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A new species of Pinus (Pinaceae) from the Miocene of Weichang, Hebei Province, China and its evolutionary significance
No full textPinus (Pinaceae) is the largest genus of the conifers, characterised by needle-leaves usually in fascicles of 2-5 and seed cones with highly specialised and diversified apophyses and umbos. Although a denticulatomucronate umbo is the most common umbo type in the subsection Pinus, genus Pinus, this type has not been well documented in the fossil record of East Asia. Here, we describe exquisitely preserved seed cones and associated needles as Pinus weichangensis sp. nov. from the early Miocene of Weichang County, Hebei Province of China. The new species is characterised by ovoid and symmetrical seed cones with flat to shortly pyramidal apophyses, avallate umbos, and predominantly denticulate and non-geniculate mucros, associated needles in fascicles of two, fascicles persistent, leaf stomata sunken and encircled by Florin rings of type B-C. The character combination of the new species supports the assignment of it to the subsection Pinus, section Pinus, subgenus Pinus, genus Pinus. Detailed comparisons with related extant and fossil species indicate that P. weichangensis has close resemblance with an extant denticulatomucronate species P. thunbergii Parl. Our study suggests that P. thunbergii, native to Japan and South Korea, may have diversified from a continental Asian species such as P. weichangensis
Depth-dependent drivers of soil microbial necromass carbon across Tibetan alpine grasslands
No full textMicrobial necromass carbon (C) has been considered an important contributor to persistent soil C pool. However, there still lacks large-scale systematic observations on microbial necromass C in different soil layers, particularly for alpine ecosystems. Besides, it is still unclear whether the relative importance of biotic and abiotic variables such as plant C input and mineral properties in regulating microbial necromass C would change with soil depth. Based on the combination of large-scale sampling along a similar to 2200 km transect across Tibetan alpine grasslands and biomarker analysis, together with a global data synthesis across grassland ecosystems, we observed a relatively low proportion of microbial-derived C in Tibetan alpine grasslands compared to global grasslands (topsoil: 45.4% vs. 58.1%; subsoil: 41.7% vs. 53.7%). We also found that major determinants of microbial necromass C depended on soil depth. In topsoil, both plant C input and mineral protection exerted dominant effects on microbial necromass C. However, in subsoil, the physico-chemical protection provided by soil clay particles, iron-aluminum oxides, and exchangeable calcium dominantly facilitated the preservation of microbial necromass C. The differential drivers over microbial necromass C between soil depths should be considered in Earth system models for accurately forecasting soil C dynamics and its potential feedback to global warming
Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics
No full textComplete and accurate reference genomes and annotations provide fundamental resources for functional genomics and crop breeding. Here we report a de novo assembly and annotation of a pea cultivar ZW6 with contig N50 of 8.98 Mb, which features a 243-fold increase in contig length and evident improvements in the continuity and quality of sequence in complex repeat regions compared with the existing one. Genome diversity of 118 cultivated and wild pea demonstrated that Pisum abyssinicum is a separate species different from P. fulvum and P. sativum within Pisum. Quantitative trait locus analyses uncovered two known Mendel's genes related to stem length (Le/le) and seed shape (R/r) as well as some candidate genes for pod form studied by Mendel. A pan-genome of 116 pea accessions was constructed, and pan-genes preferred in P. abyssinicum and P. fulvum showed distinct functional enrichment, indicating the potential value of them as pea breeding resources in the future. A high-quality genome assembly of pea cultivar ZW6 and pan-genome analyses provide insights into pea genome evolution and domestication as well as genomic resources for pea improvement
Extreme Winter Storms Have Variable Effects on the Population Dynamics of Canopy Dominant Species in an Old-Growth Subtropical Forest
No full textExtreme climatic events are predicted to increase in frequency and magnitude as global climate change continues. Extreme climatic events have profound impacts on community structure and dynamics, but their effects on the dominant species within a community remains unclear. To explore this issue, we analyzed changes in population dynamics and dead individuals' spatial pattern for several dominant species (Castanopsis eyrei, Schima superba, Pinus massoniana, and Daphniphyllum oldhamii) among different habitats in a subtropical forest before and after a significant winter storm that occurred in February 2008. Using the Gutianshan 24-ha forest plot as a representative sample, we found that the plot-level DBH of P. massoniana and C. eyrei significantly increased after the winter storm, while the plot-level basal area of P. massoniana and S. superba decreased significantly. In addition, P. massoniana was most affected by the storm (mortality: 9.08%; population change rate: -8.93%), followed by C. eyrei (mortality: 6.93%; population change rate: -4.91%). Small-diameter individuals experienced higher mortality rates, but the diameter structure of the dominant species at the population level remained basically stable. The number of individuals, the density of the dominant population, the number of mortalities, and the mortality rate of the dominant species differed among habitats. The spatial point patterns of the dead individuals at each life stage were mainly aggregated in distribution, and the degree of aggregation tended to decrease with increasing scale. In conclusion, the population dynamics of dominant species were significantly altered following the winter storm, but the extent of the changes varied with species. Our study suggests that analyzing the dominant species of a community contributes to a better understanding of the biological response of forest ecosystems in the face of extreme climatic events
DNA demethylation affects imprinted gene expression in maize endosperm
No full textBackground: DNA demethylation occurs in many species and is involved in diverse biological processes. However, the occurrence and role of DNA demethylation in maize remain unknown. Results: We analyze loss-of-function mutants of two major genes encoding DNA demethylases. No significant change in DNA methylation has been detected in these mutants. However, we detect increased DNA methylation levels in the mutants around genes and some transposons. The increase in DNA methylation is accompanied by alteration in gene expression, with a tendency to show downregulation, especially for the genes that are preferentially expressed in endosperm. Imprinted expression of both maternally and paternally expressed genes changes in F-1 hybrid with the mutant as female and the wild-type as male parental line, but not in the reciprocal hybrid. This alteration in gene expression is accompanied by allele-specific DNA methylation differences, suggesting that removal of DNA methylation of the maternal allele is required for the proper expression of these imprinted genes. Finally, we demonstrate that hypermethylation in the double mutant is associated with reduced binding of transcription factor to its target, and altered gene expression. Conclusions: Our results suggest that active removal of DNA methylation is important for transcription factor binding and proper gene expression in maize endosperm
Does the Spatial Pattern of Plants and Green Space Affect Air Pollutant Concentrations? Evidence from 37 Garden Cities in China
No full textRelevant studies have demonstrated that urban green spaces composed of various types of plants are able to alleviate the morbidity and mortality of respiratory diseases, by reducing air pollution levels. In order to explore the relationship between the spatial pattern of urban green spaces and air pollutant concentrations, this study takes 37 garden cities with subtropical monsoon climate in China as the research object and selects the urban air quality monitoring data and land use type data in 2019 to analyze the relationship between the spatial pattern and the air pollutant concentration through the landscape metrics model and spatial regression model. Moreover, the threshold effect of the impact of green space on air pollutant concentrations is estimated, as well. The results showed that the spatial pattern of urban green space was significantly correlated with the concentrations of PM2.5 (PM with aerodynamic diameters of 2.5 mmor less), NO2 (Nitrogen Dioxide), and SO2 (Sulfur dioxide) pollutants in the air, while the concentrations of PM10 (PM with aerodynamic diameters of 10 mmor less) pollutants were not significantly affected by the green space pattern. Among them, the patch shape index (LSI), patch density (PD) and patch proportion in landscape area (PLAND) of forest land can affect the concentration of PM2.5, NO2, and SO2, respectively. The PLAND, PD, and LSI of grassland and farmland can also have an additional impact on the concentration of SO2 pollutants. The study also found that there was a significant threshold effect within the impact mechanism of urban green space landscape pattern indicators (LSI, PD, PLAND) on the concentrations of PM2.5, NO2, and SO2 air pollutants. The results of this study not only clarified the impact mechanism of the spatial pattern of urban green space on air pollutant concentrations but also provided quantitative reference and scientific basis for the optimization and updating of urban green space to promote public health
An LH1-RC photocomplex from an extremophilic phototroph provides insight into origins of two photosynthesis proteins
No full textThe cryo-EM structure of the unusual light-harvesting 1-reaction center (LH1-RC) complex from Rpi. globiformis, the most acidophilic anaerobic purple bacteria, is presented, characterized and compared to other photosynthetic bacteria. Rhodopila globiformis is the most acidophilic of anaerobic purple phototrophs, growing optimally in culture at pH 5. Here we present a cryo-EM structure of the light-harvesting 1-reaction center (LH1-RC) complex from Rhodopila globiformis at 2.24 angstrom resolution. All purple bacterial cytochrome (Cyt, encoded by the gene pufC) subunit-associated RCs with known structures have their N-termini truncated. By contrast, the Rhodopila globiformis RC contains a full-length tetra-heme Cyt with its N-terminus embedded in the membrane forming an alpha-helix as the membrane anchor. Comparison of the N-terminal regions of the Cyt with PufX polypeptides widely distributed in Rhodobacter species reveals significant structural similarities, supporting a longstanding hypothesis that PufX is phylogenetically related to the N-terminus of the RC-bound Cyt subunit and that a common ancestor of phototrophic Proteobacteria contained a full-length tetra-heme Cyt subunit that evolved independently through partial deletions of its pufC gene. Eleven copies of a novel gamma-like polypeptide were also identified in the bacteriochlorophyll a-containing Rhodopila globiformis LH1 complex; gamma-polypeptides have previously been found only in the LH1 of bacteriochlorophyll b-containing species. These features are discussed in relation to their predicted functions of stabilizing the LH1 structure and regulating quinone transport under the warm acidic conditions
Species-specific coupling of tree-ring width and litter production in a temperate mixed forest
No full textTree growth is delineated into multiple processes, such as foliar growth, stem growth, and reproductive growth; however, only stem growth can store carbon in forests at a relatively long time scale. Understanding how these processes interact in response to climate change is of utmost importance for predicting the future carbon fixation ability of forests. However, it largely remains an unresolved question. To bridge this knowledge gap, we collected litter and tree-ring samples of two deciduous tree species, i.e. Larix principis-rupprechtii and Quercus liaotungensis, in a temperate mixed forest on Dongling Mountain in northern China. The influence of climate and the coupling characteristics between leaf/needle litter, fruit/cone litter, and tree-ring width (TRW) were analysed. The results highlighted that leaf/needle production was significantly and positively coupled with TRW for both species, but with one-year time lag for larch. Path analysis revealed that climate changes directly and significantly affected fruit production, which in turn indirectly affected TRW for oak trees, but such effect of cone production on TRW was not significant for larch trees. Additionally, we found that the radial growth of oak trees is more sensitive to drought stress than larch, possibly due to the close coupling between leaf biomass and TRW. Our results demonstrated that the coupling characteristics between different components of tree growth are species-specific, and understanding these relationships is of great significance for improving the tree growth model of forest ecosystems
CLE peptides: critical regulators for stem cell maintenance in plants
No full textMain conclusion Plant CLE peptides, which regulate stem cell maintenance in shoot and root meristems and in vascular bundles through LRR family receptor kinases, are novel, complex, and to some extent conserved. Over the past two decades, peptide ligands of the CLAVATA3 (CLV3) /Embryo Surrounding Region (CLE) family have been recognized as critical short- and long-distance communication signals in plants, especially for stem cell homeostasis, cell fate determination and physiological responses. Stem cells located at the shoot apical meristem (SAM), the root apical meristem (RAM) and the procambium divide and differentiate into specialized cells that form a variety of tissues such as epidermis, ground tissues, xylem and phloem. In the SAM of Arabidopsis (Arabidopsis thaliana), the CLV3 peptide restricts the number of stem cells via leucine-rich repeat (LRR)-type receptor kinases. In the RAM, root-active CLE peptides are critical negative regulators, while ROOT GROWTH FACTOR (RGF) peptides are positive regulators in stem cell maintenance. Among those root-active CLE peptides, CLE25 promotes, while CLE45 inhibits phloem differentiation. In vascular bundles, TRACHEARY ELEMENT DIFFERENTIATION INHIBITORY FACTOR (TDIF)/CLE41/CLE44 promotes procambium cell division, and prevents xylem differentiation. Orthologs of CLV3 have been identified in liverwort (Marchantia polymorpha), tomato (Solanum lycopersicum), rice (Oryza sativa), maize (Zea mays) and lotus (Lotus japonicas), suggesting that CLV3 is an evolutionarily conserved signal in stem cell maintenance. However, functional characterization of endogenous CLE peptides and corresponding receptor kinases, and the downstream signal transduction has been challenging due to their genome-wide redundancies and rapid evolution
Positive legacies of severe droughts in the Inner Mongolia grassland
No full textGlobal change-induced extreme droughts are increasing in grasslands worldwide, and drought legacies may greatly affect the responses of grassland ecosystems to these changes. However, it remains poorly understood whether and howsevere droughts have a positive legacy effect on grassland productivity. By combining a 4-year precipitation manipulation experiment with a 40-year observational study in a semiarid grassland, we showed that extreme droughts could create strong positive legacies on community productivity and that such legacies could last for multiple years. The mechanism behind thiswas the coupled effect of the drought-induced increase in annuals and the favorable precipitation pattern that facilitated the flourishing of annuals in subsequent years. This study provides experimental and observational evidence for positive drought legacies and reveals their underlying mechanisms. Our findings suggest that positive drought legacies should be incorporated into Earth system models to better predict the impact of extreme droughts on grassland ecosystems