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Relationships Between Soil Microbial Diversities Across an Aridity Gradient in Temperate Grasslands Soil Microbial Diversity Relationships
No full textSoil microbes assemble in highly complex and diverse microbial communities, and microbial diversity patterns and their drivers have been studied extensively. However, diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between microbial functional groups in arid regions remain poorly understood. Here we assessed the relationships between the diversity and abundance of bacteria, fungi, and archaea and explored how environmental factors influence these relationships. We sampled soil along a 1500-km-long aridity gradient in temperate grasslands of Inner Mongolia (China) and sequenced the 16S rRNA gene of bacteria and archaea and the ITS2 gene of fungi. The diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between different microbial functional groups were evaluated using alpha-diversity and co-occurrence networks based on microbial abundance. Our results indicate insignificant correlations among the diversity patterns of bacterial, fungal, and archaeal domains using alpha-diversity but mostly positive correlations among diversity patterns of microbial functional groups based on alpha-diversity and co-occurrence networks along the aridity gradient. These results suggest that studying microbial diversity patterns from the perspective of functional groups and co-occurrence networks can provide additional insights on patterns that cannot be accessed using only overall microbial alpha-diversity. Increase in aridity weakens the diversity correlations between bacteria and fungi and between bacterial and archaeal functional groups, but strengthens the positive diversity correlations between bacterial functional groups and between fungal functional groups and the negative diversity correlations between bacterial and fungal functional groups. These variations of the diversity correlations are associated with the different responses of microbes to environmental factors, especially aridity. Our findings demonstrate the complex responses of microbial community structure to environmental conditions (especially aridity) and suggest that understanding diversity correlations and co-occurrence patterns between soil microbial groups is essential for predicting changes in microbial communities under future climate change in arid regions
Free-ranging livestock altered the spatiotemporal behavior of the endangered North Chinese leopard (Panthera pardus japonensis) and its prey and intensified human-leopard conflicts
No full textWidespread distribution of livestock in the natural habitats of large carnivores may negatively impact carnivore populations by reducing wild prey availability and increasing human-carnivore conflicts. In this study, we used camera-trapping data collected in the temperate forests of the Taihang Mountains in North China during 2016-2019 to examine whether and how free-ranging cattle affected habitat use and Diel activity patterns of the endangered North Chinese leopard (Panthera pardus japonensis) and its 2 wild prey species, Siberian roe deer (Capreolus pygargus), and wild boar (Sus scrofa). Residents were also interviewed to record livestock depredation events by leopards during 2015-2019. We found that roe deer spatially avoided sites frequented by cattle, but wild boar did not. In the growing seasons, leopards shared habitats with cattle and tended to increase their diurnal activities where cattle were present. All 3 study species exhibited fine-scale spatial-temporal segregation to cattle. Leopards selectively preyed on calves over adult cattle and livestock depredation frequency was positively correlated with the detection rates of cattle and wild prey, but not that of leopard. These findings not only show that through behavioral adaption large carnivores and their ungulate prey may persist under livestock disturbance, but also highlight how important proper livestock management is for conserving North Chinese leopards in this region. To enhance livestock management and mitigate human-leopard conflicts, we recommend specific actions, such as better guarding of free-ranging cattle or adoption of a captive farming system
Species delimitation of the liquorice tribe (Leguminosae: Glycyrrhizeae) based on phylogenomic and machine learning analyses
No full textThe liquorice tribe Glycyrrhizeae is a leguminous herbaceous group of plants comprised of the genera Glycyrrhiza and Glycyrrhizopsis. Some Glycyrrhiza taxa contain glycyrrhizin, a pharmacologically significant sweet substance that also has applications in crafting industrial materials. Here, we utilized an expanded taxon sampling of Glycyrrhizeae to reconstruct the phylogenetic relationships in the tribe based on genome skimming data, including whole chloroplast genomes, nuclear ribosomal DNA, and low-copy nuclear DNA. We also launched machine learning analysis (MLA) for one species pair with controversial taxonomic boundary. The integrated results indicated Glycyrrhizopsis should be split from Glycyrrhiza, while the former genus Meristotropis should be treated as part of Glycyrrhiza. Glycyrrhizopsis includes two species, Glycyrrhizopsis asymmetrica and Glycyrrhizopsis flavescens, and we recognize 13 species in Glycyrrhiza: Glycyrrhiza acanthocarpa, Glycyrrhiza astragalina, Glycyrrhiza bucharica, Glycyrrhiza echinata, Glycyrrhiza foetida, Glycyrrhiza glabra, Glycyrrhiza gontscharovii, Glycyrrhiza lepidota, Glycyrrhiza macedonica, Glycyrrhiza pallidiflora, Glycyrrhiza squamulosa, Glycyrrhiza triphylla, and Glycyrrhiza yunnanensis. We propose a broader G. glabra that includes former Glycyrrhiza aspera, G. glabra s.s., Glycyrrhiza inflata, and Glycyrrhiza uralensis, and represents the glycyrrhizin-contained medicinal group. Our ancestral state inferences show the ancestor of Glycyrrhiza lacked glycyrrhizin, and the presence of glycyrrhizin evolved twice within Glycyrrhiza during the last one million years. Our integrative phylogenomics-MLA study not only provides new insights into long-standing taxonomic controversies of Glycyrrhizeae, but also represents a useful approach for future taxonomic studies on other plant taxa
Over half of threatened species require targeted recovery actions to avert human-induced extinction
No full textAverting human-induced extinctions will require strong policy commitments that comprehensively address threats to species. A new Global Biodiversity Framework is currently being negotiated by the world's governments through the Convention on Biological Diversity. Here we explored how the suggested targets in this framework could contribute to reducing threats to threatened vertebrates, invertebrates, and plants, and assessed the importance of a proposed target to implement recovery actions for threatened species. Although many of the targets benefit species, we found that extinction risk for over half (57%) of threatened species would not be reduced sufficiently without a target promoting recovery actions, including ex situ conservation, reintroductions, and other species-specific interventions. A median of 54 threatened species per country require such actions, and most countries of the world hold such species. Preventing future human-induced extinctions requires policy commitments to implement targeted recovery actions for threatened species in addition to broader efforts to mitigate threats, underpinned by transformative change
Delphinieae flowers originated from the rewiring of interactions between duplicated and diversified floral organ identity and symmetry genes
No full textSpecies of the tribe Delphinieae (Ranunculaceae) have long been the focus of morphological, ecological, and evolutionary studies due to their highly specialized, nearly zygomorphic (bilaterally symmetrical) spiral flowers with nested petal and sepal spurs and reduced petals. The mechanisms underlying the development and evolution of Delphinieae flowers, however, remain unclear. Here, by conducting extensive phylogenetic, comparative transcriptomic, expression, and functional studies, we clarified the evolutionary histories, expression patterns, and functions of floral organ identity and symmetry genes in Delphinieae. We found that duplication and/or diversification of APETALA3-3 (AP3-3), AGAMOUS-LIKE6 (AGL6), CYCLOIDEA (CYC), and DIVARICATA (DIV) lineage genes was tightly associated with the origination of Delphinieae flowers. Specifically, an AGL6-lineage member (such as the Delphinium ajacis AGL6-1a) represses sepal spur formation and petal development in the lateral and ventral parts of the flower while determining petal identity redundantly with AGL6-1b. By contrast, two CYC2-like genes, CYC2b and CYC2a, define the dorsal and lateral-ventral identities of the flower, respectively, and form complex regulatory links with AP3-3, AGL6-1a, and DIV1. Therefore, duplication and diversification of floral symmetry genes, as well as co-option of the duplicated copies into the preexisting floral regulatory network, have been key for the origin of Delphinieae flowers. The making of highly complex Delphinieae flowers involved the duplication and diversification of floral organ identity genes and floral symmetry genes, as well as the rewiring of their interactions
Soil microbial community structure dynamics shape the rhizosphere priming effect patterns in the paddy soil
No full textMicrobial community structure plays a crucial part in soil organic carbon (SOC) decomposition and variation of rhizo-sphere priming effects (RPEs) during plant growth. However, it is still uncertain how bacterial community structure regulates RPEs in soil and how RPE patterns respond to plant growth. Therefore, we conducted an experiment to ex-amine the RPE response to plant growth and nitrogen (N) addition (0 (N0), 150 (N150), and 300 (N300) kg N ha-1) using the 13C natural abundance method in a C3 soil (paddy soil) -C4 plant (maize, Zea mays L.) system; we then explored the underlying biotic mechanisms using 16S rRNA sequencing techniques. Networks were constructed to identify keystone taxa and to analyze the correlations between network functional modules of bacterial community and C decomposition. The results indicated that negative and positive RPEs occurred on Day 30 and Day 75 after maize planting, respectively. Bacterial community structure significantly changed and tended to shift from r-strategists to-ward K-strategists with changing labile C: N stoichiometry and soil pH during plant growth stages. The different net -work modules of bacterial community were aggregated in response to RPE pattern variation. Caulobacteraceae, Bacillus, and Chitinophagaceae were keystone taxa on Day 30, while Gemmatimonas, Candidatus Koribacter, and Xanthobacteraceae were keystone taxa on Day 75. Moreover, keystone taxa with different C utilization strategieswere significantly different between the two growth stages and related closely to different RPE patterns. This study provides deeper insights into the network structure of bacterial communities corresponding to RPE patterns and em-phasizes the significance of keystone taxa in RPE variation
Exogenous glutathione modulates redox homeostasis in okra (Abelmoschus esculentus) during storage
No full textGlutathione (GSH) improves the scavenging capacity of reactive oxygen species (ROS) in postharvest fruit and vegetable, but the effect of exogenous GSH in okra (Abelmoschus esculentus) has not been clarified. This study investigated the effect of GSH on ROS scavenging in postharvest okra and found that GSH treatment effectively inhibited weight loss and alleviated browning and thereby maintained the appearance and quality of the fruit. Moreover, GSH suppressed levels of hydrogen peroxide (H2O2), superoxide radical (O2- ), and malondialdehyde (MDA). Treatment with exogenous GSH increased the contents of ascorbic acid (AsA) and GSH in okra, while decreased the contents of dehydroascorbic acid (DHA) and oxidized glutathione (GSSG). GSH treatment also enhanced the ROS-scavenging ability of okra by upregulating the expression of AeAPXs, AeGRs, AeMDHARs and AeDHARs, all of which are associated with redox homeostasis. Collectively, our findings demonstrate that exogenous GSH treatment can extend the shelf life of okra by mediating redox homeostasis
High-precision early warning system for rice cadmium accumulation risk assessment
No full textRapid global industrialization has resulted in widespread cadmium contamination in agricultural soils and products. A considerable proportion of rice consumers are exposed to Cd levels above the provisional safe intake limit, raising widespread environmental concerns on risk management. Therefore, a generalized approach is urgently needed to enable correct evaluation and early warning of cadmium contaminants in rice products. Combining big data and computer science together, this study developed a system named SMART Cd Early Warning, which integrated 4 modules including genotype-to-phenotype (G2P) modelling, high-throughput sequencing, G2P prediction and rice Cd contamination risk assessment, for rice cadmium accumulation early warning. This system can rapidly assess the risk of rice cadmium accumulation by genotyping leaves at seeding stage. The parameters including statistical methods, population size, training population-testing population ratio, SNP density were assessed to ensure G2P model exhibited superior performance in terms of prediction precision (up to 0.76 +/- 0.003) and computing efficiency (within 2 h). In field trials of cadmium-contaminated farmlands in Wenling and Fuyang city, Zhejiang Province, SMART Cd Early Warning exhibited superior capability for identification risk rice varieties, suggesting a potential of SMART Cd Early-Warning system in OsGCd risk assessment and early warning in the age of smart
Disentangling a 40-year-old taxonomic puzzle: the phylogenetic position of Mimulicalyx (Lamiales)
No full textWith the disintegration of the traditionally circumscribed Scrophulariaceae, the phylogenetic placements of most genera formerly placed in that family have been resolved. However, the familial placement of the monotypic genus Mimulicalyx has not been included in any published molecular phylogenetic study. Here, we adopt a two-step approach to resolve the phylogenetic placement of Mimulicalyx using three datasets: (1) a 71 619 bp plastome alignment of Lamiales; (2) a dataset of six plastid DNA regions (atpB, matK, ndhF, rbcL, rps16 and trnL-trnF) for Phrymaceae; and (3) a dataset of the nuclear ribosomal internal and external transcribed spacer regions (nrITS, ETS) for Phrymaceae. Our analyses reveal that Mimulicalyx is a member of the tribe Mimuleae in Phrymaceae. Generic level phylogenetic relationships within Phrymaceae are further discussed, and a dichotomous key to the 15 genera currently recognized is provided
Global ubiquitinome analysis reveals the role of E3 ubiquitin ligase FaBRIZ in strawberry fruit ripening
No full textUsing ubiquitinome analysis we unravel several hundreds of ubiquitination sites on proteins in strawberry fruit, and identify a RING-type E3 ligase, FaBRIZ, which functions as an important negative regulator of ripening. Ubiquitination is an important post-translational modification that mediates protein degradation in eukaryotic cells, participating in multiple biological processes. However, the profiling of protein ubiquitination and the function of this crucial modification in fruit ripening remain largely unknown. In this study, we found that suppression of proteasome by the inhibitor MG132 retarded strawberry fruit ripening. Using K-e-GG antibody enrichment combined with high-resolution mass spectrometry, we performed a comprehensive ubiquitinome analysis in strawberry fruit. We identified 2947 ubiquitination sites for 2878 peptides within 1487 proteins, which are involved in a variety of cellular functions. The lysine at position 48 (K48)-linked poly-ubiquitin chains appeared to be the most prevalent type of modification among the identified ubiquitinated proteins. A large number of ubiquitination sites exhibited altered ubiquitination levels after proteasome inhibition, including those within ripening-related proteins associated with sugar and acid metabolism, cell wall metabolism, anthocyanin synthesis, and ABA biosynthesis and signalling. We further demonstrated that FaBRIZ, a RING-type E3 ligase, functions as a negative regulator of ripening in strawberry fruit. Our findings highlight the critical regulatory roles of protein ubiquitination in fruit ripening. The ubiquitinome data provide a basis for further exploration of the function of ubiquitination on specific proteins