leptoria phrygia, a common scleractinian coral from the Indo-Pacific. Coral colonies were sampled from two distant reef sites located in southern Taiwan that differ in temperature regimes, exemplifying a ‘variable site’ (VS) and a ‘steady site’ (SS). We investigated changes in the relative abundance of the dominant symbiont and its physiology every 3–4 months from 2016–2017. At VS, 11 of the 12 colonies were dominated by the stress-resistant Durusdinium spp. (>90% dominance) and only one colony exhibited co-dominance between Durusdinium spp. and Cladocopium spp. Every colony displayed high photochemical efficiency across all sampling periods, while showing temporal differences in symbiont density and chlorophyll a concentration. At SS, seven colonies out of 13 were dominated by Cladocopium spp., five presented co-dominance between Durusdinium spp./Cladocopium spp. and only one was dominated by Durusdinium spp. Colonies showed temporal differences in photochemical efficiency and chlorophyll a concentration during the study period. Our results suggest that VS colonies responded physiologically better to high temperature variability by associating with Durusdinium spp., while in SS there is still inter-colonial variability, a feature that might be advantageous for coping with different environmental changes. [ABSTRACT FROM AUTHOR]

Alpinia oxyphylla Miq. (A. oxyphylla) is an important edible and traditional herbal medicine. In this study, the complete chloroplast genome of A. oxyphylla was sequenced, analysed, and compared to five species in the Zingiberaceae family. The size of the A. oxyphylla chloroplast genome was 161351 bp, which consisted of a large single-copy (LSC, 87248 bp) and small single-copy (SSC, 16175 bp) region separated by a pair of inverted repeats (IRa and IRb, 28964 bp each). The genome encoded 132 unique genes, including 87 protein-coding genes, 37 tRNAs and four rRNAs. The GC content of the genome was 36.17%. A total of 53 simple sequence repeats (SSRs) and 80 long repeats were identified in the A. oxyphylla chloroplast genome. The chloroplast genome of A. oxyphylla shared the highest sequence similarity of >90% with the chloroplast genome of A. zerumbet, and six chloroplast genomes in the Zingiberaceae family were compared by using CGView Comparison Tool (CCT). According to the phylogenetic tree, the Zingiberaceae family is divided into two categories, which coincide with the classification of the characteristics of sun-like and shade-like in plants. Our results reveal the phototrophic component of NADH-dehydrogenase (ndhB and ndhC), photosystem II (psbZ) and ATP synthase (atpE, atpF) exhibit adaptive evolution under different environments, and the strength of light is an important trigger for the adaptations at the chloroplast level. [ABSTRACT FROM AUTHOR]

Recent plastid genome (plastome) studies of legumes (family Fabaceae) have shown that this family has undergone multiple atypical plastome evolutions from each of the major clades. The tribe Desmodieae belongs to the Phaseoloids, an important but systematically puzzling clade within Fabaceae. In this study, we investigated the plastome evolution of Desmodieae and analyzed its phylogenetic signaling. We sequenced six complete plastomes from representative members of Desmodieae and from its putative sister Phaseoloid genus Mucuna. Those genomes contain 128 genes and range in size from 148,450 to 153,826 bp. Analyses of gene and intron content revealed similar characters among the members of Desmodieae and Mucuna. However, there were also several distinct characters identified. The loss of the rpl2 intron was a feature shared between Desmodieae and Mucuna, whereas the loss of the rps12 intron was specific to Desmodieae. Likewise, gene loss of rps16 was observed in Mucuna but not in Desmodieae. Substantial sequence variation of ycf4 was detected from all the sequenced plastomes, but pseudogenization was restricted to the genus Desmodium. Comparative analysis of gene order revealed a distinct plastome conformation of Desmodieae compared with other Phaseoloid legumes, i.e., an inversion of an approximately 1.5-kb gene cluster (trnD-GUC, trnY-GUA, and trnE-UUC). The inversion breakpoint suggests that this event was mediated by the recombination of an 11-bp repeat motif. A phylogenetic analysis based on the plastome-scale data set found the tribe Desmodieae is a highly supported monophyletic group nested within the paraphyletic Phaseoleae, as has been found in previous phylogenetic studies. Two subtribes (Desmodiinae and Lespedezinae) of Desmodieae were also supported as monophyletic groups. Within the subtribe Lespedezinae, Lespedeza is closer to Kummerowia than Campylotropis. [ABSTRACT FROM AUTHOR]

The growth of plant organs is a complex process powered by osmosis that attracts water inside the cells; this influx induces simultaneously an elastic extension of the walls and pressure in the cells, called turgor pressure; above a threshold, the walls yield and the cells grow. Based on Lockhart’s seminal work, various models of plant morphogenesis have been proposed, either for single cells, or focusing on the wall mechanical properties. However, the synergistic coupling of fluxes and wall mechanics has not yet been fully addressed in a multicellular model. This work lays the foundations of such a model, by simplifying as much as possible each process and putting emphasis on the coupling itself. Its emergent properties are rich and can help to understand plant morphogenesis. In particular, we show that the model can display a new type of lateral inhibitory mechanism that amplifies growth heterogeneities due e.g to cell wall loosening. [ABSTRACT FROM AUTHOR]

The blooms of Noctiluca in the Gulf of Oman and the Arabian Sea have been intensifying in recent years, posing now a threat to regional fisheries and the long-term health of an ecosystem supporting a coastal population of nearly 120 million people. We present the results of a local-scale data analysis to investigate the onset and patterns of the Noctiluca blooms, which form annually during the winter monsoon in the Gulf of Oman and in the Arabian Sea. Our approach combines methods in physical and biological oceanography with machine learning techniques. In particular, we present a robust algorithm, the variable-length Linear Dynamic Systems (vLDS) model, that extracts the causal factors and latent dynamics at the local-scale along each individual drifter trajectory, and demonstrate its effectiveness by using it to generate predictive plots for all variables and test macroscopic scientific hypotheses. The vLDS model is a new algorithm specifically designed to analyze the irregular dataset from surface velocity drifters, in which the multivariate time series trajectories are having variable or unequal lengths. The test results provide local-scale statistical evidence to support and check the macroscopic physical and biological Oceanography hypotheses on the Noctiluca blooms; it also helps identify complementary local trajectory-scale dynamics that might not be visible or discoverable at the macroscopic scale. The vLDS model also exhibits a generalization capability (as a machine learning methodology) to investigate important causal factors and hidden dynamics associated with ocean biogeochemical processes and phenomena at the population-level and local trajectory-scale. [ABSTRACT FROM AUTHOR]

The article highlights the connection between Plastid–endomembrane in apicomplexan parasites. Topics discussed apicoplast is a nonphotosynthetic plastid found in most apicomplexan parasites, including Toxoplasma gondii and Plasmodium spp.; mentions the relation between apicoplast and endomembrane system; and highlights the role of Autophagy machinery and phosphoinositides in apicoplast segregation.