Yak genome database: a multi-omics analysis platform

BACKGROUND

The yak (Bos grunniens) is a large ruminant species that lives in high-altitude regions and exhibits excellent adaptation to the plateau environments. To further understand the genetic characteristics and adaptive mechanisms of yak, we have developed a multi-omics database of yak including genome, transcriptome, proteome, and DNA methylation data.

DESCRIPTION

The Yak Genome Database ( http://yakgenomics.com/ ) integrates the research results of genome, transcriptome, proteome, and DNA methylation, and provides an integrated platform for researchers to share and exchange omics data. The database contains 26,518 genes, 62 transcriptomes, 144,309 proteome spectra, and 22,478 methylation sites of yak. The genome module provides access to yak genome sequences, gene annotations and variant information. The transcriptome module offers transcriptome data from various tissues of yak and cattle strains at different developmental stages. The proteome module presents protein profiles from diverse yak organs. Additionally, the DNA methylation module shows the DNA methylation information at each base of the whole genome. Functions of data downloading and browsing, functional gene exploration, and experimental practice were available for the database.

CONCLUSION

This comprehensive database provides a valuable resource for further investigations on development, molecular mechanisms underlying high-altitude adaptation, and molecular breeding of yak.

Chemical Composition, Toxicity, and Repellency of Essential Oils from Three Hedychium Species Against Stored-Product Insects

Stored products are constantly infested by insects, so finding eco-friendly bioinsecticides for insect management is important. The work aimed to assess the insecticidal and repellent activity of essential oil (EO) from Hedychium glabrum S. Q. Tong, Hedychium coronarium Koen., and Hedychium yunnanense Gagnep. against Tribolium castaneum, Lasioderma serricorne, and Liposcelis bostrychophila. Results showed that 88 chemical components were identified in the extracted Hedychium EOs, indicating that they exhibited diversity in components. According to principal component analysis (PCA), the composition of the EO from the H. yunnanense stem and leaf (EOHYSL) was significantly different from other EOs due to the different organs and species. The biological activity also varied continuously with plant species and organs. Only the EO of H. yunnanense (EOHY) showed strong fumigant toxicity. While in the contact tests, EOHGR showed the strongest toxicity effect on L. bostrychophila, with a LC50 value of 71.76 μg/cm2, which was closest to the positive control (Pyrethrin). All EOs had remarkable repellent activities against the three target insects, and repellency increased with concentration. According to the results of the comprehensive score, EOHY had the highest potential, which ranged from 0.7999 to 0.8689. Thus, Hedychium EOs possess potential biorational traits to be biological insecticides.

Phosphorus release from newly inundated soils and variation in benthic algal nutrient limitation induced by rising water levels of Qinghai Lake, China

The mobilization of internal phosphorus (P) plays a crucial role in transitioning nutrient limitations within lake ecosystems. While previous research has extensively examined P release in littoral zones influenced by fluctuating water levels, there is a paucity of studies addressing the implications of sustained water level rise in this context, particularly as it pertains to nutrient limitations in benthic algae. To address this gap, we conducted an integrated study in Qinghai Lake. In the field sampling and microcosm experiment, we found that P concentrations are elevated in areas subjected to short-term inundation compared to those enduring prolonged inundation, primarily due to the dissolution of sedimentary P fractions. The results of nutrient diffusing substrata (NDS) bioassays indicated that benthic algae in Qinghai Lake displayed either P limitation or NP co-limitation. The transition from P limitation to NP co-limitation suggested that internal P release may serve to ameliorate nutrient limitations in benthic algae. This phenomenon could potentially contribute to the proliferation of Cladophora in the littoral zones of Qinghai Lake, thereby posing long-term implications for the lake's aquatic ecosystem, particularly under conditions of sustained water level rise.

Assessing the spatial occupation and ecological impact of human activities in Chengguan district, Lhasa city, Tibetan Plateau

In this study, the ecological impact of human activities and the space occupied by construction and arable land on the Tibetan Plateau were examined, focusing on changes in the net primary productivity (NPP) as a key indicator of ecological health. With the utilization of land use data and multiyear average NPP data from 2002 to 2020, we analyzed the effects of the conversion of zonal vegetation into construction and arable land on carbon sequestration and oxygen release in Chengguan District, Lhasa city. Our findings indicated a marked spatial difference in the NPP among different land types. Regarding the original zonal vegetation, the NPP ranged from 0.2 to 0.3 kg/m2. Construction land showed a decrease in the NPP, with values ranging from 0.16 to 0.26 kg/m2, suggesting a decrease in ecological productivity. Conversely, arable land exhibited an increase in the NPP, with average values exceeding 0.3 kg/m2. This increase suggested enhanced productivity, particularly in regions where the original zonal vegetation provided lower NPP values. However, this enhanced productivity may not necessarily indicate a positive ecological change. In fact, such increases could potentially disrupt the natural balance of ecosystems, leading to unforeseen ecological consequences. The original zonal vegetation, with NPP values ranging from 0.12 to 0.43 kg/m2, exhibited higher ecological stability and adaptability than the other land types. This wider NPP range emphasizes the inherent resilience of native vegetation, which could sustain diverse ecological functions under varying environmental conditions. These findings demonstrate the urgent need for sustainable land use management on the Tibetan Plateau. This study highlights the importance of considering the ecological impact of land use changes in regional development strategies, ensuring the preservation and enhancement in the unique and fragile plateau ecosystem.

Genetic Basis and Evolutionary Forces of Sexually Dimorphic Color Variation in a Toad-Headed Agamid Lizard

In the animal kingdom, sexually dimorphic color variation is a widespread phenomenon that significantly influences survival and reproductive success. However, the genetic underpinnings of this variation remain inadequately understood. Our investigation into sexually dimorphic color variation in the desert-dwelling Guinan population of the toad-headed agamid lizard (Phrynocephalus putjatai) utilized a multidisciplinary approach, encompassing phenotypic, ultrastructural, biochemical, genomic analyses, and behavioral experiments. Our findings unveil the association between distinct skin colorations and varying levels of carotenoid and pteridine pigments. The red coloration in males is determined by a genomic region on chromosome 14, housing four pigmentation genes: BCO2 and three 6-pyruvoyltetrahydropterin synthases. A Guinan population-specific nonsynonymous single nucleotide polymorphism in BCO2 is predicted to alter the electrostatic potential within the binding domain of the BCO2-β-carotene complex, influencing their interaction. Additionally, the gene MAP7 on chromosome 2 emerges as a potential contributor to the blue coloration in subadults and adult females. Sex-specific expression patterns point to steroid hormone-associated genes (SULT2B1 and SRD5A2) as potential upstream regulators influencing sexually dimorphic coloration. Visual modeling and field experiments support the potential selective advantages of vibrant coloration in desert environments. This implies that natural selection, potentially coupled with assortative mating, might have played a role in fixing color alleles, contributing to prevalence in the local desert habitat. This study provides novel insights into the genetic basis of carotenoid and pteridine-based color variation, shedding light on the evolution of sexually dimorphic coloration in animals. Moreover, it advances our understanding of the driving forces behind such intricate coloration patterns.

Ecological barriers: An approach to ecological conservation and restoration in China

The Chinese government has pursued comprehensive ecological conservation and restoration by establishing an ecological barrier system. However, the majority of international research tends to focus on the connectivity between habitats, overlooking the functions that ecological barriers play in ecological conservation and restoration. The existing literature lacks a systematic exploration of the theory and practice of ecological barriers. This study employed the literature analysis tool CiteSpace to present the theoretical and developmental trends in ecological barriers from various perspectives, including research fields, historical evolution, research hotspots, and major research nations. By analyzing the differences in the understanding of ecological barriers between China and other countries, examining the ecological barriers construction history in China, and exploring the types and functions of ecological barriers, this study summarizes the framework of China's ecological barriers construction system as "features-functions-problems." Constructing an ecological barrier system can help achieve ecological conservation and restoration goals in China.

A cretaceous frog with eggs from northwestern China provides fossil evidence for sexual maturity preceding skeletal maturity in anurans

Mesozoic fossils of frogs are rare in the palaeontological record, particularly those exhibiting soft tissues that offer limited insights into early life-history characteristics. Here we report on a skeletally immature frog from the Lower Cretaceous of northwest China, with egg masses in the body and eggs in the oviduct, indicative of a gravid female. CT reconstruction of the specimen allows referral to Gansubatrachus qilianensis and we assign it as a paratype complementing the diagnosis of the type species. The new fossil, which might represent a younger individual than the holotype of Gansubatrachus, shows that sexual maturation occurred before full adulthood in this frog and provides evidence of death linked to mating behaviour. We also discuss other potential sources of variation and life-history traits of Gansubatrachus. The new finding represents the oldest Early Cretaceous frog preserving in situ eggs and provides a glimpse into ancient anuran development during Mesozoic times.

MFishBT: A global database of biogeochemical tags in migratory fish

Humans have long been fascinated by the mysteries surrounding fish migrations and addressing these complex behaviors often requires large data sets. Biogeochemical tags, including trace elements and stable isotopes, are the most accessible biomarkers for tracking fish migrations. However, access to standardized biogeochemical tag data is rarely available for migratory fish, which limits our understanding of the evolutionary origins, drivers, timing, and corridors of migration. This precludes the development of conservation strategies and the implementation of management actions. Here, we present MFishBT, a global, open-access database of Migratory Fish's Biogeochemical Tags. As of April 2023, the MFishBT contains biogeochemical records from 1,305 studies, of which 53% used element-to-calcium (E/Ca) ratios, 34% used isotopic ratios, and 13% used both. The database covers 17,413 field sampling locations (inland 47% vs. marine 53%) around the globe, comprising 490 migratory fish species of four classes, 44 orders/suborders, and 137 families. In total, 77 trace elements and 11 isotope systems were measured across various fish biological archives, including otoliths, scales, eye lenses, and vertebrae. E/Ca ratios were examined more frequently than isotopic ratios, led by Sr/Ca, Mg/Ca, Ba/Ca, and 87 Sr/86 Sr, δ13 C, and δ18 O. The MFishBT compiles 27,030, 16,222, and 2,481,714 records with biogeochemical data detected in the core, edge, and core-to-edge transects for biological archives of migratory fish. This is the most globally comprehensive open-access database on biogeochemical tags in migratory fish to date, and can serve a variety of needs in scientific research, conservation, and management. We encourage researchers to add more data sets to this database in the future. This database is released for noncommercial use only. There are no copyright restrictions, and please cite this paper when using these data, or a subset of these data, for publication.

Potential of UV-B radiation in drought stress resilience: A multidimensional approach to plant adaptation and future implications

The escalating impact of climate change and ultraviolet (UV) radiation is subjecting plants to unique combinations of UV-B and drought stress. These combined stressors could have additive, synergistic, or antagonistic effects, but the precise nature of these impacts remains uncertain, hampering our ability to predict plant adaptations approach towards stressors. Our analysis of various studies shows that UV-B or drought conditions detrimentally influence plant growth and health metrics by the enhanced generation of reactive oxygen species causing damage to lipids, proteins, carbohydrates and DNA. Further reducing biomass accumulation, plant height, photosynthetic efficiency, leaf area, and water transpiration, while enhancing stress-related symptoms. In response to UV-B radiation and drought stress, plants exhibit a notable up-regulation of specific acclimation-associated metabolites, including proline, flavonoids, anthocyanins, unsaturated fatty acids, and antioxidants. These metabolites play a pivotal role in conferring protection against environmental stresses. Their biosynthesis and functional roles are potentially modulated by signalling molecules such as hydrogen peroxide, abscisic acid, jasmonic acid, salicylic acid, and ethylene, all of which have associated genetic markers that further elucidate their involvement in stress response pathways. In comparison to single stress, the combination of UV-B and drought induces the plant defence responses and growth retardation which are less-than-additive. This sub-additive response, consistent across different study environments, suggests the possibility of a cross-resistance mechanism. Our outlines imply that the adverse effects of increased drought and UV-B could potentially be mitigated by cross-talk between UV-B and drought regimes utilizing a multidimensional approach. This crucial insight could contribute significantly to refining our understanding of stress tolerance in the face of ongoing global climate change.

Lakes-scale pattern of eukaryotic phytoplankton diversity and assembly process shaped by electrical conductivity in central Qinghai-Tibet Plateau

Phytoplankton are the main primary producers in aquatic ecosystems and play an important role in food web and geochemical cycles. Its diversity, community structure, and assembly process are influenced by several factors. Alpine lake ecosystems are relatively weak and extremely sensitive to global climate change. However, the impact of climate change on phytoplankton in Qinghai-Tibet Plateau lakes and their responses are still unclear. In this study, we analyzed the diversity, environmental drivers, and assembly process of phytoplankton community in the central QTP lakes. The phytoplankton of these lakes can be primarily distinguished into freshwater and brackish types, with significant differences in species diversity and community dissimilarity. Both shared nearly same key environmental factors that significantly affecting phytoplankton such as EC, and brackish lakes were also positively correlative with TN. Stochastic process was predominant in phytoplankton assembly. Additionally, freshwater and brackish lakes were dominated by dispersal limitation and heterogeneous selection respectively. Alpine lakes had significant EC thresholds, and their diversity and assembly processes changed significantly around the thresholds. The present findings have important implications for understanding and predicting the response of lake phytoplankton communities to climate change and for making decisions to protect the ecological resources of alpine lakes.

Global biogeography and ecological implications of cobamide-producing prokaryotes

Cobamides, a class of essential coenzymes synthesized only by a subset of prokaryotes, are model nutrients in microbial interaction studies and play significant roles in global ecosystems. Yet, their spatial patterns and functional roles remain poorly understood. Herein, we present an in-depth examination of cobamide-producing microorganisms, drawn from a comprehensive analysis of 2862 marine and 2979 soil metagenomic samples. A total of 1934 nonredundant metagenome-assembled genomes (MAGs) potentially capable of producing cobamides de novo were identified. The cobamide-producing MAGs are taxonomically diverse but habitat specific. They constituted only a fraction of all the recovered MAGs, with the majority of MAGs being potential cobamide users. By mapping the distribution of cobamide producers in marine and soil environments, distinct latitudinal gradients were observed: the marine environment showed peak abundance at the equator, whereas soil environments peaked at mid-latitudes. Importantly, significant and positive links between the abundance of cobamide producers and the diversity and functions of microbial communities were observed, as well as their promotional roles in essential biogeochemical cycles. These associations were more pronounced in marine samples than in soil samples, which suggests a heightened propensity for microorganisms to engage in cobamide sharing in fluid environments relative to the more spatially restricted soil environment. These findings shed light on the global patterns and potential ecological roles of cobamide-producing microorganisms in marine and soil ecosystems, enhancing our understanding of large-scale microbial interactions.

Gut microbiota reflect adaptation of cave-dwelling tadpoles to resource scarcity

Gut microbiota are significant to the host's nutrition and provide a flexible way for the host to adapt to extreme environments. However, whether gut microbiota help the host to colonize caves, a resource-limited environment, remains unknown. The nonobligate cave frog Oreolalax rhodostigmatus completes its metamorphosis within caves for 3-5 years before foraging outside. Their tadpoles are occasionally removed from the caves by floods and utilize outside resources, providing a contrast to the cave-dwelling population. For both cave and outside tadpoles, the development-related reduction in their growth rate and gut length during prometamorphosis coincided with a shift in their gut microbiota, which was characterized by decreased Lactobacillus and Cellulosilyticum and Proteocatella in the cave and outside individuals, respectively. The proportion of these three genera was significantly higher in the gut microbiota of cave-dwelling individuals compared with those outside. The cave-dwellers' gut microbiota harbored more abundant fibrolytic, glycolytic, and fermentative enzymes and yielded more short-chain fatty acids, potentially benefitting the host's nutrition. Experimentally depriving the animals of food resulted in gut atrophy for the individuals collected outside the cave, but not for those from inside the cave. Imitating food scarcity reproduced some major microbial features (e.g. abundant Proteocatella and fermentative genes) of the field-collected cave individuals, indicating an association between the cave-associated gut microbiota and resource scarcity. Overall, the gut microbiota may reflect the adaptation of O. rhodostigmatus tadpoles to resource-limited environments. This extends our understanding of the role of gut microbiota in the adaptation of animals to extreme environments.

Molecular Biology Applications of Psychrophilic Enzymes: Adaptations, Advantages, Expression, and Prospective

Psychrophilic enzymes are primarily produced by microorganisms from extremely low-temperature environments which are known as psychrophiles. Their high efficiency at low temperatures and easy heat inactivation property have attracted extensive attention from various food and industrial bioprocesses. However, the application of these enzymes in molecular biology is still limited. In a previous review, the applications of psychrophilic enzymes in industries such as the detergent additives, the food additives, the bioremediation, and the pharmaceutical medicine, and cosmetics have been discussed. In this review, we discuss the main cold adaptation characteristics of psychrophiles and psychrophilic enzymes, as well as the relevant information on different psychrophilic enzymes in molecular biology. We summarize the mining and screening methods of psychrophilic enzymes. We finally recap the expression of psychrophilic enzymes. We aim to provide a reference process for the exploration and expression of new generation of psychrophilic enzymes.

Pervasive soil phosphorus losses in terrestrial ecosystems in China

Future phosphorus (P) shortages could seriously affect terrestrial productivity and food security. We investigated the changes in topsoil available P (AP) and total P (TP) in China's forests, grasslands, paddy fields, and upland croplands during the 1980s-2010s based on substantial repeated soil P measurements (63,220 samples in the 1980s, 2000s, and 2010s) and machine learning techniques. Between the 1980s and 2010s, total soil AP stock increased with a small but significant rate of 0.13 kg P ha-1  year-1 , but total soil TP stock declined substantially (4.5 kg P ha-1  year-1 ) in the four ecosystems. We quantified the P budgets of soil-plant systems by harmonizing P fluxes from various sources for this period. Matching trends of soil contents over the decades with P budgets and fluxes, we found that the P-surplus in cultivated soils (especially in upland croplands) might be overestimated due to the great soil TP pool compared to fertilization and the substantial soil P losses through plant uptake and water erosion that offset the P additions. Our findings of P-deficit in China raise the alarm on the sustainability of future biomass production (especially in forests), highlight the urgency of P recycling in croplands, and emphasize the critical role of country-level basic data in guiding sound policies to tackle the global P crises.

New records of the white-cheeked macaque provide range extension for the endangered primate in Gaoligong Mountains

White-cheeked macaque Macaca leucogenys is a recently described primate species discovered by camera-trap surveys in the Medog region in 2015. The species was thought to be narrowly distributed in southeastern Tibet. However, knowledge on the distribution and conservation of the species is quite limited. Based on a systematic camera-trapping survey, we report the occurrence of the species in the Gaoligong Mountains, over 350 km southeast of the nearest known population. We recorded 3025 photographs of white-cheeked macaques representing 481 independent records from 59 camera-trap stations with total trapping efforts of 18,437 camera days. Notably, part of the newly discovered locations of the white-cheeked macaque are outside of nature reserves without any formal protection and management. Our survey also confirms the occurrence of ten primate species in the Gaoligong Mountains, accounting for 35.7% of China's primates, including the Skywalker hoolock gibbon Hoolock tianxing and the Myanmar snub-nosed monkey Rhinopithecus strykeri etc. These findings reveal a new distribution record for the white-cheeked macaque and further highlight the conservation values of Gaoligong Mountains for globally threatened primate species. We also provide a preliminary report on the daily activity patterns of this endangered species, which enriches the bio-ecological data of the poorly studied species. We believe the report has significant implications for understanding the ecology of the species and improving conservation planning.

Unexpected hydroxyl radical production in brewed tea under sunlight

Tea is one of the world's most popular and widely consumed beverages. It is a common pastime to enjoy a cup of tea in the sunshine. However, little attention has been given to understanding the possible photochemical reactions occurring beneath the calm surface of brewed tea. Epigallocatechin gallate (EGCG), which is widely used in food and beverages, is the most significant active ingredient found in tea. In this study, we investigated the presence of free radicals in both an aqueous EGCG solution and brewed tea under simulated sunlight conditions. To our surprise, we unexpectedly observed the production of hydroxyl radicals (•OH) in brewed tea. It was found that sunlight irradiation played a critical role in the formation of •OH, independent of the presence of metal ions. Furthermore, we demonstrated that the •OH generated from the EGCG aqueous solution induced cell cytotoxicity and DNA damage in vitro. Considering the crucial role of •OH in various fields, including human health and the environment, it is important to further explore the practical implications of •OH production in brewed tea under sunlight. In summary, our study unveils the unexpected formation of •OH in brewed tea and emphasizes the significance of sunlight-induced reactions. The observed cytotoxic and DNA-damaging effects of •OH emphasize the importance of understanding the potential health consequences associated with tea consumption. Further research in this area will contribute to a better understanding of the broader implications of •OH production in brewed tea under sunlight.

A remote sensing method for mapping alpine grasslines based on graph-cut

Climate change has induced substantial shifts in vegetation boundaries such as alpine treelines and shrublines, with widespread ecological and climatic influences. However, spatial and temporal changes in the upper elevational limit of alpine grasslands ("alpine grasslines") are still poorly understood due to lack of field observations and remote sensing estimates. In this study, taking the Tibetan Plateau as an example, we propose a novel method for automatically identifying alpine grasslines from multi-source remote sensing data and determining their positions at 30-m spatial resolution. We first identified 2895 mountains potentially having alpine grasslines. On each mountain, we identified a narrow area around the upper elevational limit of alpine grasslands where the alpine grassline was potentially located. Then, we used linear discriminant analysis to adaptively generate from Landsat reflectance features a synthetic feature that maximized the difference between vegetated and unvegetated pixels in each of these areas. After that, we designed a graph-cut algorithm to integrate the advantages of the Otsu and Canny approaches, which was used to determine the precise position of the alpine grassline from the synthetic feature image. Validation against alpine grasslines visually interpreted from a large number of high-spatial-resolution images showed a high level of accuracy (R2 , .99 and .98; mean absolute error, 22.6 and 36.2 m, vs. drone and PlanetScope images, respectively). Across the Tibetan Plateau, the alpine grassline elevation ranged from 4038 to 5380 m (5th-95th percentile), lower in the northeast and southeast and higher in the southwest. This study provides a method for remotely sensing alpine grasslines for the first-time at large scale and lays a foundation for investigating their responses to climate change.

Chromosome-level genome assembly of the kiang (Equus kiang) illuminates genomic basis for its high-altitude adaptation

The kiang (Equus kiang) can only be observed in the Qinghai-Tibet Plateau (QTP). The kiang displayed excellent athletic performance in the high-altitude environment, which attracted wide interest in the investigation of the potential adaptive mechanisms to the extreme environment. Here, we assembled a chromosome-level genome of the kiang based on Hi-C sequencing technology. A total of 324.14 Gb clean data were generated, and the chromosome-level genome with 26 chromosomes (25 + X) and scaffold N50 of 101.77 Mb was obtained for the kiang. The genomic synteny analysis revealed large-scale chromosomal rearrangement during the evolution process of Equus species. Phylogenetic and divergence analyses revealed that the kiang was the sister branch to the ass and diverged from a common ancestor at approximately 13.5 Mya. The expanded gene families were mainly related to the hypoxia response, metabolism, and immunity. The kiang suffered a significant loss of olfaction-related genes, which might indicate decreased olfactory sensibility. Positively selected genes (PSGs) detected in the kiang were mainly associated with hypoxia response. Especially, there were two species-specific missense amino acid mutations in the PSG STAT3 annotated in the hypoxia-inducible factor 1 signal pathway, which may play an important role in the high-altitude adaptation of the kiang. Moreover, structure variations in the kiang genome were also identified, which possibly contributed to the high-altitude adaptation of the kiang. Comparative analysis revealed a lot of species-specific insertions and deletions in the kiang genome, such as PIK3CB and AKT with 3258 and 189 bp insertions in the intron region, respectively, possibly affecting the expression and regulation of hypoxia-related downstream pathways. This study provided valuable genomic resources, and our findings help a better understanding of the underlying adaptive strategies to the high-altitude environment in the kiang.

Plant Secondary Compounds Promote White Adipose Tissue Browning via Modulation of the Gut Microbiota in Small Mammals

The browning of white adipose tissue (WAT) is a promising area of research for treating metabolic disorders and obesity in the future. However, studies on plant secondary compounds promoting WAT browning are limited. Herein, we explored the effects of swainsonine (SW) on gut microbiota and WAT browning in captive pikas. SW inhibited body mass gain, increased brown adipose tissue (BAT) mass, and induced WAT browning in pikas. The 16S rDNA sequencing revealed a significant reduction in the alpha diversity and altered community structure of the gut microbiota in captive pikas. However, the addition of SW to the diet significantly increased the alpha diversity of gut microbiota and the relative abundance of Akkermansia, Prevotella, and unclassified_f__Lachnospiraceae, along with the complexity of the microbial co-occurrence network structure, which decreased in the guts of captive pikas. Functional profiles showed that SW significantly decreased the relative abundances of energy metabolism, lipid metabolism, and glycan biosynthesis and metabolism, which were enriched in captive pikas. Furthermore, SW decreased deterministic processes of gut microbiota assembly in July and increased them in November. Finally, the genera Prevotella and unclassified_f__Prevotellaceae were positively correlated with BAT mass. Our results highlighted that plant secondary compounds promote WAT browning by modulating the gut microbiota in small mammals.

Assessment of Contact Toxicity and Repellent Effects of Essential Oils from Piper Plants Piper yunnanense and Piper boehmeriifolium against Three Stored-Product Insects

Storage is a crucial part during grain production for the massive spoilage caused by stored product insects. Essential oils (EOs) of plant origin have been highly recommended to combating insects which are biodegradable and safe mode of action. Hence, to make the fullest use of natural resources, essential oils of different parts from Piper yunnanense (the whole part, PYW; fruits, PYF; leaves, PYL) and Piper boehmeriifolium (leaves, PBL) were extracted by steam distillation method in the present study. Gas chromatography-mass spectrometry (GC-MS) characterization revealed bicyclogermacrene (PYW), γ-muurolene (PYF), δ-cadinene (PYL) and methyl 4,7,10,13,16,19-docosahexaenoate (PBL) as the principal compound of each essential oil. Sesquiterpene hydrocarbons were also recognized as the richest class accounting for 56.3 %-94.9 % of the total oil. Three storage pests, Tribolium castaneum, Lasioderma serricorne and Liposceis bostrychophila, were exposed to different concentrations of EOs to determine their insecticidal effects. All tested samples performed modest contact toxicity in contrast to a bioactive ingredient pyrethrin, among which the most substantial effects were observed in PYF EOs against T. castaneum (35.84 μg/adult), PBL EOs against L. serricorne (15.76 μg/adult) and PYW EOs against L. bostrychophila (57.70 μg/cm2 ). In terms of repellency tests, essential oils of PYF at 78.63 nL/cm2 demonstrated to have a remarkable repellence against T. castaneum at 2h and 4h post-exposure. The investigations indicate diverse variations in the chemical profiles and insecticidal efficacies of P. yunnanense and P. boehmeriifolium EOs, providing more experimental evidence for the use of the Piper plants.

Leaf carbon isotope tracks the facilitation pattern of legume shrubs shaped by water availability and species replacement along a large elevation gradient in Trans-Himalayas

BACKGROUND AND AIMS

Understanding patterns and mechanisms of nurse plant facilitation is important to predict the resilience of arid/semi-arid ecosystems to climate change. We investigate whether water availability and nurse species turnover interact to shape the facilitation pattern of widespread legume shrubs along a large elevation gradient. We also investigate whether leaf δ13C of nurse plants can track the facilitation pattern.

METHODS

We measured the relative interaction index (RII) of the number of species within and outside the canopy of two widespread legume shrub species (Caragana gerardiana and Caragana versicolor) alternatively distributed along a large elevation gradient in the Trans-Himalayas. We also assessed the proportional increase of species richness (ISR) at the community level using the paired plot data. To determine site-specific water availability, we measured the leaf δ13C of nurse shrubs and calculated the Thornthwaite moisture index (MI) for each elevation site.

KEY RESULTS

Elevational variations in RII, ISR and δ13C were mainly explained by the MI when the effects of soil nitrogen and plant traits (leaf nitrogen and shrub size) were controlled. Variations in RII and ISR across the two nurse species were explained better by δ13C than by smoothly changing climatic factors along elevation. At the transition zone between the upper limit of C. gerardiana (4100 m) and the lower limit of C. versicolor (4200 m), RII and ISR were much higher in C. versicolor than in C. gerardiana under a similar MI. Such an abrupt increase in facilitation induced by nurse species replacement was well tracked by the variation of δ13C.

CONCLUSIONS

Water availability and nurse species replacement are crucial to shaping facilitation patterns by legume shrubs along a large elevation gradient in dry mountainous regions, such as the Trans-Himalayas. Turnover in nurse species under global change might significantly alter the pattern of nurse plant facilitation associated with water availability, which can be well tracked by leaf δ13C.

Genomics of Yoonia sp. Isolates (Family Roseobacteraceae) from Lake Zhangnai on the Tibetan Plateau

Understanding the genomic differentiation between marine and non-marine aquatic microbes remains a compelling question in ecology. While previous research has identified several lacustrine lineages within the predominantly marine Roseobacteraceae family, limited genomic data have constrained our understanding of their ecological adaptation mechanisms. In this study, we isolated four novel Yoonia strains from a brackish lake on the Tibetan Plateau. These strains have diverged from their marine counterparts within the same genus, indicating a recent habitat transition event from marine to non-marine environments. Metabolic comparisons and ancestral genomic reconstructions in a phylogenetic framework reveal metabolic shifts in salinity adaptation, compound transport, aromatics degradation, DNA repair, and restriction systems. These findings not only corroborate the metabolic changes commonly observed in other non-marine Roseobacters but also unveil unique adaptations, likely reflecting the localized metabolic changes in responses to Tibetan Plateau environments. Collectively, our study expands the known genomic diversity of non-marine Roseobacteraceae lineages and enhances our understanding of microbial adaptations to lacustrine ecosystems.

Climate and litter traits affect the response of litter decomposition to soil fauna

OBJECTIVES

Soil fauna plays a crucial role in contributing to litter breakdown, accelerating the decomposition rate and enhancing the biogeochemical cycle in terrestrial ecosystems. Comprehending the specific fauna role of functional species in litter decomposition is challenging due to their vast numbers and diversity. Climate and litter quality are widely acknowledged as dominant drives of litter decomposition across large spatial scales. However, the pattern of climate and litter quality modulates the effect of soil fauna on litter decomposition remains largely unexplored. To address this gap, we conducted an extensive analysis using data from 81 studies to investigate how climate and litter traits affects soil fauna in the decomposition.

DATA DESCRIPTION

The paper describes fauna body size, climate zones (tropical, subtropical and temperate), ecosystem types (forest, grassland, wetland and farmland), soil types (sand, loam and clay), decomposed duration (< 180, 180-360, > 360 days), litter initial traits, average annual temperature and precipitation. The litter traits encompass various parameters such as concentrations of carbon, nitrogen, phosphorus, potassium, lignin, cellulose, total phenol, condensed tannin, hydrolysable tannin and other nutrient traits. These comprehensive datasets provide valuable insights into the role of soil fauna on the decomposition at global scale. Furthermore, the data will give researchers keys to assess how climate, litter quality and soil fauna interact to determine decomposition rates.

Effects of ex situ conservation on diversity and function of the gut microbiota of the Tibetan wild ass (Equus kiang)

Ex situ conservation is the main method for the protection of endangered wildlife. To explore the effect of ex situ conservation on the gut microbiota of the kiang (Equus kiang), metagenomic sequencing combined with bioinformatics analysis was used to investigate the composition and function of the gut microbiota of the kiang. The results showed that ex situ conservation not only protected wildlife, but also affected the composition and function of gut microbiota, as well as the health of animals. In the zoo, the ratio of the relative abundance of Firmicutes to that of Bacteroidetes (F/B) is higher, clusters of potentially pathogenic bacteria (such as Catonella, Catonella, and Mycoplasma) are more numerous, the abundance of resistance genes is higher, and the abundance of metabolic functions is increased. The dynamic changes of the gut microbiota also played an important role in the nutritional absorption, energy metabolism, and environmental adaptation of the kiang. Improving the rearing environment and increasing food diversity play important roles for increasing the diversity of gut microbiota, reducing the spread of potentially pathogenic bacteria, and reducing diseases. In the wild, especially in winter and in food-deficient areas, food supplementation can enhance the gut microbial homeostasis of wild animals and reduce the impact of crises. In depth studies of the gut microbial function of wildlife have important implications for improving ex situ conservation.

Effects of provisioning on the activity budget and foraging strategies of black-and-white snub-nosed monkeys (Rhinopithecus bieti) in the Baima Snow Mountain Nature Reserve, Yunnan, China

Provisioning can significantly affect the ranging patterns, foraging strategies, and time budget of wild primates. In this study, we document for the first time, the effects of provisioning on the activity budget and foraging effort in an Asian colobine. Over 3-years, we used an instantaneous scanning method at 10-min intervals to collect data on the activity budget of a semiprovisioned breeding band (SPB) of black-and-white snub-nosed monkeys (Rhinopithecus bieti) (42-70 individuals) at Xiangguqing (Tacheng), Yunnan, China. We then compared the effects of provisioning in our study band with published data on a sympatric wild nonprovisioned breeding band (NPB) of R. bieti (ca. 360 monkeys) at the same field site. The SPB spent 25.6% of their daytime feeding, 17.1% traveling, 46.9% resting, and 10.3% socializing. In comparison, the NPB devoted more time to feeding (34.9%) and socializing (14.1%), less time to resting (31.3%), and was characterized by a greater foraging effort (1.74 versus 0.96, foraging effort = (feeding + traveling)/resting; see Methods). There was no difference between bands in the proportion of their activity budget devoted to traveling (15.7% vs. 17.1%). In addition, the SPB exhibited a more consistent activity budget and foraging effort across all seasons of the year compared to the NPB. These findings suggest that the distribution, availability, and productivity of naturally occurring feeding sites is a major determinant of the behavioral strategies and activity budget of R. bieti. Finally, a comparison of our results with data on six nonprovisioned R. bieti bands indicates that caution must be raised in meta-analyses or intraspecific comparisons of primate behavioral ecology that contain data generated from both provisioned and nonprovisioned groups.

Oxidative stress mediates the impact of heatwaves on survival, growth and immune status in a lizard

Climate change often includes increases in the occurrence of extreme environmental events. Among these, heatwaves affect the pace of life and performance of wildlife, particularly ectothermic animals, owing to their low thermoregulatory abilities. However, the underlying mechanisms by which this occurs remain unclear. Evidence shows that heatwaves alter the redox balance of ectotherms, and oxidative stress is a major mediator of life-history trade-offs. Therefore, oxidative stress may mediate the effect of extreme thermal conditions on the life histories of ectotherms. To test this hypothesis, a 2 × 2 experiment was conducted to manipulate the redox balance (through a mitochondrial uncoupler that alleviates oxidative stress) of the desert toad-headed agama (Phrynocephalus przewalskii) exposed to heatwave conditions. We recorded lizard growth and survival rates and quantified their redox and immune statuses. In control lizards (unmanipulated redox balance), heatwave conditions decreased growth and survival and induced oxidative damage and immune responses. By contrast, lizards with alleviated oxidative stress showed close-to-normal growth, survival, and immune status when challenged with heatwaves. These results provide mechanistic insight into the role of oxidative stress in mediating the effects of extreme temperatures on ectothermic vertebrates, which may have major eco-evolutionary implications.

Object use in insects

Insects are the most diverse group of organisms in the animal kingdom, and some species exhibit complex social behaviors. Although research on insect object use is still in its early stages, insects have already been shown to display rich object-use behaviors. This review focuses on patterns and behavioral flexibility in insect object-use behavior, and the role of cultural evolution in the development of object-use behaviors. Object use in insects is not widespread but has been documented in a diverse set of taxa. Some insects can use objects flexibly and display various object-use patterns. Like mammals and birds, insects use objects in diverse activities, including foraging, predator defense, courtship, and play. Intelligence, pre-existing manipulative behaviors, and anatomical structure affect innovations in object use. In addition, learning and imitation are the main mechanisms underlying the spread of object-use behaviors within populations. Given that insects are one of the major animal groups engaging in object use, studies of insect object use could provide general insights into object use in the animal kingdom.

Forestation at the right time with the right species can generate persistent carbon benefits in China

Previous evaluations on the biophysical potential of forest carbon sink have focused on forestation area distribution and the associated carbon stock for equilibrium-state forests after centuries-long growth. These approaches, however, have limited relevance for climate policies because they ignore the near-term and mid-term decadal carbon uptake dynamics and suitable forest species for forestation. This study developed a forestation roadmap to support China's "carbon neutrality" objective in 2060 by addressing three key questions of forestation: where, with what forest species, and when to afforest. The results yielded a high-confidence potential forestation map for China at a resolution of 1 km with the identified optimal native forest type or species. Our analysis revealed an additional 78 Mha suitable for forestation up to the 2060s, a 43% increase on the current forest area. Selecting forest species for maximal carbon stock in addition to maximizing local environmental suitability enabled almost a doubling in forest carbon sink potential. Progressive forestation of this area can fix a considerable amount of CO2 and compensate for the carbon sink decline in existing forests. Altogether, the entire forest ecosystem can support a persistent biophysical carbon sink potential of 0.4 Pg C y-1 by 2060 and 0.2 Pg C y-1 by 2100, offsetting 7 to 14% of the current national fossil CO2 emissions. Our research provides an example of building a forestation roadmap toward a sustained forest carbon sink, which creates a critical time window for the emission cuts required by the goal of carbon neutrality.

Male spiny frogs enter the underwater battlefield with loose skin exhibiting enhanced penetration of capillaries into the epidermis

The skin has multiple functions, and capillaries can penetrate the epidermis to shorten the diffusion path while allowing maintenance of overall epidermal thickness for nonrespiratory roles. However, a method for quantifying the capillary penetration extent is lacking. Such a method may facilitate making comparisons and detecting associations, potentially making the extent a useful variable in biological studies. We quantified the extent as the ratio of the average minimum thickness of epidermis overlying each capillary to the average epidermal thickness along a skin section and then explored its performance in the Emei mustache toad, Leptobrachium boringii, a species in which breeding males with loose skin call and fight each other with maxillary spines underwater. The ratio showed informative associations with other variables, such as perfused capillary density. It displayed small intragroup variation and could be more sensitive than other variables in revealing structural differences in the skin. The ratio estimates were lowest and were correlated with epidermal and stratum compactum thicknesses in breeding males, i.e., a covariation but not reinforcement against stabbing, constituting early evidence consistent with the increased extensibility of loose skin conferring a defensive advantage during combat in amphibians. In addition, our results lead to the hypothesis that high hemoglobin density along subepidermal capillaries favors the maintenance of low blood partial oxygen pressure and hence increases cutaneous oxygen uptake. We also provide evidence supporting the new idea that the cooccurrence of loose skin and underwater calling found in some frogs can be explained by the latter benefiting from a large functional respiratory surface area. Awareness of the usefulness of the ratio may promote its application and the quantification of the penetration. Regarding exchange surface design, these findings for L. boringii imply a case in which looseness increases surface area as well as prevents damage.

Stable functional structure despite high taxonomic variability across fungal communities in soils of old-growth montane forests

BACKGROUND

Major advances over the past decade in molecular ecology are providing access to soil fungal diversity in forest ecosystems worldwide, but the diverse functions and metabolic capabilities of this microbial community remain largely elusive. We conducted a field survey in montane old-growth broadleaved and conifer forests, to investigate the relationship between soil fungal diversity and functional genetic traits. To assess the extent to which variation in community composition was associated with dominant tree species (oak, spruce, and fir) and environmental variations in the old-growth forests in the Jade Dragon Snow Mountain in Yunnan Province, we applied rDNA metabarcoding. We also assessed fungal gene expression in soil using mRNA sequencing and specifically assessed the expression of genes related to organic matter decomposition and nutrient acquisition in ectomycorrhizal and saprotrophic fungi.

RESULTS

Our taxonomic profiling revealed striking shifts in the composition of the saprotrophic and ectomycorrhizal guilds among the oak-, fir-, and spruce-dominated forests. The core fungal microbiome comprised only ~ 20% of the total OTUs across all soil samples, although the overlap between conifer-associated communities was substantial. In contrast, seasonality and soil layer explained only a small proportion of the variation in community structure. However, despite their highly variable taxonomic composition, fungal guilds exhibited remarkably similar functional traits for growth-related and core metabolic pathways across forest associations, suggesting ecological redundancy. However, we found that the expression profiles of genes related to polysaccharide and protein degradation and nutrient transport notably varied between and within the fungal guilds, suggesting niche adaptation.

CONCLUSIONS

Overall, our metatranscriptomic analyses revealed the functional potential of soil fungal communities in montane old-growth forests, including a suite of specialized genes and taxa involved in organic matter decomposition. By linking genes to ecological traits, this study provides insights into fungal adaptation strategies to biotic and environmental factors, and sheds light on the importance of understanding functional gene expression patterns in predicting ecosystem functioning. Video Abstract.

Understanding Global Rice Trade Flows: Network Evolution and Implications

Rice holds a significant position as one of the world's most important food crops, and international trade plays a crucial role in regulating rice supply and demand. Analyzing the structural evolution of the global rice trade from a network perspective is paramount for understanding the global rice-trade supply chain and ensuring global food security. This study utilizes international rice-trade data from 2000 to 2021 and employs various network analysis methods to depict the spatial and temporal patterns of the global rice trade, examines the network topologies of the global rice trade, and reveals the impacts of its evolution on food security. The research findings are as follows: (1) Global rice-trade scale has increased over time, indicating a relatively stable development with the gradual formation of complex rice-trade networks. Since 2000, the global rice-trade networks have shown increasing density characterized by Asia as the primary export source and Africa as an important import market. (2) Network analysis indicators demonstrate a growing trend in the size and density of the global rice-trade networks, along with increasingly optimized network structures and improved network connectivity efficiency. Core positions in the networks are occupied by Thailand, Vietnam, India, China, Pakistan, and the United States, while import partners in European and American countries, such as Germany, France, UK, Canada, The Netherlands, and Belgium, show greater diversification. Asia, Europe, and North America form agglomeration regions for rice-exporting countries. Additionally, importing and exporting countries in the global rice-trade networks exhibit certain geographical concentrations. (3) The network backbones of the global rice trade are continuously evolving and being refined, characterized by dominant large rice-exporting countries in Asia and prominent developed countries in Europe and North America. The backbone structures revolve around India as the core, Thailand and Pakistan as the second cores, and critical nodes represented by Italy, the United States, China, and Vietnam. Regional backbone networks have also formed in Asia and Europe. Based on these findings, this paper clarifies the complex network characteristics of the global rice trade and offers insights to promote international rice-trade cooperation and safeguard global food security.

Composition, distribution, health risks, and drivers of phthalates in typical red paddy soils

The accelerated accumulation of phthalate esters (PAEs) in paddy soils poses a serious threat to human health. However, related studies mainly focus on facility vegetable fields, drylands, and orchards, and little is known about paddy soils. In this study, 125 samples were collected from typical red paddy fields to investigate the pollution characteristics, sources, health risks, and main drivers of PAEs. Soil physicochemical properties, enzyme activity, and bacterial community composition were also measured simultaneously. The results showed that eight PAE congeners were detected ranging from 0.17 to 1.97 mg kg-1. Di-n-butyl phthalate (DBP), di-(2-ethylhexyl) phthalate (DEHP), and di-isobutyl phthalate (DIBP) were the most abundant PAE congeners, accounting for 81% of the total PAEs. DEHP exhibited a potential carcinogenic risk to humans through the intake route. The main PAEs were positively correlated with soil organic matter (SOM) and soil water content (SWC) contents. Low levels of PAEs increased bacterial abundance. Furthermore, most PAE congeners were positively correlated with hydrolase activity. Soil acidity and nutrient dynamics played a dominant role in the bacterial community composition, with PAE congeners playing a secondary role. These findings suggest that there may be a threshold response between PAEs and organic matter and nutrient transformation in red paddy soils, and that microbial community should be the key driver. Overall, this study deepens the understanding of ecological risks and microbial mechanisms of PAEs in red paddy soils.

Non-symmetric responses of leaf onset date to natural warming and cooling in northern ecosystems

The northern hemisphere has experienced regional cooling, especially during the global warming hiatus (1998-2012) due to ocean energy redistribution. However, the lack of studies about the natural cooling effects hampers our understanding of vegetation responses to climate change. Using 15,125 ground phenological time series at 3,620 sites since the 1950s and 31-year satellite greenness observations (1982-2012) covering the warming hiatus period, we show a stronger response of leaf onset date (LOD) to natural cooling than to warming, i.e. the delay of LOD caused by 1°C cooling is larger than the advance of LOD with 1°C warming. This might be because cooling leads to larger chilling accumulation and heating requirements for leaf onset, but this non-symmetric LOD response is partially offset by warming-related drying. Moreover, spring greening magnitude, in terms of satellite-based greenness and productivity, is more sensitive to LOD changes in the warming area than in the cooling. These results highlight the importance of considering non-symmetric responses of spring greening to warming and cooling when predicting vegetation-climate feedbacks.

Environmental fate and ecological impact of the potentially toxic elements from the geothermal springs

Potentially toxic elements from geothermal springs can cause significant pollution of the surrounding environment and pose potential risk to the ecosystem. The fate of potentially toxic elements in the water-soil-plant system in the Yangbajain geothermal field on the Tibetan Plateau, China was investigated to assess their impact on the eco-environment. The concentrations of Be, F, As, and Tl were highly elevated in the headwaters of the Yangbajain geothermal springs, and their concentrations in the local surface water impacted by the geothermal springs reached 8.1 μg/L (Be), 23.9 mg/L (F), 3.83 mg/L (As), and 8.4 μg/L (Tl), respectively, far exceeding the corresponding thresholds for surface and drinking water. The absence of As-Fe co-precipitation, undersaturated F-, and weak adsorption on minerals at high geothermal spring pH may be responsible for the As- and F-rich drainage, which caused pollution of local river. As concentrations in the leaves of Orinus thoroldii (Stapf ex Hemsl.) Bor were up to 42.7 μg/g (dry weight basis), which is an order of magnitude higher than the allowable limit in animal feeds. The locally farmed yaks are exposed to the excessive amount of F and As with high exposure risk through water-drinking and grass-feeding.

Niche-Specific Restructuring of Bacterial Communities Associated with Submerged Macrophyte under Ammonium Stress

Submerged macrophytes and their epiphytic microbes form a "holobiont" that plays crucial roles in regulating the biogeochemical cycles of aquatic ecosystems but is sensitive to environmental disturbances such as ammonium loadings. Increasingly more studies suggest that plants may actively seek help from surrounding microbial communities whereby conferring benefits in responding to particular abiotic stresses. However, empirical evidence is scarce regarding how aquatic plants reconstruct their microbiomes as a "cry-for-help" against acute ammonium stress. Here, we investigated the temporal dynamics of the phyllosphere and rhizosphere bacterial communities of Vallisneria natans following ammonium stress and recovery periods. The bacterial community diversity of different plant niches exhibited opposite patterns with ammonium stress, that is, decreasing in the phyllosphere while increasing in the rhizosphere. Furthermore, both phyllosphere and rhizosphere bacterial communities underwent large compositional changes at the end of ammonium stress, significantly enriching of several nitrifiers and denitrifiers. Meanwhile, bacterial legacies wrought by ammonium stress were detected for weeks; some plant growth-promoting and stress-relieving bacteria remained enriched even after stress disappeared. Structural equation model analysis showed that the reshaped bacterial communities in plant niches collectively had a positive effect on maintaining plant biomass. Additionally, we applied an age-prediction model to predict the bacterial community's successional trajectory, and the results revealed a persistent change in bacterial community development under ammonium treatment. Our findings highlight the importance of plant-microbe interactions in mitigating plant stress and fostering a better understanding of the assembly of plant-beneficial microbes under ammonium stress in aquatic ecosystems. IMPORTANCE Increasing anthropogenic input of ammonium is accelerating the decline of submerged macrophytes in aquatic ecosystems. Finding efficient ways to release submerged macrophytes from ammonium stress is crucial to maintain their ecological benefits. Microbial symbioses can alleviate abiotic stress in plants, but harnessing these beneficial interactions requires a detailed understanding of plant microbiome responses to ammonium stress, especially over a continuous time course. Here, we tracked the temporal changes in bacterial communities associated with the phyllosphere and rhizosphere of Vallisneria natans during ammonium stress and recovery periods. Our results showed that severe ammonium stress triggers a plant-driven timely reshaping of the associated bacterial community in a niche-specific strategy. The reassembled bacterial communities could potentially benefit the plant by positively contributing to nitrogen transformation and plant growth promotion. These findings provide empirical evidence regarding the adaptive strategy of aquatic plants whereby they recruit beneficial microbes against ammonium stress.

The Change in Habitat Quality for the Yunnan Snub-Nosed Monkey from 1975 to 2022

The reduction in habitat quality (as shown, in part, by the increase in habitat rarity) is an important challenge when protecting the Yunnan snub-nosed monkey. We used the InVEST model to quantitatively analyze the dynamic changes in the habitat of the Yunnan snub-nosed monkey from 1975 to 2022. The results show that in the study period, the degree of habitat degradation increased, with the degradation range at its widest in the south, and the degradation intensity highest in the north, especially along a center "spine" area in the north. Over the latter part of the study period, the habitat quality of most monkey groups improved, which is conducive to the survival and reproduction of the population. However, the habitat quality and monkey populations are still at significant risk. The results provide the basis for formulating the protection of the Yunnan snub-nosed monkey and provide research cases for the protection of other endangered species.

Ethylene constrains stomatal reopening in Fraxinus chinensis post moderate drought

Clarifying the mechanisms underlying the recovery of gas exchange following drought is the key to providing insights into plant drought adaptation and habitat distribution. However, the mechanisms are still largely unknown. Targeting processes known to inhibit gas exchange during drought recovery, we measured leaf water potential, the leaf hydraulic conductance, stomatal reopening, abscisic acid (ABA) and the ethylene emission rate (EER) following moderate drought stress in seedlings of the globally pervasive woody tree Fraxinus chinensis. We found strong evidence that the slow stomatal reopening after rehydration is regulated by a slow decrease in EER, rather than changes in leaf hydraulics or foliar ABA levels. This was supported by evidence of rapid gas exchange recovery in plants after treatment with the ethylene antagonist 1-methylcyclopropene. These findings provide evidence to rigorously support ethylene as a key factor constraining stomatal reopening from moderate drought directly, thereby potentially opening new windows for understanding species drought adaptation.

Genome-wide comparison of DNA methylation patterns between yak and three cattle strains and their potential association with mRNA transcription

Yak has evolved specific adaptative mechanisms to high-altitude environment. Up to date, only a few studies reported the DNA methylation in yak. In the present study, genome-wide DNA methylome and transcriptome profiles in lung, mammary, and biceps brachii muscle tissues were compared between yak and three cattle breeds (Tibetan cattle, Sanjiang cattle, and Holstein cattle). The association between differentially expressed genes (DEGs) and differentially methylated regions (DMRs) was analyzed, and the biological functions of DEGs potentially driven by DMRs were explored by KEGG enrichment analysis. Finally, we found that yak-specific DMRs-driven DEGs were mainly involved in neuromodulation, respiration, lung development, blood pressure regulation, cardiovascular protection, energy metabolism, DNA repair, and immune functions. The higher levels of the key genes associated with these functions were observed in yak than in cattle, suggesting that DNA methylation might regulate these genes. Overall, the present study contributes basic data at the DNA methylation level to further understand the physiological metabolism in yak.

Geographic isolation and climatic heterogeneity drive population differentiation of Rosa chinensis var. spontanea complex

Global biodiversity is contracting rapidly due to potent anthropogenic activities and severe climate change. Wild populations of Rosa chinensis var. spontanea and Rosa lucidissima are rare species endemic to China, as well as important germplasm resources for rose breeding. However, these populations are at acute risk of extinction and require urgent action to ensure their preservation. We harnessed 16 microsatellite loci to 44 populations of these species and analysed population structure and differentiation, demographic history, gene flow and barrier effect. In addition, a niche overlap test and potential distribution modelling in different time periods were also carried out. The data indicate that: (1) R. lucidissima cannot be regarded as a separate species from R. chinensis var. spontanea; (2) the Yangtze River and the Wujiang River function as barriers in population structure and differentiation, and precipitation in the coldest quarter may be the key factor for niche divergence of R. chinensis var. spontanea complex; (3) historical gene flow showed a converse tendency to current gene flow, indicating that alternate migration events of R. chinensis var. spontanea complex between south and north were a response to climate oscillations; and (4) extreme climate change will decrease the distribution range of R. chinensis var. spontanea complex, whereas the opposite will occur under a moderate scenario for the future. Our results resolve the relationship between R. chinensis var. spontanea and R. lucidissima, highlight the pivotal roles of geographic isolation and climate heterogeneity in their population differentiation, and provide an important reference for comparable conservation studies on other endangered species.

Groundwater potential assessment using GIS-based ensemble learning models in Guanzhong Basin, China

Groundwater plays a crucial role in sustaining industrial and agricultural production and meeting the water demands of the growing population in the semi-arid Guanzhong Basin of China. The objective of this study was to evaluate the groundwater potential of the region through the use of GIS-based ensemble learning models. Fourteen factors, including landform, slope, slope aspect, curvature, precipitation, evapotranspiration, distance to fault, distance to river, road density, topographic wetness index, soil type, lithology, land cover, and normalized difference vegetation index, were considered. Three ensemble learning models, namely random forest (RF), extreme gradient boosting (XGB), and local cascade ensemble (LCE), were trained and cross-validated using 205 sets of samples. The models were then applied to predict groundwater potential in the region. The XGB model was found to be the best, with an area under the curve (AUC) value of 0.874, followed by the RF model with an AUC of 0.859, and the LCE model with an AUC of 0.810. The XGB and LCE models were more effective than the RF model in discriminating between areas of high and low groundwater potential. This is because most of the RF model's prediction outcomes were concentrated in moderate groundwater potential areas, indicating that RF is less decisive when it comes to binary classification. In areas predicted to have very high and high groundwater potential, the proportions of samples with abundant groundwater were 33.6%, 69.31%, and 52.45% for RF, XGB, and LCE, respectively. In contrast, in areas predicted to have very low and low groundwater potential, the proportions of samples without groundwater were 57.14%, 66.67%, and 74.29% for RF, XGB, and LCE, respectively. The XGB model required the least amount of computational resources and achieved the highest accuracy, making it the most practical option for predicting groundwater potential. The results can be useful for policymakers and water resource managers in promoting the sustainable use of groundwater in the Guanzhong Basin and other similar regions.

Relic DNA effects on the estimates of bacterial community composition and taxa dynamics in soil

DNA-based analyses have become routine methods in soil microbial research, for their high throughput and resolution in characterizing microbial communities. Yet, concerns arise regarding the interference of relic DNA in estimates of viable bacterial community composition and individual taxa dynamics in soils that recovered from post-gamma irradiation. In this study, different soil samples with varying bacterial diversity but similar soil properties were randomly selected. We split each sample into two parts: one part was treated with propidium monoazide (PMA) before DNA extraction, PMA can bind to relic DNA and inhibit PCR amplification by chemical modification; DNA of the other part was extracted following the same process but without PMA pretreatment. Then, soil bacterial abundance was quantified by quantitative polymerase chain reaction, and bacterial community structure was examined by Illumina metabarcoding sequencing of 16S rRNA gene. The results showed that the higher bacterial richness and evenness were estimated when relic DNA was present. The variation trends of bacterial abundance, alpha diversity, and beta diversity remained the same, as reflected by the significant correlations between PMA-treated and -untreated samples (P < 0.05). Moreover, as the mean abundance increased, the reproducibility of detecting individual taxa dynamics between relic DNA present and absent treatments increased. These findings provide empirical evidence that a more even distribution of species abundance derived from relic DNA would result in the overestimation of richness in the total DNA pools and also have crucial implications for guiding proper application of high-throughput sequencing to estimate bacterial community diversity and taxonomic population dynamic. KEY POINTS: • Relic DNA effects on the bacterial community in sterilized soils were assessed. • More even species abundance distribution in relic DNA overestimates true richness. • The reproducibility of individual taxa dynamics increased with their abundance.

High carbon emissions from thermokarst lakes and their determinants in the Tibet Plateau

Thermokarst lakes are potentially important sources of methane (CH₄ ) and carbon dioxide (CO₂ ). However, considerable uncertainty exists regarding carbon emissions from thermokarst lakes owing to a limited understanding of their patterns and motivators. In this study, we measured CH₄ and CO₂ diffusive fluxes in 163 thermokarst lakes in the Qinghai-Tibet Plateau (QTP) over 3 years from May to October. The median carbon emissions from the QTP thermokarst lakes were 1440 mg CO₂ m^-2 day^-1 and 60 mg CH₄ m^-2 day^-1 , respectively. The diffusive rates of CO₂ and CH₄ are related to the catchment land cover type. Sediment microbial abundance and hydrochemistry explain 51.9% and 38.3% of the total variance in CH₄ diffusive emissions, respectively, while CO₂ emissions show no significant relationship with environmental factors. When upscaling carbon emissions from the QTP thermokarst lakes, the annual average CH₄ release per lake area is equal to that of the pan-Arctic region. Our findings highlight the importance of incorporating in situ observation data with different emission pathways for different land cover types in predicting carbon emissions from thermokarst lakes in the future.

Safe Rice Production in Cd-Contaminated Paddy Soil: Strategy and Environmental Implications

This field study explored safe rice production in Cd-contaminated red paddy soil by application of the combined Si-/Se- containing foliar inhibitors (Si or Se) and the mixture amendments of quicklime (Q), polyacrylamide (A), or/and sepiolite (S) at low (1) and high (2) application rates. The results showed that all treatments increased soil pH and decreased total P and soil organic matter (excluding QSe2). With the increasing application rates, QAS significantly decreased the available Cd because of the enhanced stabilization, while QSi and QSe significantly increased the available Cd because of the inhibited plant uptake. After remediation, QA1, QSi2, and QSe2 most effectively decreased the uptake Cd by rice to meet the threshold of National Food Safety Standard of China. The treatments excluding Q1, QA1, QSi1, and QSi2 did not dramatically change the bacterial community structure in soil. Collectively, QSe2 was recommended for remediating Cd-contaminated red paddy soil.

The potential evaluation of groundwater by integrating rank sum ratio (RSR) and machine learning algorithms in the Qaidam Basin

Groundwater is a vital resource in arid areas that sustains local industrial development and environmental preservation. Mapping groundwater potential zones and determining high-potential regions are essential for the responsible use of the local groundwater resource. When utilizing machine learning or deep learning algorithms to forecast groundwater potential in arid areas, difficulties such as inaccurate and overfitting predictions might occur due to a shortage of borehole samples. In this study, a database of groundwater conditioning factors with a size of 275,157 × 9 was created in the Qaidam Basin, and 85 known borehole samples were collected. The groundwater potential was evaluated using a combination of rank sum ratio (RSR), projection pursuit regression (PPR) and random forest (RF) algorithms, resulting in four models: PPR, RSR-PPR, RSR-RF, and RF. Results indicated that the groundwater potential was higher in mountainous regions surrounding the Qaidam Basin and decreased progressively towards the central and northwestern regions where most industries and facilities are located. The two primary factors, according to the PPR and RF models, were evapotranspiration (0.246, 0.225) and landform (0.176, 0.294). In terms of their ability to accurately forecast the borehole samples, the four models ranked as follows: RF > RSR-RF > RSR-PPR > PPR. The accuracy of the four models in the low-potential area was 0.73 (PPR), 0.60 (RSR-PPR), 0.87 (RSR-RF), and 0.80 (RF), respectively. However, the RF model showed overfitting due to a lack of samples, especially in high-potential regions, which limits its applicability. The RSR-RF method was applied directly to evaluate the entire factor database, avoiding the risk of overfitting caused by a limited number of training samples. The results demonstrate that the RSR-RF model is effective for classifying groundwater potential types in samples and mapping groundwater potential of the study area. This research presents a novel approach for groundwater potential predictions in areas with insufficient sample sizes, providing a reference for policymakers and researchers.

Revisiting the mechanisms of mid-Tertiary uplift of the NE Tibetan Plateau

Contrasting views exist on timing and mechanisms of Tertiary crustal uplift in the NE Tibetan Plateau based on different approaches, with many models attributing surface uplift to crustal shortening. We carry out a comprehensive investigation of mid-Tertiary stratigraphy, sedimentology, and volcanism in the West Qinling, Hoh Xil and Qaidam basin, and the results challenge previous views. It was held that the discordance between Oligocene and Miocene strata is an angular unconformity in the West Qinling, but our field observations show that it is actually a disconformity, indicative of vertical crustal uplifting rather than crustal shortening at the Oligocene to Miocene transition. Widespread occurrence of synsedimentary normal faults in mid-Tertiary successions implicates supracrustal stretching. Miocene potassic-ultrapassic and mafic-ultramafic volcanics in the Hoh Xil and West Qinling suggest a crucial role of deep thermomechanical processes in generating crust- and mantle-sourced magmatism. Also noticeable are the continuity of mid-Tertiary successions and absence of volcanics in the Qaidam basin. Based on a holistic assessment of stratigraphic-sedimentary processes, volcanic petrogenesis, and spatial variations of lithospheric thicknesses, we speculate that small-sale mantle convection might have been operating beneath northeast Tibet in the mid-Tertiary. It is assumed that northward asthenospheric flow was impeded by thicker cratonic lithosphere of the Qaidam and Alxa blocks, thereby leading to edge convection. The edge-driven convection could bring about surface uplift, induce supracrustal stretching, and trigger vigorous volcanism in the Hoh Xil and West Qinling in the mid-Tertiary period. This mechanism satisfactorily explains many key geologic phenomena that are hardly reconciled by previous models.

Effects of food availability and climate on the activity budget of Shortridge's langur (Trachypithecus shortridgei) in the Drung Valley, Gaoligong Mountains, China

Food availability and climate represent environmental factors that affect species' social behavior, ranging patterns, diet, and activity budget. From August 2012 to September 2013, we examined the effects of seasonal changes in food availability, temperature, and rainfall on the diet and behavioral ecology of Shortridge's langur (Trachypithecus shortridgei) an Endangered primate species inhabiting moist evergreen broadleaf forests in the Eastern Himalayas. Our field site represents the northernmost latitudinal distribution of this species. Data were collected using scan sampling at 10 min intervals, and analyzed based on generalized linear models. The results indicate that the langurs experienced two feeding peaks (9:00 and 17:00) and two traveling peaks (10:00 and 19:00) during each day. Periods of rest, mainly occurred between 10:00 and 13:00, and overnight. Feeding accounted for 38.5% of the daily activity budget, followed by resting (35%), traveling (24.5%), and socializing (2%). During periods when young leaves were most available, the langurs increased feeding time on young leaves (35% vs. 4%). During periods of maximum fruit availability, the langurs decreased total time spent feeding (36.6% vs. 40.4%), devoted more time to traveling (28.1% vs. 21%), and increased time spent consuming fruit (49.1% vs. 11.8%). During the winter, the langurs increased their consumption of mature leaves (44.5%) and reduced time spent traveling (20.2% vs. 25.4%). Overall, time spent resting was greatest in the spring (47.5%), time spent feeding was greatest during the summer (51.1%), and time spent in traveling was greatest in the autumn (33.2%). The frequency of social interactions remained relatively constant throughout the year. Foraging effort was greatest in the summer, when fruits dominated the diet. Like other species of temperate langurs, T. shortridgei devoted less time to resting, more time to feeding, and was characterized by a greater year-round foraging effort than tropical/subtropical langurs.

New Fossil Evidence Suggests That Angiosperms Flourished in the Middle Jurassic

Angiosperms are a group of plants with the highest rate of evolution, the largest number of species, the widest distribution and the strongest adaptability. Needless to say, angiosperms are the most important group for the humans. The studies on the origin, evolution and systematics of angiosperms have been the major challenges in plant sciences. However, the origin and early history of angiosperms remains poorly understood and controversial among paleobotanists. Some paleobotanists insist that there were no angiosperms in the pre-Cretaceous age. However, this conclusion is facing increasing challenges from fossil evidence, especially Early Jurassic Nanjinganthus, which is based on over two hundred specimens of fossil flowers. Studying more fossil plants is the only reliable way to elucidate the origin and early evolution of angiosperms. Here, we document a new species of angiosperms, Qingganninginfructus formosa gen. et sp. nov, and provide the first detailed three-dimensional morphology of Qingganninginfructus gen. nov from the Middle Jurassic of Northwest China. A Micro-CT examination shows that the best-preserved fossil infructescence has eleven samaroid fruits, each with a single basal ovule. Since these fossils are distinct in morphology and organization from all organs of known gymnosperms and angiosperms (the latter are defined by their enclosed ovules), we interpret Qingganninginfructus as a new genus of angiosperms including a new species, Q. formosa gen. et sp. nov., and an unspecified species from the Middle Jurassic of Northwest China. The discovery of this new genus of angiosperms from the Middle Jurassic, in addition to the existing records, undermines the "no angiosperms until the Cretaceous" stereotype and updates the perspective on the origin and early history of angiosperms.

DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs

DNA barcoding has greatly facilitated studies of taxonomy, biodiversity, biological conservation, and ecology. Here, we establish a reliable DNA barcoding library for Chinese snakes, unveiling hidden diversity with implications for taxonomy, and provide a standardized tool for conservation management. Our comprehensive study includes 1638 cytochrome c oxidase subunit I (COI) sequences from Chinese snakes that correspond to 17 families, 65 genera, 228 named species (80.6% of named species) and 36 candidate species. A barcode gap analysis reveals gaps, where all nearest neighbour distances exceed maximum intraspecific distances, in 217 named species and all candidate species. Three species-delimitation methods (ABGD, sGMYC, and sPTP) recover 320 operational taxonomic units (OTUs), of which 192 OTUs correspond to named and candidate species. Twenty-eight other named species share OTUs, such as Azemiops feae and A. kharini, Gloydius halys, G. shedaoensis, and G. intermedius, and Bungarus multicinctus and B. candidus, representing inconsistencies most probably caused by imperfect taxonomy, recent and rapid speciation, weak taxonomic signal, introgressive hybridization, and/or inadequate phylogenetic signal. In contrast, 43 species and candidate species assign to two or more OTUs due to having large intraspecific distances. If most OTUs detected in this study reflect valid species, including the 36 candidate species, then 30% more species would exist than are currently recognized. Several OTU divergences associate with known biogeographic barriers, such as the Taiwan Strait. In addition to facilitating future studies, this reliable and relatively comprehensive reference database will play an important role in the future monitoring, conservation, and management of Chinese snakes.

Structure-function analyses of coiled-coil immune receptors define a hydrophobic module for improving plant virus resistance

Plant immunity relies on nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs) that detect microbial patterns released by pathogens, and activate localized cell death to prevent the spread of pathogens. Tsw is the only identified resistance (R) gene encoding an NLR, conferring resistance to tomato spotted wilt orthotospovirus (TSWV) in pepper species (Capsicum, Solanaceae). However, molecular and cellular mechanisms of Tsw-mediated resistance are still elusive. Here, we analysed the structural and cellular functional features of Tsw protein, and defined a hydrophobic module to improve NLR-mediated virus resistance. The plasma membrane associated N-terminal 137 amino acid in the coiled-coil (CC) domain of Tsw is the minimum fragment sufficient to trigger cell death in Nicotiana benthamiana plants. Transient and transgenic expression assays in plants indicated that the amino acids of the hydrophobic groove (134th-137th amino acid) in the CC domain is critical for its full function and can be modified for enhanced disease resistance. Based on the structural features of Tsw, a super-hydrophobic funnel-like mutant, TswY137W, was identified to confer higher resistance to TSWV in a SGT1 (Suppressor of G-two allele of Skp1)-dependent manner. The same point mutation in a tomato Tsw-like NLR protein also improved resistance to pathogens, suggesting a feasible way of structure-assisted improvement of NLRs.

Assessing the structural connectivity of international trade networks along the "Belt and Road"

Assessing the trade network connectivity is essential for understanding the trade network structure, optimizing trade development patterns, and improving uneven trade development along the "Belt and Road" (BRI). From the perspective of connectivity, this paper integrates the frontier algorithms in network science and constructs an analytical framework to identify the mesoscale structures, including the community structure, core-periphery structure, and backbone structure embedded in the network, and further explore the structural connectivity of the BRI trade network. The results show that: (1) The BRI trade network represents a trade pattern of "one superpower, many great powers", with three major trade groups in Southeast Asia, the Middle East, and Northern Central and Eastern Europe in terms of geographical space. China is the super core of the BRI trade network, and the most considerable trade links are all centred in China. (2) Five distinctive trade blocs have formed in the BRI trade network. Nevertheless, the structure of the trade blocs shows significant geographical proximity, indicating that geographical distance still plays a vital role in the international trade system at the regional scale. (3) The BRI trade network demonstrates a significant core-periphery structure, with apparent trade clustering among the core countries within the trade network. Among them, nine countries led by China constitute the core structure, and the peripheral structure is large, reaching forty-four. (4) The trade links with China constitute the backbone structure of the whole trade network in the BRI region. In addition, the trade links related to energy trade and re-export trade are also crucial components of the BRI backbone structure. Methodologically, the analytical framework proposed for assessing the network structural connectivity has great potential to be widely applied to other disciplines and fields.