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Background Diet analysis is essential to understanding the functional role of large bird species in food webs. Morphological analysis of regurgitated bird pellet contents is time intensive and may underestimate biodiversity. DNA metabarcoding has the ability to circumvent these issues, but has yet to be done. Methods We present a pilot study using DNA metabarcoding of MT-RNR1 and MT-CO1 markers to determine the species of origin and prey of 45 pellets collected in Qinghai and Gansu Provinces, China. Results We detected four raptor species [Eurasian Eagle Owl (Bubo bubo), Saker Falcon (Falco cherrug), Steppe Eagle (Aquila nipalensis), and Upland Buzzard (Buteo hemilasius)] and 11 unique prey species across 10 families and 4 classes. Mammals were the greatest detected prey class with Plateau Pika (Ochotona curzoniae) being the most frequent. Observed Shannon’s and Simpson’s diversity for Upland Buzzard were 1.089 and 0.479, respectively, while expected values were 1.312 ± 0.266 and 0.485 ± 0.086. For Eurasian Eagle Owl, observed values were 1.202 and 0.565, while expected values were 1.502 ± 0.340 and 0.580 ± 0.114. Interspecific dietary niche partitioning between the two species was not detected. Conclusions Our results demonstrate successful use of DNA metabarcoding for understanding diet via a novel noninvasive sample type to identify common and uncommon species. More work is needed to understand how raptor diets vary locally, and the mechanisms that enable exploitation of similar dietary resources. This approach has wide ranging applicability to other birds of prey, and demonstrates the power of using DNA metabarcoding to study species noninvasively.

Application of next-generation sequencing (NGS) to DNA metabarcoding can greatly increase the understanding of predator–prey dynamics and the conflict between wildlife and humans, but remains underutilized for carnivores such as the threatened snow leopard (Panthera uncia). To date, this technique was hindered by the difficulty in discerning closely related caprines (Caprinae). We identified a segment of mitochondrial cytochrome c oxidase subunit 1 (MT-CO1) to differentiate these prey, and used this marker in tandem with a portion of mitochondrial 12S rRNA (MT-RNR1) to determine dietary items in 165 genetically confirmed snow leopard scats from four range countries. Identified prey species consisted of ten medium to large mammals, three small mammals, and two birds. The dominant prey consumed varied by country, with markhor (Capra falconeri) most prevalent in Pakistan, Siberian ibex (C. sibirica) in Mongolia and Kyrgyzstan, and blue sheep (Pseudois nayaur) in China. Livestock comprised 31% of diet occurrences from Pakistan and 15% from Mongolia. Domestic livestock included goat (C. aegagrus hircus), sheep (Ovis aries), bovids (Bos taurus, B. grunniens, and potentially hybrids), and horse (Equus caballus). Protection and management of regionally specific wild prey is crucial for sustaining snow leopard populations, although overall dietary breadth suggests that snow leopards may exploit other species if necessary, including livestock. Additional sampling efforts across seasons, years, regions, and areas with varying degrees of livestock depredation are needed. MT-CO1 in conjunction with MT-RNR1 can be applied to other carnivore diet studies, making it an important tool for conservation and research, particularly in ecosystems with pastoral communities.

Nature reserves in China are undergoing adjustments in functional zoning. Currently, one urgent problem is determining how to delineate core conservation zones more scientifically and rationally. This case study focused on the Houhe National Nature Reserve, Wufeng County, Hubei Province, China, and was based on the distribution data of seven species (Moschus berezovskii, Elaphodus cephalophus, Muntiacus reevesi, Naemorhedus griseus, Capricornis sumatraensis, Prionailurus bengalensis, and Ursus thibetanus), vegetation types, meteorological factors, human disturbance, terrain, and hydrological variables. Species distributions were predicted through MaxEnt modeling, and MARXAN software was used for systematic conservation planning. The results showed that (1) for the MaxEnt model simulations of one critically endangered (CR) species and six vulnerable (VU) species in Houhe National Nature Reserve, the area under curve (AUC) values of seven species were all greater than 0.8, of which the AUC of M. berezovskii was 0.961, indicating a high modeling accuracy; (2) based on the analysis of the MaxEnt model, MARXAN was used to delineate the core conservation zone of Houhe National Nature Reserve. When the boundary length modifier was set as 100 and planning units as hexagons with a boundary length of 200 m, the priority conservation areas had the fewest fragments. Thus, using these parameters for conservation planning is more reasonable; and (3) among the four proposals obtained from the MARXAN analysis that were based on different conservation targets, those with a conservation target of 80% for CR species and 60% for VU species had the largest priority conservation areas. According to the principles of maintaining ecosystem integrity and habitat connectivity of species and ensuring consistent conservation management, we propose a new functional zoning plan for Houhe National Nature Reserve. In this plan, the core conservation zone will have an area of 5947.76 ha, which will be greater than the sum of the areas of the current buffer and core zones, whereas the area of the general control zone will be 4395.64 ha.

Damage to homesteads by brown bears (Ursus arctos) has become commonplace in Asia, Europe, and the Americas. Science‐based solutions for preventing damages can contribute to the establishment of mechanisms that promote human–bear coexistence. We examined the spatial distribution patterns of house break‐ins by Tibetan brown bears (U. a. pruinosus) in Zhiduo County of the Sanjiangyuan region in China. Occurrence points of bear damage were collected from field surveys completed from 2017 to 2019. The maximum entropy (MaxEnt) model was then used to assess house break‐in risk. Circuit theory modeling was used to simulate risk diffusion paths based on the risk map generated from our MaxEnt model. The results showed that (a) the total risk area of house break‐ins caused by brown bears was 11,577.91 km2, accounting for 29.85% of Zhiduo County, with most of the risk areas were distributed in Sanjiangyuan National Park, accounting for 58.31% of the total risk area; (b) regions of alpine meadow located in Sanjiangyuan National Park with a high human population density were associated with higher risk; (c) risk diffusion paths extended southeast to northwest, connecting the inside of Sanjiangyuan National Park to its outside border; and (d) eastern Suojia, southern Zhahe, eastern Duocai, and southern Jiajiboluo had more risk diffusion paths than other areas examined, indicating higher risk for brown bear break‐ins in these areas. Risk diffusion paths will need strong conservation management to facilitate migration and gene flow of brown bears and to alleviate bear damage, and implementation of compensation schemes may be necessary in risk areas to offset financial burdens. Our analytical methods can be applied to conflict reduction efforts and wildlife conservation planning across the Qinghai–Tibet Plateau., Assessing risk areas and simulating risk diffusion paths are crucial steps toward mitigating brown bear damage and provide a foundation for developing conservation programs and policies that aimed at making coexistence possible.

Extremely endangered wildlife can be effectively protected by ex situ conservation programs. Despite that, the effects of human activity on the health of captive populations are still unclear. Using reduced representation bisulfite sequencing and RNA-seq, we assessed epigenetic and gene transcriptional variations between different types of human intervention (“Custodial” and “Sanctuary” groups) and a “Wild” group of golden snub-nosed monkeys (Rhinopithecus roxellana), which is one of the most endangered primates worldwide. Consequently, we found striking genome-scale divergence of both DNA methylation and gene expression for the Custodial group, which agreed with stronger human interventions on the food supply and management of the group. KEGG pathway analyses indicated that the differentially expressed genes were enriched in a wide range of physiologically functional pathways, most of which are involved in immune and metabolic functions. In particular, a group of core genes in autophagy related pathways, e.g., ATP6V0A1 and PPM1D, were both differentially expressed and methylated. Our findings revealed that the ex situ conserved golden snub-nosed monkey exhibited significant epigenetic and transcriptional adaptation to human intervention, thereby may provide a foundation for future biomarker development that can be used to evaluate the unintended risks of ex situ conservation programs for endangered animal species.

The Sichuan snub-nosed monkey (Rhinopithecus roxellana) is an endangered species endemic to China, where the smallest population resides in Shennongjia National Park, Hubei Province. In this study, the genetic diversity of the Sichuan snub-nosed monkeys from two areas, Qianjiaping (QJP) and Dalongtan (DLT) in Shennongjia National Park was evaluated using single nucleotide polymorphisms (SNPs) data derived from restriction site-associated DNA sequencing (RAD-seq). A total of 41,260 SNP loci were found in 29 Sichuan snub-nosed monkey individuals. The genome-wide nucleotide diversity (π) of the Shennongjia population was 0.001842. The genetic differentiation (FST) between the QJP and DLT subpopulations was 0.034. The heterozygosity of individuals from QJP was 0.3475 ± 0.03696 and 0.3148 ± 0.03501 for individuals from DLT. Although the DLT and QJP subpopulations did not show significant genetic differences, genetic differentiation between the two subpopulations was confirmed using Bayesian cluster analysis, neighbor-joining trees and principal component analysis. These results suggest that the Shennongjia population of Sichuan snub-nosed monkey has relatively low genetic diversity at the genomic level. The little genetic differentiation noted between the DLT and QJP subpopulations likely due to natural and anthropogenic barriers which may exacerbate loss of genetic diversity of this endangered subpopulation.

The wild Bactrian camel is one of the world’s rarest and most endangered animals and is facing hybridization threat due to human encroachment. Although captive breeding programs of the wild camel have been undertaken to save it from extinction, to succeed, we need to take into account many factors, e.g., maintain genetic diversity of captive populations similar to that found in wild populations. We applied restriction-site associated DNA sequencing (RAD-Seq) on a captive population in the most important wild camel conservation center in China—Gansu endangered animal conservation center—to investigate the genetic diversity, potential hybridization and inbreeding threats, and thus further guide population management. We sequenced a total of 44 Bactrian camels including 13 wild camels and 31 domestic camels and generated a genome-wide polymorphism dataset with 679,195 high-quality SNPs. This enabled us to detect wild camel individuals with recent genetic introgression from domestic camels. In addition, it revealed that the studied captive population suffers from inbreeding. We therefore suggest practical measures to improve the management of the wild camel and to protect its natural gene pool.

Understanding animals’ migration, distribution and activity patterns is vital for the development of effective conservation action plans; however, such data for many species are lacking. In this study, we used camera trapping to document the spatial and temporal activity patterns of golden takins (Budorcas taxicolor bedfordi) in Changqing National Nature Reserve in the Qinling mountains, China, from April 2014 to October 2017. Our study obtained 3,323 independent detections (from a total of 12,351 detections) during a total camera trapping effort of 93,606 effective camera trap days at 573 sites. Results showed that: (1) the golden takin’s utilization distributions showed seasonal variation, with larger utilization distributions during spring and autumn compared to summer and winter; (2) the species was recorded at the highest elevations in July, and lowest elevations in December, with the species moving to higher-elevations in summer, lower-elevations in spring and autumn; (3) during all four seasons, golden takins showed bimodal activity peaks at dawn and dusk, with activity intensity higher in the second peak than the first, and overall low levels of activity recorded from 20:00–06:00; and (4) there were two annual activity peaks, the first being in April and the second in November, with camera capture rate during these two months higher than in other months, and activity levels in spring and autumn higher than in summer and winter. This study is the first application of camera traps to assess the spatial and temporal activity patterns of golden takins at a population level. Our findings suggest that the proposed national park should be designed to include golden takin habitat and that ongoing consistent monitoring efforts will be crucial to mitigating novel and ongoing threats to the species.

Personal injury and property loss caused by wildlife often deteriorates the relationship between humans and animals, prompting retaliatory killings that threaten species survival. Conflicts between humans and Tibetan brown bears (Ursus arctos pruinosus) (Human-Bear Conflicts, HBC) in the Sanjiangyuan region have recently dramatically increased, seriously affecting community enthusiasm for brown bears and the conservation of other species. In order to understand the driving mechanisms of HBC, we proposed six potential drivers leading to increased occurrences of HBC. We conducted field research in Zhiduo County of the Sanjiangyuan region from 2017 to 2019 to test hypotheses through semi-constructed interviews, marmot (Marmota himalayana) density surveys and brown bear diet analysis based on metagenomic sequencing. Analysis of herder perceptions revealed that the driving factors of HBC were related to changes in their settlement practice and living habits, changes in foraging behavior of brown bears and recovery of the brown bear population. Since the establishment of winter homes, brown bears have gradually learned to utilize the food in unattended homes. Although 91.4% (n = 285) of the respondents no longer store food in unattended homes, brown bears were reported to still frequently approach winter homes for food due to improper disposal of dead livestock and household garbage. The frequency and abundance of marmots were found to be high in brown bear diet, indicating that marmots were the bears' primary food. However, marmot density had no significant effect on brown bears utilizing human food (P = 0.329), and HBC appears to not be caused by natural food shortages. Distance to rocky outcrops (P = 0.022) and winter homes (P = 0.040) were the key factors linked to brown bears pursuing human food. The number of brown bears has increased over the past decade, and HBC is likely linked to its population recovery. Our findings will provide scientific basis for formulating effective mitigation measures and protection countermeasures for brown bears.

Cornus elliptica is a species of the Cornus, an evergreen tree endemic to China. Here, we report a complete chloroplast genome sequence of C. elliptica. The chloroplast genome was found to be 157,4...

Actinobacteria are widely distributed in various ecological environments and play essential roles in the carbon and nitrogen cycles in natural ecosystems. Understanding the community composition, structure and distribution of Actinobacteria is not only fundamentally important for studying their functions to ecosystem, but also conducive to protecting Actinobacteria resources. Furthermore, studies regarding the distribution of Actinobacteria in specific areas would also help us understand the impact of global environmental changes on the world's microbial communities. In this study, six alpine grassland sites, from 3220 m and 4790 m in elevation, were selected in Sanjiangyuan National Natural Reserve, which is located in the center of Qinghai-Tibetan Plateau. Then, using 16S rDNA high-throughput sequencing, the composition and elevational distribution patterns of soil Actinobacterial communities were analyzed. A total of 5052 OTUs were detected, which could attributed to 230 genera, 52 families, 9 orders and 5 subclasses of Actinobacteria, and the Actinobacterial communities were significantly ( P 80% of relative abundances, indicating that Actinobacteridae and Rubrobacteridae were the most important subclasses in the alpine grasslands. Through analysis of Actinobacterial ɑ-diversity of the six samples, the number of OTUs ranged from 447.23 ± 52.83 to 675.00 ± 114.69, and the Shannon index ranged from 5.35 ± 0.15 to 5.78 ± 0.11. Both of the measures exhibited strong negative correlations ( P P

We examined the landscape suitability of the region currently occupied by the Sichuan golden money (Rhinopithecus roxellana) using occupancy models constructed in Maxent with presence-only data and environmental variables. The aim of the study was to estimate potential dispersal corridors between presently disjunct populations. Least-cost path analysis was used to estimate its dispersal paths across the fragmented landscape. The results indicate that core areas of suitable habitat are located in the Qinling, Dabashan, and Minshan Mountains, as well as small patches in the Qionglai, Daxiangling and Liangshan Mountains; the most suitable habitats are in nature reserves of the Minshan Mountain. Elevation and density of the human settlements were the most important factors for identifying suitable habitat; and we identified location of less populated areas where some suitable forest patches offer the potential for dispersal corridors for this species. The study implies that there is potential for expansion of the species distribution, if steps are taken to preserve current forest patches that maybe too small for residency but suitable for dispersal.

The snow leopard, Panthera uncia, is an elusive high-altitude specialist that inhabits vast, inaccessible habitat across Asia. We conducted the first range-wide genetic assessment of snow leopards based on noninvasive scat surveys. Thirty-three microsatellites were genotyped and a total of 683 bp of mitochondrial DNA sequenced in 70 individuals. Snow leopards exhibited low genetic diversity at microsatellites (AN = 5.8, HO = 0.433, HE = 0.568), virtually no mtDNA variation, and underwent a bottleneck in the Holocene (∼8000 years ago) coinciding with increased temperatures, precipitation, and upward treeline shift in the Tibetan Plateau. Multiple analyses supported 3 primary genetic clusters: (1) Northern (the Altai region), (2) Central (core Himalaya and Tibetan Plateau), and (3) Western (Tian Shan, Pamir, trans-Himalaya regions). Accordingly, we recognize 3 subspecies, Panthera uncia irbis (Northern group), Panthera uncia uncia (Western group), and Panthera uncia uncioides (Central group) based upon genetic distinctness, low levels of admixture, unambiguous population assignment, and geographic separation. The patterns of variation were consistent with desert-basin "barrier effects" of the Gobi isolating the northern subspecies (Mongolia), and the trans-Himalaya dividing the central (Qinghai, Tibet, Bhutan, and Nepal) and western subspecies (India, Pakistan, Tajikistan, and Kyrgyzstan). Hierarchical Bayesian clustering analysis revealed additional subdivision into a minimum of 6 proposed management units: western Mongolia, southern Mongolia, Tian Shan, Pamir-Himalaya, Tibet-Himalaya, and Qinghai, with spatial autocorrelation suggesting potential connectivity by dispersing individuals up to ∼400 km. We provide a foundation for global conservation of snow leopard subspecies, and set the stage for in-depth landscape genetics and genomic studies.

Climate change might pose an additional threat to the already vulnerable giant panda (Ailuropoda melanoleuca). Effective conservation efforts require projections of vulnerability of the giant panda in facing climate change and proactive strategies to reduce emerging climate‐related threats. We used the maximum entropy model to assess the vulnerability of giant panda to climate change in the Qinling Mountains of China. The results of modeling included the following findings: (1) the area of suitable habitat for giant pandas was projected to decrease by 281 km2 from climate change by the 2050s; (2) the mean elevation of suitable habitat of giant panda was predicted to shift 30 m higher due to climate change over this period; (3) the network of nature reserves protect 61.73% of current suitable habitat for the species, and 59.23% of future suitable habitat; (4) current suitable habitat mainly located in Chenggu, Taibai, and Yangxian counties (with a total area of 987 km2) was predicted to be vulnerable. Assessing the vulnerability of giant panda provided adaptive strategies for conservation programs and national park construction. We proposed adaptation strategies to ameliorate the predicted impacts of climate change on giant panda, including establishing and adjusting reserves, establishing habitat corridors, improving adaptive capacity to climate change, and strengthening monitoring of giant panda.

Evergreen broad‐leaved (EBF) and deciduous broad‐leaved (DBF) forests are two important vegetation types in terrestrial ecosystems that play key roles in sustainable biodiversity and global carbon (C) cycling. However, little is known about their associated soil fungal community and the potential metabolic activities involved in biogeochemical processes. In this study, soil samples were collected from EBF and DBF in Shennongjia Mountain, China, and soil fungal community structure and functional gene diversity analyzed based on combined Illumina MiSeq sequencing with GeoChip technologies. The results showed that soil fungal species richness (p = 0.079) and fungal functional gene diversity (p, Evergreen broad‐leaved (EBF) and deciduous broadleaved (DBF) forests soil samples were collected and soil fungal community structure and functional gene diversity were analyzed combined Illumina MiSeq sequencing with GeoChip technologies. The results showed the soil fungal community structure and potential metabolic activity had marked divergence in different broadleaved forest types, and the higher relative abundance of genes involved in C cycling in DBF caused soil organic C release or loss of the soils.

International audience; Using a case study of an isolated management unit of Sichuan snub‐nosed monkey (Rhinopithecus roxellana), we assess the extent that climate change will impact the species’ habitat distribution in the current period and projected into the 2050s. We identify refugia that could maintain the population under climate change and determine dispersal paths for movement of the population to future suitable habitats. Hubei Province, China. We identified climate refugia and potential movements by integrating bioclimatic models with circuit theory and least‐cost model for the current period (1960–1990) and the 2050s (2041–2060). We coupled a maximum entropy algorithm to predict suitable habitat for the current and projected future periods. Suitable habitat areas that were identified during both time periods and that also satisfied home range and dispersal distance conditions were delineated as refugia. We mapped potential movements measured as current flow and linked current and future habitats using least‐cost corridors. Our results indicate up to 1,119 km2 of currently suitable habitat within the study range. Based on our projections, a habitat loss of 67.2% due to climate change may occur by the 2050s, resulting in a reduced suitable habitat area of 406 km2 and very little new habitat. The refugia areas amounted to 286 km2 and were located in Shennongjia National Park and Badong Natural Reserve. Several connecting corridors between the current and future habitats, which are important for potential movements, were identified. Our assessment of the species predicted a trajectory of habitat loss following anticipated future climate change. We believe conservation efforts should focus on refugia and corridors when planning for future species management. This study will assist conservationists in determining high‐priority regions for effective maintenance of the endangered population under climate change and will encourage increased habitat connectivity.

Climate change threatens endangered species and challenges current conservation strategies. Effective conservation requires vulnerability assessments for species susceptible to climate change and adaptive strategies to mitigate threats associated with climate. In this paper, we used the Maxent to model the impacts of climate change on habitat suitability of Sichuan golden monkey Rhinopithecus roxellana. Our results showed that (i) suitable habitat for Sichuan golden monkey was predicted to decrease by 37% in 2050s under climate change; (ii) the mean elevations of suitable habitat in the 2050s was estimated to shift 160 m higher; (iii) nature reserves protect 62% of current suitable habitat and 56% of future suitable habitat; and (iv) 49% of current suitable habitat was predicted to be vulnerable to future climate change. Given these results, we proposed conservation implications to mitigate the impacts of climate change on Sichuan golden monkey, including adjusting range of national park, establishing habitat corridors, and conducting long-term monitoring.

As two major forest types in the subtropics, broadleaved evergreen and broadleaved deciduous forests have long interested ecologists. However, little is known about their belowground ecosystems despite their ecological importance in driving biogeochemical cycling. Here, we used Illumina MiSeq sequencing targeting 16S rRNA gene and a microarray named GeoChip targeting functional genes to analyse microbial communities in broadleaved evergreen and deciduous forest soils of Shennongjia Mountain of Central China, a region known as 'The Oriental Botanic Garden' for its extraordinarily rich biodiversity. We observed higher plant diversity and relatively richer nutrients in the broadleaved evergreen forest than the deciduous forest. In odds to our expectation that plant communities shaped soil microbial communities, we found that soil organic matter quantity and quality, but not plant community parameters, were the best predictors of microbial communities. Actinobacteria, a copiotrophic phylum, was more abundant in the broadleaved evergreen forest, while Verrucomicrobia, an oligotrophic phylum, was more abundant in the broadleaved deciduous forest. The density of the correlation network of microbial OTUs was higher in the broadleaved deciduous forest but its modularity was smaller, reflecting lower resistance to environment changes. In addition, keystone OTUs of the broadleaved deciduous forest were mainly oligotrophic. Microbial functional genes associated with recalcitrant carbon degradation were also more abundant in the broadleaved deciduous forests, resulting in low accumulation of organic matters. Collectively, these findings revealed the important role of soil organic matter in shaping microbial taxonomic and functional traits.

Understanding biological diversity elevational pattern and the driver factors are indispensable to develop the ecological theories. Elevational gradient may minimize the impact of environmental factors and is the ideal places to study soil microbial elevational patterns. In this study, we selected four typical vegetation types from 1000 to 2800m above the sea level on the northern slope of Shennongjia Mountain in central China, and analysed the soil bacterial community composition, elevational patterns and the relationship between soil bacterial diversity and environmental factors by using the 16S rRNA Illumina sequencing and multivariate statistical analysis. The results revealed that the dominant bacterial phyla were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Verrucomicrobia, which accounted for over 75% of the bacterial sequences obtained from tested samples, and the soil bacterial operational taxonomic unit (OTU) richness was a significant monotonous decreasing (P

There are significant gaps in our knowledge of wild camel ecology; especially the activity patterns that allow them to adapt to desert environments. The wild Bactrian camel (Camelus bactrianus) is a critically endangered species that survives in the extreme desert conditions of Central Asia. We conducted camera trapping surveys at seven watering sites in the northern piedmont of the Altun Mountains from 2010 to 2012. We analyzed the frequency of photo-captures to elucidate the wild camels’ diel activity patterns, and the seasonal variation in their activity at watering sites. We found that these wild camels were predominantly diurnal at watering sites, with an increase in relative activity from sunrise, reaching a peak toward midday, and then gradually decreasing in activity until sunset. The camels visited watering sites more often in winter than in summer. These results provide a guide for water development in the conservation of ungulates in arid areas.

© 2017 John Wiley & Sons Ltd Land-cover change has long been recognized as having marked effect on the amount of soil organic carbon (SOC). However, the microbially mediated processes and mechanisms on SOC are still unclear. In this study, the soil samples in a degenerative succession from alpine meadow to alpine steppe meadow in the Qinghai–Tibetan Plateau were analysed using high-throughput technologies, including Illumina sequencing and geochip functional gene arrays. The soil microbial community structure and diversity were significantly (p

Taxus chinensis is a rare and endangered shrub, highly sensitive to temperature changes and widely known for its potential in cancer treatment. How gene expression of T. chinensis responds to low temperature is still unknown. To investigate cold response of the genus Taxus, we obtained the transcriptome profiles of T. chinensis grown under normal and low temperature (cold stress, 0°C) conditions using Illumina Miseq sequencing. A transcriptome including 83,963 transcripts and 62,654 genes were assembled from 4.16 Gb of reads data. Comparative transcriptomic analysis identified 2,025 differently expressed (DE) isoforms at p < 0.05, of which 1,437 were up-regulated by cold stress and 588 were down-regulated. Annotation of DE isoforms indicated that transcription factors (TFs) in the MAPK signaling pathway and TF families of NAC, WRKY, bZIP, MYB, and ERF were transcriptionally activated. This might have been caused by the accumulation of secondary messengers, such as reactive oxygen species (ROS) and Ca2+. While accumulation of ROS will have caused damages to cells, our results indicated that to adapt to low temperatures T. chinensis employed a series of mechanisms to minimize these damages. The mechanisms included: (i) cold-enhanced expression of ROS deoxidant systems, such as peroxidase and phospholipid hydroperoxide glutathione peroxidase, to remove ROS. This was further confirmed by analyses showing increased activity of POD, SOD, and CAT under cold stress. (ii) Activation of starch and sucrose metabolism, thiamine metabolism, and purine metabolism by cold-stress to produce metabolites which either protect cell organelles or lower the ROS content in cells. These processes are regulated by ROS signaling, as the “feedback” toward ROS accumulation.

The reindeer (Rangifer tarandus tarandus) is listed as a species of “least concern” on the Red List of Threatened Species of the World Conservation Union (IUCN). It is distributed in the northern part of China and semi-domesticated in the region. Here we present a comparison of the historical and current distribution and numbers of reindeer in China, as well as an assessment of the factors limiting population growth. Based on this information we explore potential protective measures for reindeer in China. The reindeer has been herded extensively by the Ewenki people, the only people to do so in China. Reindeer in China originated from the Wenduosenlin tundra highlands of Siberia. Capable of migrating more than 3000 km/year, the reindeer moved from the highlands to the Weitimu river during the 16th century and on to the Northeast area of China in 1654. Since 1957, 600 reindeer have settled in Qiqian in Inner Mongolia, and from 1965 more than 900 reindeer migrated from there to Mangui. In response to frequent flooding and a fluctuating reindeer population in the Mangui region, in 2003 the Ewenki people and more than 260 reindeer translocated from there to Aoluguya. Currently, eight meta-populations of reindeer comprising 773 individuals inhabit in the Arctic region of China. The reindeer population peaked in the 1970s at more than 1080 animals, but declined markedly from 1998 onwards mainly as a result of inbreeding, poaching, predation and tourism. The Chinese government's interest in wildlife protection is increasing, as evidenced by the introduction of wildlife protection laws and regulations, the importation of new reindeer varieties from Russia and the joining of the Association of World Reindeer Herders. However, natural reserves and national parks have still not been established within the reindeer's range in China to conserve this fragile population.

Psoriasis is a chronic and persistent inflammatory skin disease seriously affecting the quality of human life. In this study, we reported an ancient formula of Chinese folk medicine, the natural plant antimicrobial solution (PAMs) for its anti-inflammatory effects and proposed the primary mechanisms on inhibiting the inflammatory response in TNF-α/IFN-γ-induced HaCaT cells and imiquimod-induced psoriasis-like skin disease mouse model. Two main functional components of hydroxysafflor Yellow A and allantoin in PAMs were quantified by HPLC to be 94.2±2.2 and 262.9±12.5 μg/mL respectively. PAMs could significantly reduce the gene expression and inflammatory cytokines production of Macrophage-Derived Chemokine (MDC), IL-8 and IL-6 in TNF-α/IFN-γ-induced HaCaT cells. PAMs also significantly ameliorates the psoriatic-like symptoms in a mouse model with the evaluation scores for both the single (scales, thickness, erythema) and cumulative features were in the order of blank control < Dexamethasone < PAMs < 50% ethanol < model groups. The results were further confirmed by hematoxylin-eosin staining, RT-qPCR and immunohistochemistry. The down-regulated gene expression of IL-8, TNF-α, ICAM-1 and IL-23 in mouse tissues was consistent with the results from those of the HaCaT cells. The inhibition of psoriasis-like skin inflammation by PAMs was correlated with the inactivation of the translocation of P65 protein into cellular nucleus, indicating the inhibition of the inflammatory NF-κB signaling pathway. Taken together, these findings suggest that PAMs may be a promising drug candidate for the treatment of inflammatory skin disorders, such as psoriasis.

Microorganisms play key roles in ecosystem processes and biogeochemical cycling, however, the relationship between soil microbial taxa diversity and their function in natural ecosystems is largely unknown. To determine how soil bacteria community and function are linked from the local to regional scale, we studied soil bacteria community composition, potential function and environmental conditions in natural and mature broadleaf forests along a latitudinal gradient in China, using the Illumina 16S rRNA sequencing and GeoChip technologies. The results showed strong biogeographic endemism pattern in soil bacteria were existed, and the spatial distance and climatic variables were the key controlling factors for this pattern. Therefore, dispersal limitation and environmental selection may represent two key processes in generating and maintaining the soil bacterial biogeographic pattern. By contrast, the soil bacterial potential function is highly convergent along the latitudinal gradient and there were highly differing bacterial community compositions, and the soil chemistry may include the main factors active in shaping the soil bacterial potential function. Therefore, the soil bacterial potential function may be affected by local gradients in resource availability, and predicting soil bacterial potential function requires knowledge of abiotic and biotic environmental factors.

Group-living animals may need to spend less time being vigilant, consequently, having more time for other important activities such as foraging (i.e., group size effect). Przewalski’s gazelle (Procapra przewalskii) is a group-living social animal, and a study was conducted in Qinghai Province of China during June–August 2006 by using a continuous focal sampling method to investigate the influences of group size, sex, within-group spatial position, and nearest-neighbor distance on individual vigilance level (defined as scanning frequency per minute). Male gazelles were more vigilant than females. The gazelle’s vigilance level decreased with group size (group size effect), but only for females. The individuals at the central positions within a group were less vigilant than those at the peripheral positions, but the nearest-neighbor distance did not have any significant influence on the individual vigilance level. Our results support the hypotheses of group size effect and edge effects, but the sexual difference in vigilance level and in the response to group size effect on vigilance suggests that there may be sexual difference in the function and targets of vigilance behavior of Przewalski’s gazelles, which warrants more investigation, with incorporation of within-group spatial position, to better understand the mechanism underlying the group size effect and edge effect.

Background Tropical rainforests cover over 50 % of all known plant and animal species and provide a variety of key resources and ecosystem services to humans, largely mediated by metabolic activities of soil microbial communities. A deep analysis of soil microbial communities and their roles in ecological processes would improve our understanding on biogeochemical elemental cycles. However, soil microbial functional gene diversity in tropical rainforests and causative factors remain unclear. GeoChip, contained almost all of the key functional genes related to biogeochemical cycles, could be used as a specific and sensitive tool for studying microbial gene diversity and metabolic potential. In this study, soil microbial functional gene diversity in tropical rainforest was analyzed by using GeoChip technology. Results Gene categories detected in the tropical rainforest soils were related to different biogeochemical processes, such as carbon (C), nitrogen (N) and phosphorus (P) cycling. The relative abundance of genes related to C and P cycling detected mostly derived from the cultured bacteria. C degradation gene categories for substrates ranging from labile C to recalcitrant C were all detected, and gene abundances involved in many recalcitrant C degradation gene categories were significantly (P

The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth’s biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P

To understand the composition and structure of nitrogen-fixing bacterial communities from the Sanjiangyuan Nature Reserve on the Tibetan Plateau, the molecular diversity of nifH genes from soil obtained at six sites was examined using a PCR-based cloning approach. Six samples were collected from different regions at an altitude of 3907–4824 m above sea level, and a principal component analysis (PCA) showed that they had different biogeochemical properties. A total of 446 clones and 162 unique RFLP patterns were found. PCA of the RFLP patterns and their biogeochemical parameters showed that the content of soil organic carbon (C), total nitrogen (N) and altitude were the most important factors affecting the nitrogen-fixing bacteria community. Fifty-nine nifH clones were sequenced and their nucleotide identity varied from 64% to 98%, subdivisible into four groups in our phylogenetic tree. Some of the clone sequences were related to nifH genes belonging to four phylogenetic subdivisions (α, β, γ and δ subclasses of the Proteobacteria), while most of the clones were closely related to the genes of the uncultured bacteria. The tree also showed that the sequence distributions were not clearly related to the sample sites.

This is the first time to describe the diversity of denitrifying bacteria in Sanjiangyuan natural reserve in Tibet Plateau by investigating the molecular diversity and phylogenetic analysis of nirK and nosZ genes using PCR-RFLP and sequencing. Four soil samples were collected from alpine meadow communities from over an altitude of 4600 m which had different physicochemical properties by principal component analysis (PCA). For the genes fragment of nirK and nosZ, the diverse PCR products were characterized by cloning, restriction fragment length polymorphism (RFLP) analysis and sequenced. A total of 253 nirK clones and 283 nosZ clones were received in four samples, and 78 operational taxonomic units (OTUSs) of nirK and 120 OTUs of nosZ by the restriction enzymes Mspl and Rsal digested. The analysis of environmental factors showed that altitude and C/N ratio in soil may be the key factors to the denitrifying bacteria community. 36 nirK clones and 17 nosZ clones were sequenced, and their levels of nucleotide identity were from 69% to 98% and 57% to 97%, respectively. The phylogenetic tree was constructed using the Clustal W and Mega softwares, and all the sequenced clones could be subdivided into 4 groups. Some of clone sequences were related to the nirK and nosZ genes belonging to three phylogenetic subdivisions (α-, β-and γ subclasses of the Proteobacteria), while most of the clones were closely related to the genes of the uncultured bacteria. The sequence distributions were not clear relating to the sample sites in the tree.

The Przewalski's gazelle, Procapra przewalskii, is now isolated in four local populations on the east and northwest shores of Qinghai Lake. We have been being conducting field surveys in the Qinghai Lake region since 1994. Based on the information we gathered from those surveys, we carried out a Population Viability Analysis (PVA) on the Przewalski's gazelle. We discovered that the Przewalski's gazelle would be extinct within 200 years if no management measures were taken. Since the local population size of the gazelle is small, the most effective measures are to control the wolf density and to reduce the impact of climatic catastrophes. In order to increase the population of the gazelle, we should also take measures to increase primary production of the grassland, to establish a habitat corridor, and to increase the rate of migration of individuals among different local populations.

To examine soil microbial functional gene diversity and causative factors in tropical rainforests, we used a microarray-based metagenomic tool named GeoChip 5.0 to profile it. We found that high microbial functional gene diversity and different soil microbial metabolic potential for biogeochemical processes were considered to exist in tropical rainforest. Soil available nitrogen was the most associated with soil microbial functional gene structure. Here, we mainly describe the experiment design, the data processing, and soil biogeochemical analyses attached to the study in details, which could be published on BMC microbiology Journal in 2015, whose raw data have been deposited in NCBI's Gene Expression Omnibus (accession number GSE69171).

Acidobacteria is one of the most dominant and abundant phyla in soil, and was believed to have a wide range of metabolic and genetic functions. Relatively little is known about its community structure and elevational diversity patterns. We selected four elevation gradients from 1000 to 2800 m with typical vegetation types of the northern slope of Shennongjia Mountain in central China. The vegetation types were evergreen broadleaved forest, deciduous broadleaved forest, coniferous forest and sub-alpine shrubs. We analyzed the soil acidobacterial community composition, elevational patterns and the relationship between Acidobacteria subdivisions and soil enzyme activities by using the 16S rRNA meta-sequencing technique and multivariate statistical analysis. The result found that 19 known subdivisions as well as an unclassified phylotype were presented in these forest sites, and Subdivision 6 has the highest number of detectable operational taxonomic units (OTUs). A significant single peak distribution pattern (P

Background GeoChip 3.0, a microbial functional gene array, containing ~28,000 oligonucleotide probes and targeting ~57,000 sequences from 292 functional gene families, provided a powerful tool for researching microbial community structure in natural environments. The alpine meadow is a dominant plant community in the Qinghai-Tibetan plateau, hence it is important to profile the unique geographical flora and assess the response of the microbial communities to environmental variables. In this study, Geochip 3.0 was employed to understand the microbial functional gene diversity and structure, and metabolic potential and the major environmental factors in shaping microbial communities structure of alpine meadow soil in Qinghai-Tibetan Plateau. Results A total of 6143 microbial functional genes involved in carbon degradation, carbon fixation, methane oxidation and production, nitrogen cycling, phosphorus utilization, sulphur cycling, organic remediation, metal resistance, energy process and other category were detected in six soil samples and high diversity was observed. Interestingly, most of the detected genes associated with carbon degradation were derived from cultivated organisms. To identify major environmental factors in shaping microbial communities, Mantel test and CCA Statistical analyses were performed. The results indicated that altitude, C/N, pH and soil organic carbon were significantly (P Conclusions High overall functional genes and phylogenetic diversity of the alpine meadow soil microbial communities existed in the Qinghai-Tibetan Plateau. Most of the genes involved in carbon degradation were derived from characterized microbial groups. Microbial composition and structures variation were significantly impacted by local environmental conditions, and soil C/N is the most important factor to impact the microbial structure in alpine meadow in Qinghai-Tibetan plateau.

The matK genes of 10 samples in Paris from Hunan, Yunnan and Jilin provinces were sequenced and compared. The phylogenetic tree was constructed based on the matK gene sequences and the ten pairs samples were divided into four groups. The results did not support the reality of four taxa named P. polyphylla var. pseudothibetica, P. polyphylla var. yunnanensis, P. polyphylla var. appendiculata and P. polyphylla var. chinenis. They are supposed to be treated as different forms of P. polyphylla var. polyphylla.

Soil microbial metabolic potential and ecosystem function have received little attention owing to difficulties in methodology. In this study, we selected natural mature forest and natural secondary forest and analyzed the soil microbial community and metabolic potential combing the high-throughput sequencing and GeoChip technologies. Phylogenetic analysis based on 16S rRNA sequencing showed that one known archaeal phylum and 15 known bacterial phyla as well as unclassified phylotypes were presented in these forest soils, and Acidobacteria, Protecobacteria, and Actinobacteria were three of most abundant phyla. The detected microbial functional gene groups were related to different biogeochemical processes, including carbon degradation, carbon fixation, methane metabolism, nitrogen cycling, phosphorus utilization, sulfur cycling, etc. The Shannon index for detected functional gene probes was significantly higher (P