Photosynthesis Genes Research Articles

Photosynthetic responses of Arabidopsis to SO2 were related to photosynthetic pigments, photosynthesis gene expression and redox regulation

Sulfur dioxide (SO2) is one of the most common and harmful air pollutants. High concentrations of SO2 can induce a series of defensive responses in Arabidopsis plants. However, the role of photosynthesis in the plant response to SO2 stress is not clear. Here, we report the photosynthetic responses of Arabidopsis plants to SO2 stress. Exposure to 30 mg/m3 SO2 decreased stomatal conductance (Gs) and transpiration rate (Tr) but increased photosynthetic pigments and net photosynthetic rate (Pn). The contents of carbohydrates and sucrose were not altered. The transcript levels of most genes related to photosystem II (PSII), cytochrome b6/f (Cytb6f), photosystem I (PSI) and carbon fixation were upregulated, revealing one important regulatory circuit for the maintenance of chloroplast homeostasis under SO2 stress. Exposure to SO2 triggered reactive oxygen species (ROS) generation, accompanied by increases in superoxide dismutase (SOD) activity and the contents of cysteine (Cys), glutathione (GSH) and non-protein thiol (NPT), which maintained cellular redox homeostasis. Together, our results indicated that chloroplast photosynthesis was involved in the plant response to SO2 stress. The photosynthetic responses were related to photosynthetic pigments, photosynthesis gene expression and redox regulation.

Degradation of key photosynthetic genes in the critically endangered semi-aquatic flowering plant Saniculiphyllum guangxiense (Saxifragaceae)

BackgroundPlastid gene loss and pseudogenization has been widely documented in parasitic and mycoheterotrophic plants, which have relaxed selective constraints on photosynthetic function. More enigmatic are sporadic reports of pseudogenization and loss of important photosynthesis genes in lineages thought to be fully photosynthetic. Here we report the complete plastid genome of Saniculiphyllum guangxiense, a critically endangered and phylogenetically isolated plant lineage, along with genomic evidence of reduced chloroplast function. We also report 22 additional plastid genomes representing the diversity of its containing clade Saxifragales, characterizing gene content and placing variation in a broader phylogenetic context.ResultsWe find that the plastid genome of Saniculiphyllum has experienced pseudogenization of five genes of the ndh complex (ndhA, ndhB, ndhD, ndhF, and ndhK), previously reported in flowering plants with an aquatic habit, as well as the surprising pseudogenization of two genes more central to photosynthesis (ccsA and cemA), contrasting with strong phylogenetic conservatism of plastid gene content in all other sampled Saxifragales. These genes participate in photooxidative protection, cytochrome synthesis, and carbon uptake. Nuclear paralogs exist for all seven plastid pseudogenes, yet these are also unlikely to be functional.ConclusionsSaniculiphyllum appears to represent the greatest degree of plastid gene loss observed to date in any fully photosynthetic lineage, perhaps related to its extreme habitat specialization, yet plastid genome length, structure, and substitution rate are within the variation previously reported for photosynthetic plants. These results highlight the increasingly appreciated dynamism of plastid genomes, otherwise highly conserved across a billion years of green plant evolution, in plants with highly specialized life history traits.

Complete chloroplast genome sequence and phylogenetic analysis of Annona reticulata

Annona reticulata is native to South and Central America which has many phytochemical and pharmacological activities suggesting a wide range of clinical application in lieu of cancer chemotherapy. This study provides abundant genomic data for the genetic relationship study, germplasm resources evaluation and varieties selection of A. reticulata. The complete chloroplast genome of A. reticulata was sequenced, assembled, and annotated in this study. The genome size was 201,906 bp and was divided into four regions: a large single-copy region of 69,650 bp, a small single-copy region of 3,014 bp, and two inverted repeat regions of 64,621 bp. A total number of 164 genes were annotated, including 115 protein-coding genes, one pseudogene, 40 tRNA genes, and eight rRNA genes. In terms of gene function, the 164 genes were divided into four major groups: genes for self-replication, photosynthesis, unknown function, and other genes. A maximum likelihood tree based on the chloroplast genome sequences of 24 plant species was constructed. The result of phylogenetic analysis showed that A. cherimola had the closest relationship with A. reticulate.

Diazotroph Genomes and Their Seasonal Dynamics in a Stratified Humic Bog Lake.

Aquatic N-fixation is generally associated with the growth and mass development of Cyanobacteria in nitrogen-deprived photic zones. However, sequenced genomes and environmental surveys suggest active aquatic N-fixation also by many non-cyanobacterial groups. Here, we revealed the seasonal variation and genomic diversity of potential N-fixers in a humic bog lake using metagenomic data and nif gene clusters analysis. Groups with diazotrophic operons were functionally divergent and included Cholorobi, Geobacter, Desulfobacterales, Methylococcales, and Acidobacteria. In addition to nifH (a gene that encodes the dinitrogenase reductase component of the molybdenum nitrogenase), we also identified sequences corresponding to vanadium and iron-only nitrogenase genes. Within the Chlorobi population, the nitrogenase (nifH) cluster was included in a well-structured retrotransposon. Furthermore, the presence of light-harvesting photosynthesis genes implies that anoxygenic photosynthesis may fuel nitrogen fixation under the prevailing low-irradiance conditions. The presence of rnf genes (related to the expression of H+/Na+-translocating ferredoxin: NAD+ oxidoreductase) in Methylococcales and Desulfobacterales suggests that other energy-generating processes may drive the costly N-fixation in the absence of photosynthesis. The highly reducing environment of the anoxic bottom layer of Trout Bog Lake may thus also provide a suitable niche for active N-fixers and primary producers. While future studies on the activity of these potential N-fixers are needed to clarify their role in freshwater nitrogen cycling, the metagenomic data presented here enabled an initial characterization of previously overlooked diazotrophs in freshwater biomes.

Light Regulation of Chlorophyll and Glycoalkaloid Biosynthesis During Tuber Greening of Potato S. tuberosum.

Potato, S. tuberosum, is one of the most important global crops, but has high levels of waste due to tuber greening under light, which is associated with the accumulation of neurotoxic glycoalkaloids. However, unlike the situation in de-etiolating seedlings, the mechanisms underlying tuber greening are not well understood. Here, we have investigated the effect of monochromatic blue, red, and far-red light on the regulation of chlorophyll and glycoalkaloid accumulation in potato tubers. Blue and red wavelengths were effective for induction and accumulation of chlorophyll, carotenoids and the two major potato glycoalkaloids, α-solanine and α-chaconine, whereas none of these accumulated in darkness or under far-red light. Key genes in chlorophyll biosynthesis (HEMA1, encoding the rate-limiting enzyme glutamyl-tRNA reductase, GSA, CHLH and GUN4) and six genes (HMG1, SQS, CAS1, SSR2, SGT1 and SGT2) required for glycoalkaloid synthesis were also induced under white, blue, and red light but not in darkness or under far-red light. These data suggest a role for both cryptochrome and phytochrome photoreceptors in chlorophyll and glycoalkaloid accumulation. The contribution of phytochrome was further supported by the observation that far-red light could inhibit white light-induced chlorophyll and glycoalkaloid accumulation and associated gene expression. Transcriptomic analysis of tubers exposed to white, blue, and red light showed that light induction of photosynthesis and tetrapyrrole-related genes grouped into three distinct groups with one group showing a generally progressive induction by light at both 6 h and 24 h, a second group showing induction at 6 h in all light treatments, but induction only by red and white light at 24 h and a third showing just a very moderate light induction at 6 h which was reduced to the dark control level at 24 h. All glycoalkaloid synthesis genes showed a group one profile consistent with what was seen for the most light regulated chlorophyll synthesis genes. Our data provide a molecular framework for developing new approaches to reducing waste due to potato greening.

Genetic manipulation of Soc1-like genes promotes photosynthesis in flowers and leaves and enhances plant tolerance to high temperature.

Genetic manipulation of Soc1-like genes promotes photosynthesis in flowers and leaves and enhances plant tolerance to high temperature.

Shifts in the Bacterial Population and Ecosystem Functions in Response to Vegetation in the Yellow River Delta Wetlands.

Vegetation represents probably the most crucial step for the ecosystem functions of wetlands, but it is unclear how microbial populations and functions shift along with vegetation. In this study, we found that the richness and diversity of soil bacteria increased with vegetation levels and that the community composition was distinctly shifted from bare to vegetative places. The bare land displayed an extremely high abundance of Cyanobacteria as a monospecies genus, while a Gemmatimonadetes genus was predominant as multiple species in all the vegetative wetlands, suggesting their important ecosystem functions and potential mechanisms. Expression of the genes related to photosynthesis was enriched exclusively in bare land. Genes involved in biological organic carbon metabolism and the cycling of main elements (C, N, S, and P) were highly expressed in vegetative wetlands and were mostly included in the metagenome-assembled genome (MAG) of Gemmatimonadetes Some compounds identified from soil metabolomic results also corresponded to pathways involving these key active genes. Cyanobacteria is thus responsible for the carbon sink in early infertile wetlands, and Gemmatimonadetes plays a crucial role in ecosystem functions in vegetative wetlands. Our results highlight that the soil microbial populations execute ecosystem functions for wetlands and that vegetation is the determinant for the population and functional shifts in the coastal estuarine wetland of the Yellow River Delta.IMPORTANCE Vegetation probably represents the most crucial step for the ecosystem functions of wetlands, but it is unclear how microbial populations and functions shift in pace with the colonization and succession of vegetation. In this study, we found that a Cyanobacteria monospecies genus and a Gemmatimonadetes multispecies genus are fastidiously predominant in the bare and vegetative wetlands of the Yellow River Delta, respectively. Consistently, photosynthesis genes were enriched exclusively in bare land, while genes involved in biological organic carbon metabolism and the cycling of main elements were highly expressed in vegetative wetlands, were mostly included in the MAG of Gemmatimonadetes, and were consistent with soil metabolomic results. Our results provide insight into the adaptive succession of predominant bacterial species and their ecosystem functions in response to the presence of vegetation.

Overexpression of maize transcription factor mEmBP-1 increases photosynthesis, biomass, and yield in rice.

Identifying new options to improve photosynthetic capacity is a major approach to improve crop yield potential. Here we report that overexpression of the gene encoding the transcription factor mEmBP-1 led to simultaneously increased expression of many genes in photosynthesis, including genes encoding Chl a,b-binding proteins (Lhca and Lhcb), PSII (PsbR3 and PsbW) and PSI reaction center subunits (PsaK and PsaN), chloroplast ATP synthase subunit, electron transport reaction components (Fd1 and PC), and also major genes in the Calvin-Benson-Bassham cycle, including those encoding Rubisco, glyceraldehyde phosphate dehydrogenase, fructose bisphosphate aldolase, transketolase, and phosphoribulokinase. These increased expression of photosynthesis genes resulted in increased leaf chlorophyll pigment, photosynthetic rate, biomass growth, and grain yield both in the greenhouse and in the field. Using EMSA experiments, we showed that mEmBP-1a protein can directly bind to the promoter region of photosynthesis genes, suggesting that the direct binding of mEmBP-1a to the G-box domain of photosynthetic genes up-regulates expression of these genes. Altogether, our results show that mEmBP-1a is a major regulator of photosynthesis, which can be used to increase rice photosynthesis and yield in the field.

Over-Expression of HDA710 Delays Leaf Senescence in Rice (Oryza sativa L.).

Histone deacetylases (HDACs) influence chromatin state and gene expression. Eighteen HDAC genes with important biological functions have been identified in rice. In this study, we surveyed the gene presence frequency of all 18 rice HDAC genes in 3,010 rice accessions. HDA710/OsHDAC2 showed insertion/deletion (InDel) polymorphisms in almost 98.8% japonica accessions but only 1% indica accessions. InDel polymorphism association analysis showed that accessions with partial deletions in HDA710 tended to display early leaf senescence. Further transgenic results confirmed that HDA710 delayed leaf senescence in rice. The over-expression of HDA710 delayed leaf senescence, and the knock-down of HDA710 accelerated leaf senescence. Transcriptome analysis showed that photosynthesis and chlorophyll biosynthesis related genes were up-regulated in HDA710 over-expression lines, while some programmed cell death and disease resistance related genes were down-regulated. Co-expression network analysis with gene expression view revealed that HDA710 was co-expressed with multiple genes, particularly OsGSTU12, which was significantly up-regulated in 35S::HDA710-sense lines. InDels in the promoter region of OsGSTU12 and in the gene region of HDA710 occurred coincidentally among more than 90% accessions, and we identified multiple W-box motifs at the InDel position of OsGSTU12. Over-expression of OsGSTU12 also delayed leaf senescence in rice. Taken together, our results suggest that both HDA710 and OsGSTU12 are involved in regulating the process of leaf senescence in rice.

Temperature-regulated anatomical and gene-expression changes in Sinopodophyllum hexandrum seedlings

Sinopodophyllum hexandrum is a high-altitude perennial medicinal plant that produces the economically-valued anticancer metabolite, podophyllotoxin (PPT). While gene profiling under elevated altitude and low temperature conditions have identified transcriptions associated with increased PPT accumulation, changes in cell structure, with adaptive low-temperature conditions have yet to be identified. In this study, anatomical features including leaf micro- and ultra-structure were investigated by monitoring traits when S. hexandrum seedlings were grown under a cooler temperature (15 °C). Differences in leaf micro- and ultra-structure parameters including stomatal density and shape, chloroplast density as well as the abundance of starch grain, osmiophilic granule and thylakoid grana were observed with the lower temperature. Greater chlorophyll content and higher tissue amounts (e.g. leaf area, number of petioles and root size) were also observed at the cooler temperature. These anatomical and morphological changes were associated with elevated PPT levels on a dry weight and per plant basis, as well increased whole plant fresh and dry weights. To link anatomical and morphological changes with elevated PPT levels, mRNA transcripts encoding for photosynthesis, glyco-metabolism, stress response and PPT biosynthesis select genes were monitored and found to be differentially regulated at 15 versus 22 °C. These cool-temperature anatomical/morphological changes are consistent with S. hexandrum’s capacity to biosynthesize and accumulate elevated PPT in cooler environments.

High salinity acclimatization alleviated cadmium toxicity in Dunaliella salina: Transcriptomic and physiological evidence

In the present study, we tested the hypothesis that high salinity acclimatization can mitigate cadmium (Cd) toxicity in the microalga Dunaliella salina. To this end, microalgal cells were subjected to high salinity (60 g/L) for 12 weeks until the growth rate remained stable between generations and were then exposed to 2.5 mg/L of Cd for 4 days. Acute Cd toxicity impaired cell growth by increasing Cd bioaccumulation and lipid peroxidation, which reduced cellular pigment, total protein, and glutathione content. It also significantly weakened photosynthetic efficiency and total antioxidant capacity. However, acclimatization to high salinity alleviated these negative effects under Cd stress. To understand the potential mechanisms behind this phenomenon, 12 cDNA libraries from control, Cd-exposed (Cd), high salinity-acclimated (Salinity), and high salinity-acclimated with Cd exposure (Salinity + Cd) cells were derived using RNA sequencing. A total of 2019, 1799, 2150 and 1256 differentially expressed genes (DEGs) were identified from sample groups Salinity / Control, Cd / Control, Salinity + Cd / Control, and Salinity + Cd / Cd, respectively. Some of these DEGs were significantly enriched in ribosome, photosynthesis, stress defense, and photosynthesis-antenna proteins. Among these genes, 82 ribosomal genes were up-regulated in Salinity / Control (corrected P = 3.8 × 10−28), while 81 were down-regulated in Cd / Control (corrected P = 1.1 × 10-24). Moreover, high salinity acclimatization up-regulated 8 photosynthesis genes and 18 stress defense genes compared with the control. Additionally, 3 photosynthesis genes, 11 stress defense genes and 11 genes encoding light harvesting proteins were up-regulated by high salinity acclimatization under Cd exposure. Overall, high salinity acclimatization mitigated Cd toxicity, possibly by up-regulating the transcription of photosynthesis, stress defense, and ribosomal genes. These results provide new insights on cross-tolerance in microalgae.

Phytoplankton transcriptomic and physiological responses to fixed nitrogen in the California current system.

Marine phytoplankton are responsible for approximately half of photosynthesis on Earth. However, their ability to drive ocean productivity depends on critical nutrients, especially bioavailable nitrogen (N) which is scarce over vast areas of the ocean. Phytoplankton differ in their preferences for N substrates as well as uptake efficiencies and minimal N requirements relative to other critical nutrients, including iron (Fe) and phosphorus. In this study, we used the MicroTOOLs high-resolution environmental microarray to examine transcriptomic responses of phytoplankton communities in the California Current System (CCS) transition zone to added urea, ammonium, nitrate, and also Fe in the late summer when N depletion is common. Transcript level changes of photosynthetic, carbon fixation, and nutrient stress genes indicated relief of N limitation in many strains of Prochlorococcus, Synechococcus, and eukaryotic phytoplankton. The transcriptomic responses helped explain shifts in physiological and growth responses observed later. All three phytoplankton groups had increased transcript levels of photosynthesis and/or carbon fixation genes in response to all N substrates. However, only Prochlorococcus had decreased transcript levels of N stress genes and grew substantially, specifically after urea and ammonium additions, suggesting that Prochlorococcus outcompeted other community members in these treatments. Diatom transcript levels of carbon fixation genes increased in response to Fe but not to Fe with N which might have favored phytoplankton that were co-limited by N and Fe. Moreover, transcription patterns of closely related strains indicated variability in N utilization, including nitrate utilization by some high-light adapted Prochlorococcus. Finally, up-regulation of urea transporter genes by both Prochlorococcus and Synechococcus in response to filtered deep water suggested a regulatory mechanism other than classic control via the global N regulator NtcA. This study indicated that co-existing phytoplankton strains experience distinct nutrient stresses in the transition zone of the CCS, an understudied region where oligotrophic and coastal communities naturally mix.

The Organelle Genomes in the Photosynthetic Red Algal Parasite Pterocladiophila hemisphaerica (Florideophyceae, Rhodophyta) Have Elevated Substitution Rates and Extreme Gene Loss in the Plastid Genome.

Comparative organelle genome studies of parasites can highlight genetic changes that occur during the transition from a free-living to a parasitic state. Our study focuses on a poorly studied group of red algal parasites, which are often closely related to their red algal hosts and from which they presumably evolved. Most of these parasites are pigmented and some show photosynthetic capacity. Here, we assembled and annotated the complete organelle genomes of the photosynthetic red algal parasite, Pterocladiophila hemisphaerica. The plastid genome is the smallest known red algal plastid genome at 68,701bp. The plastid genome has many genes missing, including all photosynthesis-related genes. In contrast, the mitochondrial genome is similar in architecture to that of other free-living red algae. Both organelle genomes show elevated mutation rates and significant changes in patterns of selection, measured as dN/dS ratios. This caused phylogenetic analyses, even of multiple aligned proteins, to be unresolved or give contradictory relationships. Full plastid datasets interfered by selected best gene evolution models showed the supported relationship of P.hemisphaerica within the Ceramiales, but the parasite was grouped with support as sister to the Gracilariales when interfered under the GHOST model. Nuclear rDNA showed a supported grouping of the parasite within a clade containing several red algal orders including the Gelidiales. This photosynthetic parasite, which is unable to photosynthesize with its own plastid due to the total loss of all photosynthesis genes, raises intriguing questions on parasite-host organelle genome capabilities and interactions.

Emerging from the darkness: interplay between light and plastid signaling during chloroplast biogenesis.

Chloroplast biogenesis is a highly complex process that requires carefully coordinated communication between the nucleus and the chloroplast to integrate light signaling and information about the state of the plastid through retrograde signals. Most studies on plastid development have been performed using dark-grown seedlings and have focused on the transition from etioplast to chloroplast in response to light. Some advances are now also being made to understand the transition directly from proplastids to chloroplasts as it occurs in the shoot apical meristems. Recent reports have highlighted the importance of repressive mechanisms to block premature chloroplast development in dark, both at the transcriptional and post-transcriptional level. A group of new proteins with dual plastid and nuclear localization were shown to take part in the light triggered degradation of PHYTOCHROME INTERACTING FACTORs (PIFs) in the nucleus and thereby release the suppression of the nuclear photosynthesis associated genes. These dually localized proteins are also required to activate transcription of photosynthesis genes in the plastid in response to light, emphasizing the close link between the nucleus and the plastids during early light response. Furthermore, development of a fully functional chloroplast requires a plastid signal but the nature of this signal(s) is still unknown. GENOMES UNCOUPLED1 (GUN1) is a plastid protein pivotal for retrograde signal(s) during early seedling development, and recent reports have revealed multiple interactors of GUN1 from different plastid processes. These new GUN1 interactors could reveal the true molecular function of the enigmatic character, GUN1, under naturally occurring adverse growth conditions.

A high-quality genome provides insights into the new taxonomic status and genomic characteristics of Cladopus chinensis (Podostemaceae)

The Podostemaceae are ecologically and morphologically unusual aquatic angiosperms that survive only in rivers with pristine hydrology and high water quality and are at a relatively high risk of extinction. The taxonomic status of Podostemaceae has always been controversial. Here, we report the first high-quality genome assembly for Cladopus chinensis of Podostemaceae, obtained by incorporating Hi-C, Illumina and PacBio sequencing. We generated an 827.92 Mb genome with a contig N50 of 1.42 Mb and 27,370 annotated protein-coding genes. The assembled genome size was close to the estimated size, and 659.42 Mb of the assembly was assigned to 29 superscaffolds (scaffold N50 21.22 Mb). A total of 59.20% repetitive sequences were identified, among which long terminal repeats (LTRs) were the most abundant class (28.97% of the genome). Genome evolution analysis suggested that the divergence time of Cladopus chinensis (106 Mya) was earlier than that of Malpighiales (82 Mya) and that this taxon diverged into an independent branch of Podestemales. A recent whole-genome duplication (WGD) event occurred 4.43 million years ago. Comparative genomic analysis revealed that the expansion and contraction of oxidative phosphorylation, photosynthesis and isoflavonoid metabolism genes in Cladopus chinensis are probably related to the genomic characteristics of this growing submerged species. Transcriptome analysis revealed that upregulated genes in the shoot group compared to the root group were enriched in the NAC gene family and transcription factors associated with shoot development and defense responses, including WUSCHEL (WUS), ASYMMETRIC LEAVES (ASL), SHOOT MERISTEMLESS (STM), NAC2, NAC8, NAC29, NAC47, NAC73, NAC83 and NAC102. These findings provide new insights into the genomic diversity of unusual aquatic angiosperms and serve as a valuable reference for the taxonomic status and unusual shoot apical meristem of Podostemaceae.

Influence of Exogenous Hydrogen Peroxide on Plant Physiology, Leaf Anatomy and Rubisco Gene Expression of the Ficus deltoidea Jack var. Deltoidea

This study was carried out to investigate the regulatory effects of hydrogen peroxide (H2O2) on the growth, photosynthesis, biochemical properties, leaf anatomy and Rubisco gene expression in Ficus deltoidea var. deltoidea, a slow-growing medicinal herb. Results showed that 20-mM H2O2 treatment increased plant height, net photosynthetic rate, stomatal conductance and chlorophyll content of the plants by 10%, 20%, 127% and 57%, respectively, than a control plant. In addition, 20 mM H2O2 treatment significantly increased the carotene, total phenolic, total flavonoid and total sugar content than the control plant. The applications of H2O2 did not produce any negative effects on the leaf area, chlorophyll fluorescence, quantum yield or antioxidant activity of F. deltoidea plants. In regard to leaf anatomy, it was observed that the applications of H2O2 at 15 mM significantly improved cellular structure, leaf veins and promoted cell proliferation. Treated leaves developed a palisade layer, thickened leaf surface, the widest stomatal openings and a well-developed vascular bundle when compared to the control plant. Employing reverse transcription polymerase chain reaction (RT-PCR), the study showed that the Rubisco gene was expressed at a higher level in 15 mM H2O2 treatments than in 20 mM H2O2 treatments. The results indicate that H2O2 increased the Rubisco expression ratio up to 16-fold when compared to the untreated plants. It was conclusive that spraying 15 mM and 20 mM H2O2 twice a week enhanced growth, photosynthesis, the stomatal aperture, improved leaf anatomy and helped to regulate the expression of the Rubisco gene.

Biogeography of American Northwest Hot Spring A/B'-Lineage Synechococcus Populations.

Previous analyses have shown how diversity among unicellular cyanobacteria inhabiting island-like hot springs is structured relative to physical separation and physiochemical differences among springs, especially at local to regional scales. However, these studies have been limited by the low resolution provided by the molecular markers surveyed. We analyzed large datasets obtained by high-throughput sequencing of a segment of the photosynthesis gene psaA from samples collected in hot springs from geothermal basins in Yellowstone National Park, Montana, and Oregon, all known from previous studies to contain populations of A/B′-lineage Synechococcus. The fraction of identical sequences was greater among springs separated by <50 km than among springs separated by >50 km, and springs separated by >800 km shared sequence variants only rarely. Phylogenetic analyses provided evidence for endemic lineages that could be related to geographic isolation and/or geochemical differences on regional scales. Ecotype Simulation 2 was used to predict putative ecotypes (ecologically distinct populations), and their membership, and canonical correspondence analysis was used to examine the geographical and geochemical bases for variation in their distribution. Across the range of Oregon and Yellowstone, geographical separation explained the largest percentage of the differences in distribution of ecotypes (9.5% correlated to longitude; 9.4% to latitude), with geochemical differences explaining the largest percentage of the remaining differences in distribution (7.4–9.3% correlated to magnesium, sulfate, and sulfide). Among samples within the Greater Yellowstone Ecosystem, geochemical differences significantly explained the distribution of ecotypes (6.5–9.3% correlated to magnesium, boron, sulfate, silicon dioxide, chloride, and pH). Nevertheless, differences in the abundance and membership of ecotypes in Yellowstone springs with similar chemistry suggested that allopatry may be involved even at local scales. Synechococcus populations have diverged both by physical isolation and physiochemical differences, and populations on surprisingly local scales have been evolving independently.

Enhancement of salt tolerance in maize (Zea mays L.) using locally isolated Bacillus sp. SR-2-1/1

The current study was aimed at enhancement of salt tolerance of maize by using a halotolerant plant growth promoting rhizobacterium. Maize seeds (FH-1137) were grown under salt stress with and without inoculation of a locally isolated Bacillus sp. SR-2-1/1. Inoculation of Bacillus sp. SR-2-1/1 significantly augmented the salt tolerance of maize plants which was reflected by increased contents of chlorophyll, total phenolics and proline. Moreover, inoculation of strain SR-2-1/1 resulted in less oxidative damage in terms of H2O2 production and lipid peroxidation. This was further supported by higher catalase and peroxidase production in these plants. Bacillus sp. SR-2-1/1 exhibited positive effects on the expression of photosynthesis (RBCL), antioxidants status (CAT1, APX1, APX2) and plant ion homeostasis (NHX1, SOS1, H+-PPase, and HKT1) related genes. To the best of our knowledge, this is the first study reporting enhancement of salt tolerance in maize genotype FH-1137 by using plant growth promoting rhizobacterium. The use of Bacillus sp. SR-2-1/1 as bio-inoculant seems to be a sustainable alternative to alleviate salt-induced damages in maize. This approach can be applied to other plant species to increase salt tolerance.

Ectopic expression of C4 photosynthetic pathway genes improves carbon assimilation and alleviate stress tolerance for future climate change.

Alteration in atmospheric carbon dioxide concentration and other environmental factors are the significant cues of global climate change. Environmental factors affect the most fundamental biological process including photosynthesis and different metabolic pathways. The feeding of the rapidly growing world population is another challenge which imposes pressure to improve productivity and quality of the existing crops. C4 plants are considered the most productive, containing lower photorespiration, and higher water-use & N-assimilation efficiencies, compared to C3 plants. Besides, the C4-photosynthetic genes not only play an important role in carbon assimilation but also modulate abiotic stresses. In this review, fundamental three metabolic processes (C4, C3, and CAM) of carbon dioxide assimilation, the evolution of C4-photosynthetic genes, effect of elevated CO2 on photosynthesis, and overexpression of C4-photosynthetic genes for higher photosynthesis were discussed. Kranz-anatomy is considered an essential prerequisite for the terrestrial C4 carbon assimilation, but single-celled C4 plant species changed this well-established paradigm. C4 plants are insensitive to an elevated CO2 stress condition but performed better under stress conditions. Overexpression of essential C4-photosynthetic genes such as PEPC, PPDK, and NADP-ME in C3 plants like Arabidopsis, tobacco, rice, wheat, and potato not only improved photosynthesis but also provided tolerance to various environmental stresses, especially drought. The review provides useful information for sustainable productivity and yield under elevated CO2 environment, which to be explored further for CO2 assimilation and also abiotic stress tolerance. Additionally, it provides a better understanding to explore C4-photosynthetic gene(s) to cope with global warming and prospective adverse climatic changes.

Tissue-specific changes in the RNA structurome mediate salinity response in Arabidopsis.

Little is known concerning the effects of abiotic factors on in vivo RNA structures. We applied Structure-seq to assess the in vivo mRNA structuromes of Arabidopsis thaliana under salinity stress, which negatively impacts agriculture. Structure-seq utilizes dimethyl sulfate reactivity to identify As and Cs that lack base-pairing or protection. Salt stress refolded transcripts differentially in root versus shoot, evincing tissue specificity of the structurome. Both tissues exhibited an inverse correlation between salt stress-induced changes in transcript reactivity and changes in abundance, with stress-related mRNAs showing particular structural dynamism. This inverse correlation is more pronounced in mRNAs wherein the mean reactivity of the 5′UTR, CDS, and 3′UTR concertedly change under salinity stress, suggesting increased susceptibility to abundance control mechanisms in transcripts exhibiting this phenomenon, which we name “concordancy.” Concordant salinity-induced increases in reactivity were notably observed in photosynthesis genes, thereby implicating mRNA structural loss in the well-known depression of photosynthesis by salt stress. Overall, changes in secondary structure appear to impact mRNA abundance, molding the functional specificity of the transcriptome under stress.