Publications by authors named "Diqiang Li"

34 Publications

The complete chloroplast genome sequences of (Cornaceae).

Mitochondrial DNA B Resour 2021 Mar 16;6(3):931-932. Epub 2021 Mar 16.

Environment and Protection, The Chinese Academy of Forestry, The Research Institute of Forest Ecology, Beijing, China.

is a species of the , an evergreen tree endemic to China. Here, we report a complete chloroplast genome sequence of . The chloroplast genome was found to be 157,400bp in length, and G-C contents were 38.1%. The sequence contained 115 unique genes, including 31 tRNA, 4 rRNA, and 80 protein-coding genes. Phylogenetic framework of is consistent with previous studies.
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http://dx.doi.org/10.1080/23802359.2021.1888333DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7971275PMC
March 2021

Implementing a comprehensive approach to study the causes of human-bear (Ursus arctos pruinosus) conflicts in the Sanjiangyuan region, China.

Sci Total Environ 2021 Jun 2;772:145012. Epub 2021 Feb 2.

Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China. Electronic address:

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.
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http://dx.doi.org/10.1016/j.scitotenv.2021.145012DOI Listing
June 2021

Spatial and temporal activity patterns of Golden takin () recorded by camera trapping.

PeerJ 2020 26;8:e10353. Epub 2020 Nov 26.

Chinese Academy of Forestry, Research Institute of Forest Ecology, Environment and Protection, Beijing, China.

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 () 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.
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http://dx.doi.org/10.7717/peerj.10353DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7700736PMC
November 2020

Identifying the risk regions of house break-ins caused by Tibetan brown bears () in the Sanjiangyuan region, China.

Ecol Evol 2019 Dec 8;9(24):13979-13990. Epub 2019 Dec 8.

Research Institute of Forest Ecology, Environment and Protection Chinese Academy of Forestry Beijing China.

Damage to homesteads by brown bears () 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 () 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 km, 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.
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http://dx.doi.org/10.1002/ece3.5835DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6953560PMC
December 2019

Identifying climate refugia and its potential impact on Tibetan brown bear () in Sanjiangyuan National Park, China.

Ecol Evol 2019 Dec 14;9(23):13278-13293. Epub 2019 Nov 14.

Research Institute of Forest Ecology, Environment and Protection Chinese Academy of Forestry Beijing China.

Climate change has direct impacts on wildlife and future biodiversity protection efforts. Vulnerability assessment and habitat connectivity analyses are necessary for drafting effective conservation strategies for threatened species such as the Tibetan brown bear (). We used the maximum entropy (MaxEnt) model to assess the current (1950-2000) and future (2041-2060) habitat suitability by combining bioclimatic and environmental variables, and identified potential climate refugia for Tibetan brown bears in Sanjiangyuan National Park, China. Next, we selected Circuit model to simulate potential migration paths based on current and future climatically suitable habitat. Results indicate a total area of potential suitable habitat under the current climate scenario of approximately 31,649.46 km, of which 28,778.29 km would be unsuitable by the 2050s. Potentially suitable habitat under the future climate scenario was projected to cover an area of 23,738.6 km. Climate refugia occupied 2,871.17 km, primarily in the midwestern and northeastern regions of Yangtze River Zone, as well as the northern region of Yellow River Zone. The altitude of climate refugia ranged from 4,307 to 5,524 m, with 52.93% lying at altitudes between 4,300 and 4,600 m. Refugia were mainly distributed on bare rock, alpine steppe, and alpine meadow. Corridors linking areas of potentially suitable brown bear habitat and a substantial portion of paths with low-resistance value were distributed in climate refugia. We recommend various actions to ameliorate the impact of climate change on brown bears, such as protecting climatically suitable habitat, establishing habitat corridors, restructuring conservation areas, and strengthening monitoring efforts.
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http://dx.doi.org/10.1002/ece3.5780DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6912912PMC
December 2019

Genetic diversity of the Sichuan snub-nosed monkey (Rhinopithecus roxellana) in Shennongjia National Park, China using RAD-seq analyses.

Genetica 2019 Aug 24;147(3-4):327-335. Epub 2019 Jul 24.

Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, and the Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Beijing, 100091, China.

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 (F) 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.
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http://dx.doi.org/10.1007/s10709-019-00073-3DOI Listing
August 2019

Broad-leaved forest types affect soil fungal community structure and soil organic carbon contents.

Microbiologyopen 2019 10 19;8(10):e874. Epub 2019 Jun 19.

Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China.

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 < 0.01) were higher in DBF than EBF. Zygomycota was the most dominant phylum in both broad-leaved forests, and the most dominant genera found in each forest varied (Umbelopsis dominated in DBF, whereas Mortierella dominated in EBF). A total of 4, 439 soil fungi associated functional gene probes involved in C and nitrogen (N) cycling were detected. Interestingly, the relative abundance of functional genes related to labile C degradation (e.g., starch, pectin, hemicellulose, and cellulose) was significantly higher (p < 0.05) in DBF than EBF, and the functional gene relative abundance involved in C cycling was significantly negatively correlated with soil labile organic C (r = -0.720, p = 0.002). In conclusion, the soil fungal community structure and potential metabolic activity showed marked divergence in different broad-leaved forest types, and the higher relative abundance of functional genes involved in C cycling in DBF may be caused by release of loss of organic C in the soil.
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http://dx.doi.org/10.1002/mbo3.874DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6813455PMC
October 2019

Identifying refugia and corridors under climate change conditions for the Sichuan snub-nosed monkey () in Hubei Province, China.

Ecol Evol 2019 Feb 8;9(4):1680-1690. Epub 2019 Feb 8.

Chinese Academy of Forestry/Key Laboratory of Biodiversity of National Forestry and Grassland Administration Research Institute of Forest Ecology Environment and Protection Beijing China.

Using a case study of an isolated management unit of Sichuan snub-nosed monkey (), 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 km 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 km and very little new habitat. The refugia areas amounted to 286 km 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.
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http://dx.doi.org/10.1002/ece3.4815DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6392490PMC
February 2019

Identifying potential refugia and corridors under climate change: A case study of endangered Sichuan golden monkey (Rhinopithecus roxellana) in Qinling Mountains, China.

Am J Primatol 2018 11;80(11):e22929

Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry/Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Haidian, Beijing, China.

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.
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http://dx.doi.org/10.1002/ajp.22929DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6644296PMC
November 2018

Assessing vulnerability of giant pandas to climate change in the Qinling Mountains of China.

Ecol Evol 2017 06 25;7(11):4003-4015. Epub 2017 Apr 25.

Research Institute of Forest Ecology, Environment and Protection Chinese Academy of Forestry/Key Laboratory of Forest Ecology and Environment of State Forestry Administration Haidian Beijing China.

Climate change might pose an additional threat to the already vulnerable giant panda (). 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 km 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 km) 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.
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http://dx.doi.org/10.1002/ece3.2981DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5468157PMC
June 2017

Transcriptomic Response of Chinese Yew () to Cold Stress.

Front Plant Sci 2017 28;8:468. Epub 2017 Apr 28.

Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Institute of Forest Ecology, Environment, and Protection, Chinese Academy of ForestryBeijing, China.

is a rare and endangered shrub, highly sensitive to temperature changes and widely known for its potential in cancer treatment. How gene expression of responds to low temperature is still unknown. To investigate cold response of the genus , we obtained the transcriptome profiles of 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 < 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 Ca. While accumulation of ROS will have caused damages to cells, our results indicated that to adapt to low temperatures 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.
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http://dx.doi.org/10.3389/fpls.2017.00468DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408010PMC
April 2017

Range-Wide Snow Leopard Phylogeography Supports Three Subspecies.

J Hered 2017 Sep;108(6):597-607

Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282; Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China; The Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Beijing, China; Institute of General and Experimental Biology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia, Irbis Mongolia, Ulaanbaatar, Mongolia; Bhutan Foundation, Washington, DC; Wildlife Biology Program, University of Montana, Missoula, MT; Center for Molecular Dynamics, Kathmandu, Nepal; Panthera, New York, NY; Center for Nature and Society, College of Life Sciences, Peking University, Beijing, China; Department of Environmental Science, Policy and Management, University of California, Berkeley, CA; Shan Shui Conservation Center, Beijing, China; Snow Leopard Trust, Seattle, WA; Center for Cellular and Molecular Biology, Hyderabad, India; Trinity College, Hartford, CT; Baltistan Wildlife Conservation and Development Organization, Skardu, Pakistan; Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX; Research Institute of Wildlife Ecology, Vienna, Austria; American Museum of Natural History, New York, NY; Department of Biology, Texas A&M University, College Station, TX; University of Adelaide, Adelaide, Australia; and Snow Leopard Conservancy, Sonoma, CA 95476.

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.
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http://dx.doi.org/10.1093/jhered/esx044DOI Listing
September 2017

PAMs ameliorates the imiquimod-induced psoriasis-like skin disease in mice by inhibition of translocation of NF-κB and production of inflammatory cytokines.

PLoS One 2017 2;12(5):e0176823. Epub 2017 May 2.

School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, China.

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.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0176823PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5413058PMC
September 2017

The microbially mediated soil organic carbon loss under degenerative succession in an alpine meadow.

Mol Ecol 2017 Jul 16;26(14):3676-3686. Epub 2017 May 16.

CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.

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 < .05) different between alpine meadow and alpine steppe meadow; the microbial ɑ-diversity in alpine steppe meadow was significantly (p < .01) higher than in alpine meadow. Molecular ecological network analysis indicated that the microbial community structure in alpine steppe meadow was more complex and tighter than in the alpine meadow. The relative abundance of soil microbial labile carbon degradation genes (e.g., pectin and hemicellulose) was significantly higher in alpine steppe meadow than in alpine meadow, but the relative abundance of soil recalcitrant carbon degradation genes (e.g., chitin and lignin) showed the opposite tendency. The Biolog Ecoplate experiment showed that microbially mediated soil carbon utilization was more active in alpine steppe meadow than in alpine meadow. Consequently, more soil labile carbon might be decomposed in alpine steppe meadow than in alpine meadow. Therefore, the degenerative succession of alpine meadow because of climate change or anthropogenic activities would most likely decrease SOC and nutrients medicated by changing soil microbial community structure and their functional potentials for carbon decomposition.
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http://dx.doi.org/10.1111/mec.14148DOI Listing
July 2017

Variations of Soil Microbial Community Structures Beneath Broadleaved Forest Trees in Temperate and Subtropical Climate Zones.

Front Microbiol 2017 10;8:200. Epub 2017 Feb 10.

State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University Beijing, China.

Global warming has shifted climate zones poleward or upward. However, understanding the responses and mechanism of microbial community structure and functions relevant to natural climate zone succession is challenged by the high complexity of microbial communities. Here, we examined soil microbial community in three broadleaved forests located in the Wulu Mountain (WLM, temperate climate), Funiu Mountain (FNM, at the border of temperate and subtropical climate zones), or Shennongjia Mountain (SNJ, subtropical climate). Although plant species richness decreased with latitudes, the microbial taxonomic α-diversity increased with latitudes, concomitant with increases in soil total and available nitrogen and phosphorus contents. Phylogenetic NRI (Net Relatedness Index) values increased from -0.718 in temperate zone (WLM) to 1.042 in subtropical zone (SNJ), showing a shift from over dispersion to clustering likely caused by environmental filtering such as low pH and nutrients. Similarly, taxonomy-based association networks of subtropical forest samples were larger and tighter, suggesting clustering. In contrast, functional α-diversity was similar among three forests, but functional gene networks of the FNM forest significantly ( < 0.050) differed from the others. A significant correlation ( = 0.616, < 0.001) between taxonomic and functional β-diversity was observed only in the FNM forest, suggesting low functional redundancy at the border of climate zones. Using a strategy of space-for-time substitution, we predict that poleward climate range shift will lead to decreased microbial taxonomic α-diversities in broadleaved forest.
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http://dx.doi.org/10.3389/fmicb.2017.00200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5300970PMC
February 2017

Soil bacterial endemism and potential functional redundancy in natural broadleaf forest along a latitudinal gradient.

Sci Rep 2016 06 30;6:28819. Epub 2016 Jun 30.

Institute of Forestry Ecology, Environment and Protection, and the Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Chinese Academy of Forestry, Beijing 100091, China.

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.
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http://dx.doi.org/10.1038/srep28819DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4928066PMC
June 2016

Analyses of the influencing factors of soil microbial functional gene diversity in tropical rainforest based on GeoChip 5.0.

Genom Data 2015 Sep 15;5:397-8. Epub 2015 Jul 15.

Institute of Forestry Ecology, Environment and Protection, and the Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Chinese Academy of Forestry, Beijing 100091, China.

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).
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http://dx.doi.org/10.1016/j.gdata.2015.07.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4583697PMC
September 2015

Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests.

Mol Ecol 2015 Oct 14;24(20):5175-85. Epub 2015 Oct 14.

State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.

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.
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http://dx.doi.org/10.1111/mec.13384DOI Listing
October 2015

Available nitrogen is the key factor influencing soil microbial functional gene diversity in tropical rainforest.

BMC Microbiol 2015 Aug 20;15:167. Epub 2015 Aug 20.

Institute of Forestry Ecology, Environment and Protection, and the Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Chinese Academy of Forestry, Beijing, 100091, China.

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 < 0.05) different among three sampling sites. The relative abundance of genes related to N cycling detected was significantly (P < 0.05) different, mostly derived from the uncultured bacteria. The gene categories related to ammonification had a high relative abundance. Both canonical correspondence analysis and multivariate regression tree analysis showed that soil available N was the most correlated with soil microbial functional gene structure.

Conclusions: Overall high microbial functional gene diversity and different soil microbial metabolic potential for different biogeochemical processes were considered to exist in tropical rainforest. Soil available N could be the key factor in shaping the soil microbial functional gene structure and metabolic potential.
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http://dx.doi.org/10.1186/s12866-015-0491-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4546036PMC
August 2015

Soil bacterial diversity patterns and drivers along an elevational gradient on Shennongjia Mountain, China.

Microb Biotechnol 2015 Jul 29;8(4):739-46. Epub 2015 May 29.

Institute of Forestry Ecology, Environment and Protection, Key Laboratory of Forest Ecology and Environment of State Forestry Administration, The Chinese Academy of Forestry, Beijing, 100091, China.

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 2800 m 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 < 0.01) trend with the elevational increasing. The similarity of soil bacterial population composition decreased significantly (P < 0.01) with elevational distance increased as measured by the Jaccard and Bray-Curtis index. Canonical correspondence analysis and Mantel test analysis indicated that plant diversity and soil pH were significantly correlated (P < 0.01) with the soil bacterial community. Therefore, the soil bacterial diversity on Shennongjia Mountain had a significant and different elevational pattern, and plant diversity and soil pH may be the key factors in shaping the soil bacterial spatial pattern.
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http://dx.doi.org/10.1111/1751-7915.12288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4476828PMC
July 2015

Systemic Screening of Strains of the Lion's Mane Medicinal Mushroom Hericium erinaceus (Higher Basidiomycetes) and Its Protective Effects on Aβ-Triggered Neurotoxicity in PC12 Cells.

Int J Med Mushrooms 2015 ;17(3):219-29

laboratory of Molecular Evolution and Applied Biology, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China.

Hericium erinaceus possesses multiple medicinal values. To date, however, there have been few studies of the systemic screening of H. erinaceus strains, and the neuroprotective effects of H. erinaceus prepared from homogenized, fresh fruiting bodies are not fully understood. In this study, 4 random primers were selected and used in random amplified polymorphic DNA (RAPD) polymerase chain reaction (PCR) to screen and evaluate the genetic diversity of 19 commercial strains of H. erinaceus from different localities in China. A total of 66 bands were obtained, and the percentage of polymorphic loci reached 80.30%. Five dendrograms were constructed based on RAPD by Jaccard cluster and within-group linkage analysis. Primer S20 as well as all 4 primers had great potential as specific primers for RAPD-PCR molecular identification and differentiation of H. erinaceus strains. Based on the results of submerged culture and fruiting body cultivation, strains HT-N, HT-J1, HT-C, and HT-M were identified as superior among the 19 H. erinaceus strains. Further study showed that the oral preparation of homogenized, fresh fruiting bodies of H. erinaceus could attenuate the Aβ25-35-triggered damage in PC12 cells by significantly increasing cell viability and by decreasing the release of lactate dehydrogenase. In conclusion, RAPD-PCR combined with liquid and solid cultures can be used well in the screening and identification of H. erinaceus strains, and products prepared from homogenized, fresh fruiting bodies of H. erinaceus had neuroprotective effects on PC12 cells.
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http://dx.doi.org/10.1615/intjmedmushrooms.v17.i3.20DOI Listing
January 2016

Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession.

Sci Rep 2015 May 6;5:10007. Epub 2015 May 6.

Institute of Forestry Ecology, Environment and Protection, and the Key Laboratory of Forest Ecology and Environment of State Forestry Administration, the Chinese Academy of Forestry, Beijing 100091, China.

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 < 0.05) higher than those of CF and MBF, rendering their microbial community compositions markedly different. Consistently, microbial functional diversity was also highest in the DBF. Furthermore, a network analysis of microbial carbon and nitrogen cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession.
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http://dx.doi.org/10.1038/srep10007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4421864PMC
May 2015

Integrated metagenomics and network analysis of soil microbial community of the forest timberline.

Sci Rep 2015 Jan 23;5:7994. Epub 2015 Jan 23.

State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.

The forest timberline responds quickly and markedly to climate changes, rendering it a ready indicator. Climate warming has caused an upshift of the timberline worldwide. However, the impact on belowground ecosystem and biogeochemical cycles remain elusive. To understand soil microbial ecology of the timberline, we analyzed microbial communities via 16s rRNA Illumina sequencing, a microarray-based tool named GeoChip 4.0 and a random matrix theory-based association network approach. We selected 24 sampling sites at two vegetation belts forming the timberline of Shennongjia Mountain in Hubei Province of China, a region with extraordinarily rich biodiversity. We found that temperature, among all of measured environmental parameters, showed the most significant and extensive linkages with microbial biomass, microbial diversity and composition at both taxonomic and functional gene levels, and microbial association network. Therefore, temperature was the best predictor for microbial community variations in the timberline. Furthermore, abundances of nitrogen cycle and phosphorus cycle genes were concomitant with NH4(+)-N, NO3(-)-N and total phosphorus, offering tangible clues to the underlying mechanisms of soil biogeochemical cycles. As the first glimpse at both taxonomic and functional compositions of soil microbial community of the timberline, our findings have major implications for predicting consequences of future timberline upshift.
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http://dx.doi.org/10.1038/srep07994DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4303876PMC
January 2015

Cloning and characterization of 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) gene from Paris fargesii Franch.

Indian J Biochem Biophys 2014 Jun;51(3):201-6

3-Hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR) plays an important role in catalyzing the first committed step of isoprenoids biosynthesis in mevalonic acid (MVA) pathway. Here, we cloned a full-length transcript of Paris fargesii Franch. The full-length cDNA of P. fargesii HMGR (Pf-HMGR, GenBank accession no. JX508638) was 1,973 bp and contained a 1,728 bp ORF encoding 576 amino acids. Sequence analysis revealed that the deduced Pf-HMGR had high similarity with HMGRs from other plants, including Ricinus communis (77%), Litchi chinensis (76%), Michelia chapensis (75%) and Panax quinquefolius (72%). It had a calculated molecular mass of about 62.13 kDa and an isoelectric point (pI) of 8.47. It contained two transmembrane domains, two putative HMGR binding sites and two NADP(H)-binding sites. The predicted 3-D structure revealed that Pf-HMGR had a similar spatial structure with other plant HMGRs. Three catalytic regions, including L-domain, N-domain and S-domain were detected by structural modeling of HMGR. Tissue expression analysis revealed that Pf-HMGR was strongly expressed in roots and stems than in leaves. Taken together, our data laid a foundation for further investigation of HMGR's functions and regulatory mechanisms in plants.
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June 2014

Community structure and elevational diversity patterns of soil Acidobacteria.

J Environ Sci (China) 2014 Aug 23;26(8):1717-24. Epub 2014 Jun 23.

Institute of Forestry Ecology, Environment and Protection, Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Chinese Academy of Forestry, Beijing 100091, China. Electronic address:

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<0.05) between the OTU number and the elevation was observed. The Jaccard and Bray-Curtis index analysis showed that the soil Acidobacteria compositional similarity significantly decreased (P<0.01) with the increase in elevation distance. Mantel test analysis showed the most of the soil Acidobacteria subdivisions had the significant relationship (P<0.01) with different soil enzymes. Therefore, soil Acidobacteria may be involved in different ecosystem functions in global elemental cycles. Partial Mantel tests and CCA analysis showed that soil pH, soil temperature and plant diversity may be the key factors in shaping the soil Acidobacterial community structure.
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http://dx.doi.org/10.1016/j.jes.2014.06.012DOI Listing
August 2014

Optimized spatial priorities for biodiversity conservation in China: a systematic conservation planning perspective.

PLoS One 2014 29;9(7):e103783. Epub 2014 Jul 29.

School of Nature Reserve, Beijing Forestry University, Beijing, China.

By addressing several key features overlooked in previous studies, i.e. human disturbance, integration of ecosystem- and species-level conservation features, and principles of complementarity and representativeness, we present the first national-scale systematic conservation planning for China to determine the optimized spatial priorities for biodiversity conservation. We compiled a spatial database on the distributions of ecosystem- and species-level conservation features, and modeled a human disturbance index (HDI) by aggregating information using several socioeconomic proxies. We ran Marxan with two scenarios (HDI-ignored and HDI-considered) to investigate the effects of human disturbance, and explored the geographic patterns of the optimized spatial conservation priorities. Compared to when HDI was ignored, the HDI-considered scenario resulted in (1) a marked reduction (∼9%) in the total HDI score and a slight increase (∼7%) in the total area of the portfolio of priority units, (2) a significant increase (∼43%) in the total irreplaceable area and (3) more irreplaceable units being identified in almost all environmental zones and highly-disturbed provinces. Thus the inclusion of human disturbance is essential for cost-effective priority-setting. Attention should be targeted to the areas that are characterized as moderately-disturbed, <2,000 m in altitude, and/or intermediately- to extremely-rugged in terrain to identify potentially important regions for implementing cost-effective conservation. We delineated 23 primary large-scale priority areas that are significant for conserving China's biodiversity, but those isolated priority units in disturbed regions are in more urgent need of conservation actions so as to prevent immediate and severe biodiversity loss. This study presents a spatially optimized national-scale portfolio of conservation priorities--effectively representing the overall biodiversity of China while minimizing conflicts with economic development. Our results offer critical insights for current conservation and strategic land-use planning in China. The approach is transferable and easy to implement by end-users, and applicable for national- and local-scale systematic conservation prioritization practices.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0103783PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114974PMC
November 2015

An integrated study to analyze soil microbial community structure and metabolic potential in two forest types.

PLoS One 2014 17;9(4):e93773. Epub 2014 Apr 17.

Institute of Forestry Ecology, Environment and Protection, and the Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Chinese Academy of Forestry, Beijing, China.

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<0.05) at natural secondary forest site. The regression analysis showed that a strong positive (P<0.05) correlation was existed between the soil microbial functional gene diversity and phylogenetic diversity. Mantel test showed that soil oxidizable organic carbon, soil total nitrogen and cellulose, glucanase, and amylase activities were significantly linked (P<0.05) to the relative abundance of corresponded functional gene groups. Variance partitioning analysis showed that a total of 81.58% of the variation in community structure was explained by soil chemical factors, soil temperature, and plant diversity. Therefore, the positive link of soil microbial structure and composition to functional activity related to ecosystem functioning was existed, and the natural secondary forest soil may occur the high microbial metabolic potential. Although the results can't directly reflect the actual microbial populations and functional activities, this study provides insight into the potential activity of the microbial community and associated feedback responses of the terrestrial ecosystem to environmental changes.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0093773PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3990527PMC
January 2015

Geochip-based analysis of microbial communities in alpine meadow soils in the Qinghai-Tibetan plateau.

BMC Microbiol 2013 Mar 29;13:72. Epub 2013 Mar 29.

Institute of Forestry Ecology, Environment and Protection, and the Key Laboratory of Forest Ecology and Environment of State Forestry Administration, the Chinese Academy of Forestry, Beijing 100091, China.

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 < 0.05) correlated with the microbial functional structure and a total of 80.97% of the variation was significantly explained by altitude, C/N and pH. The C/N contributed 38.2% to microbial functional gene variation, which is in accordance with the hierarchical clustering of overall microbial functional genes.

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.
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http://dx.doi.org/10.1186/1471-2180-13-72DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617080PMC
March 2013

Habitat evaluation of wild Amur tiger (Panthera tigris altaica) and conservation priority setting in north-eastern China.

J Environ Manage 2011 Jan 9;92(1):31-42. Epub 2010 Sep 9.

College of Nature Conservation, Beijing Forestry University, Beijing 100083, China.

The Amur Tiger (Panthera tigris altaica) is one of the world's most endangered species. Recently, habitat fragmentation, food scarcity and human hunting have drastically reduced the population size and distribution areas of Amur tigers in the wild, leaving them on the verge of extinction. Presently, they are only found in the north-eastern part of China. In this study, we developed a reference framework using methods and technologies of analytic hierarchy process (AHP), remote sensing (RS), geographic information system (GIS), GAP analysis and Natural Break (Jenks) classification to evaluate the habitat and to set the conservation priorities for Amur tigers in eastern areas of Heilongjiang and Jilin Provinces of northeast China. We proposed a Habitat Suitability Index (HSI) incorporating 7 factors covering natural conditions and human disturbance. Based on the HSI values, the suitability was classified into five levels from the most to not suitable. Finally, according to results of GAP analysis, we identified six conservation priorities and designed a conservation landscape incorporating four new nature reserves, enlarging two existing ones, and creating four linkages for Amur tigers in northeast China. The case study showed that the core habitats (the most suitable and highly suitable habitats) identified for Amur tigers covered 35,547 km(2), accounting for approximately 26.71% of the total study area (1,33,093 km(2)). However, existing nature reserves protected only (7124 km(2) or) 20.04% of the identified core habitats. Thus, enlargement of current reserves is necessary and urgent for the tiger's conservation and restoration. Moreover, the establishment of wildlife corridors linking core habitats will provide an efficient reserve network for tiger conservation to maintain the evolutionary potential of Amur tigers facing environmental changes.
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http://dx.doi.org/10.1016/j.jenvman.2010.08.001DOI Listing
January 2011