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Ecological adaptation shaped the genetic structure of homoploid ferns against strong dispersal capacity
No full textThe formation of spatial genetic structure with the presence of extensive gene flow, an evolutionary force which is generally expected to eliminate population-specific variation and maintain genetic homogeneity, remains poorly understood. Homosporous ferns, which spread by spores through wind and possess long distance dispersal capacity, provide an ideal system to investigate such a process. Here, using a homoploid fern lineage, the Athyrium sinense complex, we used reduced-representation genomic data to examine spatial genetic structure and explored potential driving forces including geographical distance, environment, climatic history and external dispersal constraints. Our findings showed a clear north-south divergence at the genetic, morphological and ecological levels between both sides of 35 degrees N in East Asia. Fluctuant and heterogeneous climatic condition was demonstrated to play a crucial role during the formation of the divergence. Our results suggested that this lineage was able to migrate southward and colonize new habitat as a result of the Quaternary climatic fluctuation. Furthermore, the present genetic structure is attributed to adaptation to heterogeneous environments, especially temperature difference. In addition to ecological adaptation, we found clues showing that canopy density, wind direction as well as habitat continuity were all likely to constrain the effect of gene flow. These results demonstrated a diversification process without ploidy changes in ferns providing new insights for our present knowledge on ferns' spatio-temporal evolutionary pattern. In particular, our study highlights the influence of environmental heterogeneity in driving genetic divergence against strong dispersal capacity
TIME FOR COFFEE regulates phytochrome A-mediated hypocotyl growth through dawn-phased signaling
No full textTo enhance plant fitness under natural conditions, the circadian clock is synchronized and entrained by light via photoreceptors. In turn, the circadian clock exquisitely regulates the abundance and activity of photoreceptors via largely uncharacterized mechanisms. Here we show that the clock regulator TIME FOR COFFEE (TIC) controls the activity of the far-red light photoreceptor phytochrome A (phyA) at multiple levels in Arabidopsis thaliana. Null mutants of TIC displayed dramatically increased sensitivity to light irradiation with respect to hypocotyl growth, especially to far-red light. RNA-sequencing demonstrated that TIC and phyA play largely opposing roles in controlling light-regulated gene expression at dawn. Additionally, TIC physically interacts with the transcriptional repressor TOPLESS (TPL), which was associated with the significantly increased PHYA transcript levels in the tic-2 and tpl-1 mutants. Moreover, TIC interacts with phyA in the nucleus, thereby affecting phyA protein turnover and the formation of phyA nuclear speckles following light irradiation. Genetically, phyA was found to act downstream of TIC in regulating far red light-inhibited growth. Taken together, these findings indicate that TIC acts as a major negative regulator of phyA by integrating transcriptional and post-translational mechanisms at multiple levels. TIME FOR COFFEE positively regulates far-red light inhibited hypocotyl growth in Arabidopsis by managing the accumulation of the dawn-phased photoreceptor phytochrome A
Different facets of bacterial and fungal communities drive soil multifunctionality in grasslands spanning a 3500 km transect
No full textSoil microbial communities are essential in regulating ecosystem functions and services. However, the importance of bacterial and fungal communities as predictors of multiple soil functions (i.e. soil multifunctionality) in grassland ecosystems has not been studied systematically. Here, we measured soil microbial diversity, community composition, biomass and multiple soil functions of 41 sites in five grassland ecosystems spanning a 3500 km northeast-southwest transect. The random forest algorithm was adopted to determine the importance of geographical location, climatic, altitude, edaphic, plant and microbial predictors in driving a proxy of soil multifunctionality (seven soil functions in this study). Moreover, structural equation models were employed to examine the direct and indirect effects of those predictors on soil multifunctionality. Our results demonstrated that soil multifunctionality was positively driven by soil fungal diversity but not by bacterial diversity. Fungal phylogenetic diversity (presence of different evolutionary lineages) showed stronger positive relationships with soil multifunctionality than taxonomic diversity (richness of species). Dominant bacterial taxa, particularly of phyla Actinobacteria and Proteobacteria, were positively associated with soil multifunctionality, while none of the fungal taxa were found to regulate soil multifunctionality. Furthermore, both fungal and bacterial biomass had significant effects on soil multifunctionality, while the effect of microbial biomass was weaker than that of fungal diversity and bacterial taxa. Importantly, the direct positive effects of soil fungal diversity, dominant bacterial taxa, and fungal and bacterial biomass were maintained after accounting for multiple predictors in grassland ecosystems. This study provided strong empirical evidence that soil multifunctionality was driven by different facets of the bacterial and fungal communities in the grassland ecosystems. Our results also highlighted that any loss of fungal diversity, dominant bacterial taxa and microbial biomass might reduce soil multifunctionality, exacerbating ecosystem functions and services such as soil fertility, primary production and climate mitigation in grassland ecosystems. Read the free Plain Language Summary for this article on the Journal blog
Stocking rate changed the magnitude of carbon sequestration and flow within the plant-soil system of a meadow steppe ecosystem
No full textAims Livestock grazing is one of the most common utilization methods and exerts a significant effect on the carbon allocations between the above- and belowground components of a grassland ecosystem. The major aim of this study were to evaluate the proportions of C-13 allocation to various C pools of the plant-soil system of a meadow steppe ecosystem in response to changes of stocking rate. Methods In situ stable C-13 isotope pulse labeling was conducted in a long-term grazing experiment with 4 stocking rate. Plant materials and soil samples were taken at eight occasions (0, 3, 10, 18, 31, 56 and 100 days after labeling) to analyze the decline in C-13 over time, and their composition signature of C-13 were analyzed by the isotope ratio mass spectrometer technique. Results We found a significantly greater decline in assimilated C-13 of shoot and living root for the heavily grazed swards compared to other stocking rates, with the highest relocation rate of C-13 into soil C pool compared to other fractions. In addition, light grazing significantly allocated C-13 assimilates in the belowground pool compared to other stocking rates, especially in the live root and topsoil C-pools. Conclusions In this study, the effects of grazing on the carbon transfers and stocks within the plant-soil system of the meadow steppe were highly grazing pressure dependent. Plant-soil system in light stocking rate presented the highest C utilization efficiency, however, plants allocated more C to soil C pools with heavily stocking rate
Genome-wide association study and metabolic pathway prediction of barrenness in maize as a response to high planting density
No full textIncreasing the planting density is one way to enhance grain production in maize. However, high planting density brings about growth and developmental defects such as barrenness, which is the major factor limiting grain yield. In this study, the barrenness was characterized in an association panel comprising 280 inbred lines under normal (67 500 plants ha-1, ND) and high (120 000 plants ha-1, HD) planting densities in 2017 and 2018. The population was genotyped using 776 254 single nucleotide polymorphism (SNP) markers with criteria of minor allele frequency >5% and <20% missing data. A genome-wide association study (GWAS) was conducted for barrenness under ND and HD, as well as the barrenness ratio (HD/ND), by applying a Mixed Linear Model that controls both population structure and relative kinship (Q+K). In total, 20 SNPs located in nine genes were significantly (P<6.44x10-8) associated with barrenness under the different planting densities. Among them, seven SNPs for barrenness at ND and HD were located in two genes, four of which were common under both ND and HD. In addition, 13 SNPs for the barrenness ratio were located in seven genes. A complementary pathway analysis indicated that the metabolic pathways of amino acids, such as glutamate and arginine, and the mitogen-activated protein kinase (MAPK) signaling pathway might play important roles in tolerance to high planting density. These results provide insights into the genetic basis of high planting density tolerance and will facilitate high yield maize breeding
Scaling-up and proteomic analysis reveals photosynthetic and metabolic insights toward prolonged H2 photoproduction in Chlamydomonas hpm91 mutant lacking proton gradient regulation 5 (PGR5)
No full textClean and sustainable H-2 production is crucial to a carbon-neutral world. H-2 generation by Chlamydomonas reinhardtii is an attractive approach for solar-H-2 from H2O. However, it is currently not large-scalable because of lacking desirable strains with both optimal H-2 productivity and sufficient knowledge of underlying molecular mechanism. We hereby carried out extensive and in-depth investigations of H-2 photoproduction of hpm91 mutant lacking PGR5 (Proton Gradient Regulation 5) toward its up-scaling and fundamental mechanism issues. We show that hpm91 is at least 100-fold scalable (up to 10 L) with continuous H-2 collection of 7287 ml H-2/10L-HPBR in averagely 26 days under sulfur deprivation. Also, we show that hpm91 is robust and active during sustained H-2 photoproduction, most likely due to decreased intracellular ROS relative to wild type. Moreover, we obtained quantitative proteomic profiles of wild type and hpm91 at four representing time points of H-2 evolution, leading to 2229 and 1350 differentially expressed proteins, respectively. Compared to wild type, major proteome alterations of hpm91 include not only core subunits of photosystems and those related to anti-oxidative responses but also essential proteins in photosynthetic antenna, C/N metabolic balance, and sulfur assimilation toward both cysteine biosynthesis and sulfation of metabolites during sulfur-deprived H-2 production. These results reveal not only new insights of cellular and molecular basis of enhanced H-2 production in hpm91 but also provide additional candidate gene targets and modules for further genetic modifications and/or in artificial photosynthesis mimics toward basic and applied research aiming at advancing solar-H-2 technology
Transgenerational effects of elevated CO2 on rice photosynthesis and grain yield
No full textKey message The maternal carbon dioxide environment affected the responses of offspring to elevated carbon dioxide with regard to stomatal density, photosynthesis and yield. The responses of crops to rising carbon dioxide concentration ([CO2]) are often validated using single-generation short-term experiments. However, the transgenerational effects of elevated [CO2] on rice growth have received little attention. Here, we set up ambient [CO2] (a[CO2]) and elevated [CO2] (e[CO2], a[CO2] + 200 mu mol mol(-1)) treatments using open-top chamber (OTC). Rice was cultivated in different [CO2] treatments over five growing seasons in 2016-2020. Beginning in 2017, rice seeds harvested in the previous year under a[CO2] and e[CO2] conditions were planted in their respective growing environments. In 2021, seedlings derived from a[CO2] maternal treatment (a[CO2](m)) and e[CO2] maternal treatment (e[CO2](m)) were planted with both a[CO2] offspring (a[CO2](o)) and e[CO2] offspring (e[CO2](o)) conditions to investigate the transgenerational effects of e[CO2]. Leaf gas exchange and grain yield under different conditions were determined in 2021. The results showed that light-saturated net photosynthesis (A(sat)) and stomatal conductance of offspring from e[CO2](m) were significantly lower at the heading and grain-filling stages under e[CO2](o) compared with a[CO2](m), and the corresponding stomatal density was also significantly lower. Moreover, A(sat) was positively correlated with stomatal density. These results suggest that transgenerational effects induce a decrease in stomatal density and thus cause a lower benefit of A(sat) from e[CO2](o). These findings contribute new insights into predicting crop growth and yield in the future
Diversity, phylogeny, and adaptation of bryophytes: insights from genomic and transcriptomic data
No full textWe review recent advances in the knowledge of bryophyte diversity, phylogeny, and adaptation made using genomic and transcriptomic data, and particularly emphasize their adaptation to early land environments and modern ecosystems. Bryophytes including mosses, liverworts, and hornworts are among the earliest land plants, and occupy a crucial phylogenetic position to aid in the understanding of plant terrestrialization. Despite their small size and simple structure, bryophytes are the second largest group of extant land plants. They live ubiquitously in various habitats and are highly diversified, with adaptive strategies to modern ecosystems on Earth. More and more genomes and transcriptomes have been assembled to address fundamental questions in plant biology. Here, we review recent advances in bryophytes associated with diversity, phylogeny, and ecological adaptation. Phylogenomic studies have provided increasing supports for the monophyly of bryophytes, with hornworts sister to the Setaphyta clade including liverworts and mosses. Further comparative genomic analyses revealed that multiple whole-genome duplications might have contributed to the species richness and morphological diversity in mosses. We highlight that the biological changes through gene gain or neofunctionalization that primarily evolved in bryophytes have facilitated the adaptation to early land environments; among the strategies to adapt to modern ecosystems in bryophytes, desiccation tolerance is the most remarkable. More genomic information for bryophytes would shed light on key mechanisms for the ecological success of these 'dwarfs' in the plant kingdom
Sharing of nitrogen between connected ramets of Alternanthera philoxeroides in homogeneous environments
No full textPurpose Benefits of clonal integration have been widely documented in clonal species, but quantitative tests of the translocation of resources in both directions between older and younger ramets (e.g., transport rate and partitioning pattern) are still scarce. Methods A control experiment, using a clonal species Alternanthera philoxeroides as plant material and the technique of N-15 isotope, was conducted to quantify the transport rate of nitrogen (N) in two opposite directions (i.e., from younger to older ramets or the other way around) within a clone, and the partitioning proportion of N in recipient ramets. Results The amount of N-15 transported toward the apical part was markedly reduced at the higher external N level, whereas the amount of N-15 transported toward the basal part was unrelated to the external N levels. The rate of N-15 acropetal transport basically averaged 20.9%, and the rate of N-15 basipetal transport generally ranged between 0.2% and 6.3%, both being negatively dependent of Delta PNC (i.e., difference in plant N concentration [PNC] between apical and basal parts). The proportion of N-15 in stems and leaves averaged 74.7% and 18.1%, respectively; the proportion of root N-15 in the apical part significantly decreased from 7.6% to 0.4% when acropetal transport occurred. Conclusion These results suggest that N sharing between connected ramets tended to be acropetal and the partitioning pattern of N is organ-specific in A. philoxeroides, which potentially contributes to the early development of young ramets, and also to the spread of A. philoxeroides in limited N conditions
Arabidopsis F-BOX STRESS INDUCED 4 is required to repress excessive divisions in stomatal development
No full textDuring the terminal stage of stomatal development, the R2R3-MYB transcription factors FOUR LIPS (FLP/MYB124) and MYB88 limit guard mother cell division by repressing the transcript levels of multiple cell-cycle genes. In Arabidopsis thaliana possessing the weak allele flp-1, an extra guard mother cell division results in two stomata having direct contact. Here, we identified an ethylmethane sulfonate-mutagenized mutant, flp-1 xs01c, which exhibited more severe defects than flp-1 alone, producing giant tumor-like cell clusters. XS01C, encoding F-BOX STRESS-INDUCED 4 (FBS4), is preferentially expressed in epidermal stomatal precursor cells. Overexpressing FBS4 rescued the defective stomatal phenotypes of flp-1 xs01c and flp-1 mutants. The deletion or substitution of a conserved residue (Proline166) within the F-box domain of FBS4 abolished or reduced, respectively, its interaction with Arabidopsis Skp1-Like1 (ASK1), the core subunit of the Skp1/Cullin/F-box E3 ubiquitin ligase complex. Furthermore, the FBS4 protein physically interacted with CYCA2;3 and induced its degradation through the ubiquitin-26S proteasome pathway. Thus, in addition to the known transcriptional pathway, the terminal symmetric division in stomatal development is ensured at the post-translational level, such as through the ubiquitination of target proteins recognized by the stomatal lineage F-box protein FBS4