of Botany,Chinese Academy Of Sciences
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Global soil profiles indicate depth-dependent soil carbon losses under a warmer climate
No full textSoil organic carbon (SOC) changes under future climate warming are difficult to quantify in situ. Here we apply an innovative approach combining space-for-time substitution with meta-analysis to SOC measurements in 113,013 soil profiles across the globe to estimate the effect of future climate warming on steady-state SOC stocks. We find that SOC stock will reduce by 6.0 +/- 1.6% (mean +/- 95% confidence interval), 4.8 +/- 2.3% and 1.3 +/- 4.0% at 0-0.3, 0.3-1 and 1-2 m soil depths, respectively, under 1 degrees C air warming, with additional 4.2%, 2.2% and 1.4% losses per every additional 1 degrees C warming, respectively. The largest proportional SOC losses occur in boreal forests. Existing SOC level is the predominant determinant of the spatial variability of SOC changes with higher percentage losses in SOC-rich soils. Our work demonstrates that warming induces more proportional SOC losses in topsoil than in subsoil, particularly from high-latitudinal SOC-rich systems. The response of soil organic carbon to climate warming may be soil depth-dependent, but remains unquantified in situ. Here the authors show that warming induces more proportional soil carbon losses in topsoil than in subsoil, particularly from high-latitudinal carbon-rich soils
Tree species richness as an important biotic factor regulates the soil phosphorus density in China's mature natural forests
No full textTree species richness has been recognized as an underlying driving factor for regulating soil phosphorus (P) status in many site-specific studies. However, it remains poorly understood whether this is true at broad scales where soil P strongly rely on climate, soil type and vegetation type. Here, based on the data of 946 mature natural forest sites from a nationwide field survey in China, we analyzed the impact of tree species richness on soil P density of China's mature natural forests (deciduous coniferous forest, DCF; evergreen coniferous forest, ECF; deciduous broad-leaved forest, DBF; evergreen broad-leaved forest, EBF; and mixed coniferous and broad-leaved forest, MF). Our results showed that tree species richness had a negative effect on soil P density in China's mature natural forests. The Random Forest regression model showed that the relative importance of tree species richness to soil P density was second only to the climate factors (mean annual temperature, MAT; mean annual precipitation, MAP). In addition, the structura
A chromosome-scale genome and transcriptomic analysis of the endangered tropical tree Vatica mangachapoi (Dipterocarpaceae)
No full textVatica mangachapoi is a tropical tree species native to Southeast Asia. It has long been valued as a timber species because the wood resists decay, but it is now considered vulnerable to extinction due to habitat loss and overexploitation. Here, we present the first chromosome-level genome assembly of V. mangachapoi that we created by combining data from PacBio long read sequencing with Hi-C proximity ligation and Illumina short-read sequencing. The assembled genome was 456.21 Mb, containing 11 chromosome and a BUSCO score of 93.4%. From the newly assembled genome, 46,811 protein-coding genes were predicted. Repetitive DNA accounted for 53% of the genome. Phylogenomic and gene family analyses showed that V. mangachapoi diverged from a common ancestor of Gossypium raimondii 70 million years ago. Transcriptome analyses found 227 genes that were differentially expressed in the leaves of plants grown in normal soil relative to plants grown in dry, coastal, sandy soil. For these genes, we identified three significantly enriched with GO terms: responses to organonitrogen compounds, chitin-triggered immunity, and wound response. This genome provides an important comparative benchmark not only for future conservation work on V. mangachapoi but also for phylogenomics work on Dipterocarpaceae
Soil pH and aridity influence distributions of branched tetraether lipids in grassland soils along an aridity transect
No full textBranched glycerol dialkyl glycerol tetraethers (brGDGTs) are membrane lipids of certain soil bacteria, and their relative distributions are used as a proxy for air temperature and soil pH. While temperature is recorded by the degree of methylation, soil pH is reflected by the amount of internal cyclization and the relative abundance of 6-methyl isomers. Since the exact producers of brGDGTs remain enigmatic, the mechanisms underlying their empirical relationships with temperature and soil pH, and thus the reliability of brGDGT-based paleorecords, are not well understood, especially in arid regions where mean annual precipitation (MAP) is less than 500 mm. Here, we evaluate the influence of soil pH and aridity on brGDGT distributions in grassland soils along an aridity transect (MAP = 173-415 mm) in Inner Mongolia. While the absolute and fractional abundance of 6-methyl brGDGTs increases with increasing soil pH and aridity, following the trend in the global surface soil calibra-tion dataset, the degree of cyclization does not. This indicates that in arid regions, soil pH reconstructions based on the relative contribution of 6-methyl brGDGTs are likely more reliable than those based on the degree of cyclization. Furthermore, 5-and 6-methyl brGDGTs respond differently to aridity, supporting prior suggestions that the distribution of brGDGTs could be the result of changes in bacterial community composition instead of the direct physiological alteration of molecular structures by the source organisms. Analysis of the bacterial community composition in the same soil transect indicates that the relative abundance of Acidobacteria, the phylum hosting potential brGDGT source-organisms, shows a poor relationship with aridity. Instead, Verruco-microbia (r(2) = 0.70, p < 0.01), and its subclass Spartobacteria (r(2) = 0.70, p < 0.01) in particular, show a sig-nificant negative correlation with aridity, resembling that of 5-methyl brGDGTs. Similarly, Actinobacteria are positively correlated with aridity (r(2) = 0.59, p < 0.01), following the same trend as that of 6-methyl brGDGTs. The ability of certain cultures of Verrucomicrobia and Actinobacteria to produce iso-C15:0 fatty acids that could serve as building blocks for brGDGTs hints that Verrucomicrobia and Actinobacteria could possibly produce brGDGTs in arid soils
Phylogenomic Analysis Reconstructed the Order Matoniales from Paleopolyploidy Veil
No full textPhylogenetic conflicts limit our understanding of the evolution of terrestrial life under multiple whole genome duplication events, and the phylogeny of early terrestrial plants remains full of controversy. Although much incongruence has been solved with so-called robust topology based on single or lower copy genes, the evolutionary mechanisms behind phylogenetic conflicts such as polyploidization remain poorly understood. Here, through decreasing the effects of polyploidization and increasing the samples of species, which represent all four orders and eight families that comprise early leptosporangiate ferns, we have reconstructed a robust phylogenetic tree and network with 1125 1-to-1 orthologs based on both coalescent and concatenation methods. Our data consistently suggest that Matoniales, as a monophyletic lineage including Matoniaceae and Dipteridaceae, should be redefined as an ordinal rank. Furthermore, we have identified and located at least 11 whole-genome duplication events within the evolutionary history of four leptosporangiates lineages, and associated polyploidization with higher speciation rates and mass extinction events. We hypothesize that paleopolyploidization may have enabled leptosporangiate ferns to survive during mass extinction events at the end Permian period and then flourish throughout the Mesozoic era, which is supported by extensive fossil records. Our results highlight how ancient polyploidy can result in rapid species radiation, thus causing phylogenetic conflicts yet allowing plants to survive and thrive during mass extinction events
Photoprotective energy quenching in the red alga Porphyridium purpureum occurs at the core antenna of the photosystem II but not at its reaction center
No full textPhotosynthetic organisms have evolved light-harvesting antennae over time. In cyanobacteria, external phycobilisomes (PBSs) are the dominant antennae, whereas in green algae and higher plants, PBSs have been replaced by proteins of the Lhc family that are integrated in the membrane. Red algae represent an evolutionary intermediate between these two systems, as they employ both PBSs and membrane LHCR proteins as light-harvesting units. Understanding how red algae cope with light is not only interesting for biotechnological applications, but is also of evolutionary interest. For example, energy-dependent quenching (qE) is an essential photoprotective mechanism widely used by species from cyanobacteria to higher plants to avoid light damage; however, the quenching mechanism in red algae remains largely unexplored. Here, we used both pulse amplitude-modulated (PAM) and time-resolved chlorophyll fluorescence to characterize qE kinetics in the red alga Porphyridium purpureum. PAM traces confirmed that qE in P. purpureum is activated by a decrease in the thylakoid lumen pH, whereas time-resolved fluorescence results further revealed the quenching site and ultrafast quenching kinetics. We found that quenching exclusively takes place in the photosystem II (PSII) complexes and preferentially occurs at PSII's core antenna rather than at its reaction center, with an overall quenching rate of 17.6 +/- 3.0 ns(-1). In conclusion, we propose that qE in red algae is not a reaction center type of quenching, and that there might be a membrane-bound protein that resembles PsbS of higher plants or LHCSR of green algae that senses low luminal pH and triggers qE in red algae
Petrocosmea purpureomaculata sp. nov. and P. wui sp. nov. (Gesneriaceae) from Yunnan, China with additions to P. coerulea and P. parryorum
No full textTwo new species of Petrocosmea (Gesneriaceae), P. purpureomaculata M.Q. Han, J. Cai & J. D. Ya from Jinping County and P. wui M.Q. Han, J. Cai & J. D. Ya from Eshan County, Yunnan Province, China, are described and illustrated. Petrocosmea wui was previously misidentified as P. coerulea due to its shield-shaped leaf base, but can be distinguished by several salient characters. Petrocosmea purpureomaculata is most similar to but distinguishable from P. parryorum. Additions and revisions of previously published descriptions of P. coerulea and P. parryorum, are also provided
Oxidosqualene Cyclases Involved in the Biosynthesis of Diverse Triterpenes in Camellia sasanqua
No full textCamellia sasanqua is an important economic plant that is rich in lipophilic triterpenols with pharmacological activities including antiallergic, anti-inflammatory, and anticancer activities. However, the key enzymes related to triterpene biosynthesis have seldom been studied in C. sasanqua. Oxidosqualene cyclases (OSCs) are the rate-limiting enzymes related to triterpene biosynthesis. In this study, seven putative OSC genes (CsOSC1-7) were mined from the C. sasanqua transcriptome. Six CsOSCs were characterized for the biosynthesis of diverse triterpene skeletons, including alpha-amyrin, beta-amyrin, delta-amyrin, dammarenediol-II, psi taraxasterol, taraxasterol, and cycloartenol by the heterologous expression system. CsOSC3 was a multiple functional alpha-amyrin synthase. Three key residues, Trp260, Tyr262, and Phe415, are critical to the catalytic performance of CsOSC3 judging from the results of molecular docking and site-directed mutagenesis. These findings provide important insights into the biosynthesis pathway of triterpenes in C. sasanqua
Multispecies forest plantations outyield monocultures across a broad range of conditions
No full textMultispecies tree planting has long been applied in forestry and landscape restoration in the hope of providing better timber production and ecosystem services; however, a systematic assessment of its effectiveness is lacking. We compiled a global dataset of matched single-species and multispecies plantations to evaluate the impact of multispecies planting on stand growth. Average tree height, diameter at breast height, and aboveground biomass were 5.4, 6.8, and 25.5% higher, respectively, in multispecies stands compared with single-species stands. These positive effects were mainly the result of interspecific complementarity and were modulated by differences in leaf morphology and leaf life span, stand age, planting density, and temperature. Our results have implications for designing afforestation and reforestation strategies and bridging experimental studies of biodiversity-ecosystem functioning relationships with real-world practices
The Cycas genome and the early evolution of seed plants
No full textCycads represent one of the most ancient lineages of living seed plants. Identifying genomic features uniquely shared by cycads and other extant seed plants, but not non-seed-producing plants, may shed light on the origin of key innovations, as well as the early diversification of seed plants. Here, we report the 10.5-Gb reference genome of Cycas panzhihuaensis, complemented by the transcriptomes of 339 cycad species. Nuclear and plastid phylogenomic analyses strongly suggest that cycads and Ginkgo form a clade sister to all other living gymnosperms, in contrast to mitochondrial data, which place cycads alone in this position. We found evidence for an ancient whole-genome duplication in the common ancestor of extant gymnosperms. The Cycas genome contains four homologues of the fitD gene family that were likely acquired via horizontal gene transfer from fungi, and these genes confer herbivore resistance in cycads. The male-specific region of the Y chromosome of C. panzhihuaensis contains a MADS-box transcription factor expressed exclusively in male cones that is similar to a system reported in Ginkgo, suggesting that a sex determination mechanism controlled by MADS-box genes may have originated in the common ancestor of cycads and Ginkgo. The C. panzhihuaensis genome provides an important new resource of broad utility for biologists. The study assembled a chromosome-level genome of Cycas panzhihuaensis, the last major lineage of seed plants for which a high-quality genome assembly was lacking. The study closes an important gap in our understanding of genome structure and evolution in seed plants