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A single degenerated primer significantly improves COX1 barcoding performance in soil nematode community profiling

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Soil Ecology Letters 2024年第2期6卷 31-44页

作者： Yincai Ren Dorota L. Porazinska Quanhui Ma Shuhan Liu Hongmei Li Xue Qing Department of Plant Pathology Nanjing Agricultural UniversityNanjing210095China Department of Entomology and Nematology University of FloridaGainesvilleFL32611USA Institute of grassland Science Key Laboratory of Vegetation Ecology of the Ministry of EducationJilin Songnen Grassland Ecosystem National Observation and Research StationNortheast Normal UniversityChangchun130024China

A new COX1 primer for soil nematode metabarcoding was designed,and this primer outperforms other commonly used COX1 primer pairs in species recovery and quantity of PCR products.•The lack of reference database is the main reason that led to the low species recovery in COX1 metabarcoding.•We expanded current NCBI database by adding 51 newly generated COX1 reference sequences.Microscopic nematodes play important roles in soil ecosystems and often serve as bioindicators of soil health.The identification of soil nematodes is often difficult due to their limited diagnostic characters and high phenotypic plasticity.DNA barcoding and metabarcoding techniques are promising but lack universal primers,especially for mitochondrial COX1 gene.In this study a degenerated COX1 forward primer COIFGED was developed.The primer pair(COIFGED/JB5GED)outperforms other four commonly used COX1 primer pairs in species recovery and quantity of polymerase chain reaction(PCR)products.In metabarcoding analysis,the reads obtained from the new primer pair had the highest sequencing saturation threshold and amplicon sequence variant(ASV)diversity in comparison to other COX1 as well as 18S rRNA primers.The annotation of ASVs suggested the new primer pair initially recovered 9 and 6 out of 25 genera from mock communities,respectively,outperformed other COX1 primers,but underperformed the widely used 18S NF1/18Sr2b primers(16 out of 25 genera).By supplementing the COX1 database with our reference sequences,we recovered an additional 6 mock community species bringing the tally closer to that obtained with 18S primers.In summary,our newly designed COX1 primers significantly improved species recovery and thus can be supplementary or alternative to the conventional 18S metabarcoding.

关键词： degenerated primers DNA metabarcoding mitochondrial cytochrome oxidase c subunit I gene phylogeny ribosomal RNA gene soil nematodes

The storage and utilization of carbohydrates in response to elevation mediated by tree organs in subtropical evergreen broad-leaved forests

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Forest ecosystems 2024年第1期11卷 52-61页

作者： Bin Xu Xueli Jiang Yingying Zong G.Geoff Wang Fusheng Chen Zhenyu Zhao Xiangmin Fang Key Laboratory of National Forestry and grassland Administration on Forest ecosystem Protection and Restoration of Poyang Lake Watershed College of ForestryJiangxi Agricultural UniversityNanchang330045China Jiulianshan National observation and research station of Chinese Forest ecosystem College of ForestryJiangxi Agricultural UniversityNanchang330045China Department of Forestry and Environmental Conservation Clemson UniversityClemsonSC29634USA

Global climate change can affect tree growth and carbon sink function by influencing plant carbohydrate synthesis and utilization,while elevation can be used as an ideal setting under natural conditions to simulate climate change effects.The effect of elevation on tree growth may depend on organ type.However,the allocation patterns of nonstructural and structural carbohydrates(NSCs and SCs,respectively)in different tree organs and their response to elevation remain unclear.We selected four dominant tree species,Schima superba,Castanopsis eyrei,Castanopsis fargesii and Michelia maudiae,along an elevation gradient from 609 to 1,207 m in subtropical evergreen broad-leaved forests and analyzed leaf,trunk,and fine root NSCs,carbon(C),nitrogen(N)and phosphorus(P)concentrations and the relative abundance of SCs.Leaf NSCs increased initially and then decreased,and trunk NSCs increased with increasing elevation.However,root NSCs decreased with increasing elevation.The relative abundance of SCs in leaves and trunks decreased,while the relative abundance of root SCs increased with increasing elevation.No significant correlations between SCs and NSCs in leaves were detected,while there were negative correlations between SCs and NSCs in trunks,roots,and all organs.Hierarchical partitioning analysis indicated that plant C/N and C/P were the main predictors of changes in SCs and NSCs.Our results suggest that tree organs have divergent responses to elevation and that increasing elevation will inhibit the aboveground part growth and enhance the root growth of trees.A tradeoff between the C distribution used for growth and storage was confirmed along the elevation gradient,which is mainly manifested in the"sink"organs of NSCs.Our results provide insight into tree growth in the context of global climate change scenarios in subtropical forest ecosystems.

关键词： Nonstructural carbohydrates Structural carbohydrates Elevation Subtropical evergreen broad-leaved forests Tree organs

Deterministic processes drive turnover-dominated beta diversity of breeding birds along the central Himalayan elevation gradient

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Avian research 2024年第2期15卷 163-171页

作者： Zhifeng Ding Jianchao Liang Le Yang Cong Wei Huijian Hu Xingfeng Si Guangdong Key Laboratory of Animal Conservation and Resource Utilization Institute of ZoologyGuangdong Academy of SciencesGuangzhouGuangdong510260China Tibet Plateau Institute of Biology Lhasa850001China Zhejiang Zhoushan Island ecosystem observation and research station Institute of Eco-ChongmingZhejiang Tiantong Forest Ecosystem National Observation and Research StationSchool of Ecological and Environmental SciencesEast China Normal UniversityShanghai200241China

Beta diversity,the variation of community composition among sites,bridges alpha and gamma diversity and can reveal the mechanisms of community assembly through applying distance-decay models and/or partitioning beta diversity into turnover and nestedness components from functional and phylogenetic perspectives.Mountains as the most natural experiment system provide good opportunities for exploring beta diversity patterns and the underlying ecological processes.Here,we simultaneously consider distance-decay models and multiple di-mensions of beta diversity to examine spatial variations of bird communities,and to evaluate the relative importance of niche-based and neutral community assembly mechanisms along a 3600-m elevational gradient in the central Himalayas,China.Our results showed that species turnover dominates taxonomic,functional,and phylogenetic beta diversity.We observed strongest evidence of spatial distance decays in taxonomic similarities of birds,followed by its phylogenetic and functional analogues.Turnover component was highest in taxonomic beta diversity,while nestedness component was highest in functional beta diversity.Further,all correlations of assemblage similarity with climatic distance were higher than that with spatial distances.Standardized values of overall taxonomic,functional,and phylogenetic beta diversity and their turnover components increase with increasing elevational distance,while the standardized values of taxonomic and phylogenetic nestedness decreased with increasing elevational distance.Our results highlighted the niche-based deterministic processes in shaping elevational bird diversity patterns that were determined by the relative roles of decreasing trend of environmental filtering and increasing trend of limiting similarity along elevation distances.

关键词： Beta diversity Bird Community assembly Functional trait Himalaya Nestedenss Phylogenetic distance Turnover

Identification and Molecular Characterization of the Alkaloid Biosynthesis Gene Family in Dendrobium catenatum

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Phyton-International Journal of Experimental Botany 2024年第1期93卷 81-96页

作者： Liping Yang Xin Wan Runyang Zhou Yingdan Yuan College of Horticulture and Landscape Architecture Yangzhou UniversityYangzhouChina Jiangsu Academy of Forestry NanjingChina Jiangsu Yangzhou Urban Forest ecosystem National observation and research station YangzhouChina

As one of the main active components of Dendrobium catenatum, alkaloids have high medicinal value. The physicochemicalproperties, conserved domains and motifs, phylogenetic analysis, and cis-acting elements of the genefamily members in the alkaloid biosynthesis pathway of D. catenatum were analyzed by bioinformatics, and theexpression of the genes in different years and tissues was analyzed by qRT-PCR. There are 16 gene families,including 25 genes, in the D. catenatum alkaloid biosynthesis pathway. The analysis of conserved domains andmotifs showed that the types, quantities, and orders of domains and motifs were similar among members ofthe same family, but there were significant differences among families. Phylogenetic analysis indicated that thegene family members showed some evolutionary conservation. Cis-acting element analysis revealed that therewere a large number of light-responsive elements and MYB (v-myb avian myeloblastosis viral oncogene homolog)-related elements in these genes. qRT-PCR showed that expressions of gene family members involved in alkaloidsynthesis were different in different years and tissues of D. catenatum. This study provides a theoretical basisfor further exploration of the regulatory mechanisms of these genes in the alkaloid biosynthesis of D. catenatum.

关键词： Dendrobium catenatum gene family alkaloid biosynthesis

ACBP4-WRKY70-RAP2.12 module positively regulates submergence-induced hypoxia response in Arabidopsis thaliana

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Journal of Integrative Plant Biology 2024年第6期66卷 1052-1067页

作者： Mengyun Guo Yingjun Yao Kangqun Yin Luna Tan Meng Liu Jing Hou Han Zhang Ruyun Liang Xinran Zhang Heng Yang Xiaoxiao Chen Jinrui Tan Yan Song Shangling Lou Liyang Chen Xuejing Liu Si Tang Yongqi Hu Jin Yan Wensen Fu Kai Yang Ruijia Zhang Xuerui Li Yao Liu Zhen Yan Wei Liu Yu Han Jianquan Liu Kangshan Mao Huanhuan Liu Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station Key Laboratory for Bio-resource and Eco-environment of Ministry of Education College of Life Sciences Sichuan University

ACYL-CoA-BINDING PROTEINs(ACBPs) play crucial regulatory roles during plant response to hypoxia, but their molecular mechanisms remain poorly understood. Our study reveals that ACBP4 serves as a positive regulator of the plant hypoxia response by interacting with WRKY70,influencing its nucleocytoplasmic shuttling in Arabidopsis thaliana. Furthermore, we demonstrate the direct binding of WRKY70 to the ACBP4 promoter, resulting in its upregulation and suggesting a positive feedback loop. Additionally, we pinpointed a phosphorylation site at Ser638 of ACBP4, which enhances submergence tolerance, potentially by facilitating WRKY70's nuclear shuttling. Surprisingly, a natural variation in this phosphorylation site of ACBP4 allowed A.thaliana to adapt to humid conditions during its historical demographic expansion. We further observed that both phosphorylated ACBP4 and oleoyl-Co A can impede the interaction between ACBP4 and WRKY70, thus promoting WRKY70's nuclear translocation. Finally, we found that the overexpression of orthologous Bna C5.ACBP4and Bna A7.WRKY70 in Brassica napus increases submergence tolerance, indicating their functional similarity across genera. In summary, our research not only sheds light on the functional significance of the ACBP4 gene in hypoxia response, but also underscores its potential utility in breeding flooding-tolerant oilseed rape varieties.

关键词： ACBP4 Arabidopsis thaliana humid adaptation natural variation RAP2.12 WRKY70

Effects of nitrogen and phosphorus additions on soil nematode community of soybean farmland

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Soil Ecology Letters 2024年第2期6卷 45-55页

作者： Huiying Zhang Mengyang Tian Meiguang Jiang Jingyuan Yang Qi Xu Ying Zhang Minglu Ji Yuteng Yao Cancan Zhao Yuan Miao International Joint research Laboratory for Global Change Ecology School of Life SciencesHenan UniversityKaifeng475004China Henan Dabieshan National Field observation and research station of Forest ecosystem Xinyang Academy of Ecological ResearchXinyang464000China

The nitrogen(N)and phosphorus(P)addition promotes the abundance of soybean soil nematodes.The addition of nitrogen can alleviate the suppression of phosphorus on nematodes.Phosphorus addition affects nematode abundanc... 详细信息

关键词： soil nematodes nitrogen addition phosphorus addition soil food web soybean

Dynamics of iron and aluminum storages in a subtropical forest headwater stream

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Journal of Mountain Science 2024年第7期21卷 2193-2205页

作者： YI Qiumeng MA Diting PENG Yan ZHAO Zemin YUAN Chaoxiang YUAN Ji NI Xiangyin WU Fuzhong YUE Kai AN Nannan Key Laboratory of Humid Subtropical Eco-geographical Processes of Ministry of Education School of Geographical SciencesFujian Normal UniversityFuzhou 350117China Fujian Sanming Forest ecosystem National observation and research station Sanming 365002China

The forest headwater streams are important hubs for connecting terrestrial and aquatic ecosystems,with plant litter and sediments as the major carriers for material migrations;however,until now we knew little about the dynamics of trace elements such as iron(Fe)and aluminum(Al)in forest headwater streams.Here,we quantitatively identified the spatiotemporal dynamics of Fe and Al storages in plant litter and sediments and their influencing factors in a subtropical forest headwater stream,and assessed the potential pollution risk.The results showed that:(1)the mean concentrations of Fe and Al in plant litter(sediments)were 5.48 and 8.46(7.39 and 47.47)g·kg^(-1),and the mean storages of Fe and Al in plant litter(sediments)were 0.26 and 0.43(749.04 and 5030.90)g·m^(-2),respectively;(2)the storages of Fe and Al in plant litter and sediments significantly fluctuated from January to December,and showed a decreasing pattern from the source to mouth;and(3)storages of Fe and Al had no significant correlation with riparian forest type and the present of tributary and the Fe and Al storages in plant litter were mainly affected by water temperature and water alkalinity,and their storages in sediments were mainly affected by water temperature and frequency of rainfall;and(4)there were no anthropogenic pollution in Fe and Al in the forest headwater stream.Our study revealed the primary factors of concentrations and storages of Fe and Al in plant litter and sediments in a forest headwater stream,which will improve our understanding of the role of headwater streams in forest nutrient storage and cycling along with hydrological processes.

关键词： Plant litter Sediments Storage Forest headwater stream Stream characteristics Trace element

Impacts of Aggregation Methods and Trophospecies Number on the Structure and Function of Marine Food Webs

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Journal of Ocean University of China 2024年第1期23卷 190-198页

作者： LI Pengcheng ZHANG Chongliang XU Binduo JI Yupeng LI Fan REN Yiping XUE Ying Laboratory of Fisheries ecosystem Monitoring and Assessment College of FisheriesOcean University of ChinaQingdao 266003China Field observation and research station of Haizhou Bay Fishery ecosystem Ministry of EducationQingdao 266003China Shandong Marine Resources and Environment research Institute Shandong Provincial Key Laboratory of Restoration for Marine EcologyYantai 264006China Laboratory for Marine Fisheries Science and Food Production Processes Laoshan LaboratoryQingdao 266237China

Aggregation of species with similar ecological properties is one of the effective methods to simplify food web researches.However,species aggregation will affect not only the complexity of modeling process but also the accuracy of models’outputs.Selection of aggregation methods and the number of trophospecies are the keys to study the simplification of food web.In this study,three aggregation methods,including taxonomic aggregation(TA),structural equivalence aggregation(SEA),and self-organizing maps(SOM),were analyzed and compared with the linear inverse model–Markov Chain Monte Carlo(LIM-MCMC)model.Impacts of aggregation methods and trophospecies number on food webs were evaluated based on the robustness and unitless of ecological net-work indices.Results showed that aggregation method of SEA performed better than the other two methods in estimating food web structure and function indices.The effects of aggregation methods were driven by the differences in species aggregation principles,which will alter food web structure and function through the redistribution of energy flow.According to the results of mean absolute percentage error(MAPE)which can be applied to evaluate the accuracy of the model,we found that MAPE in food web indices will increase with the reducing trophospecies number,and MAPE in food web function indices were smaller and more stable than those in food web structure indices.Therefore,trade-off between simplifying food webs and reflecting the status of ecosystem should be con-sidered in food web studies.These findings highlight the importance of aggregation methods and trophospecies number in the analy-sis of food web simplification.This study provided a framework to explore the extent to which food web models are affected by dif-ferent species aggregation,and will provide scientific basis for the construction of food webs.

关键词： LIM-MCMC model species aggregation trophospecies number aggregation methods food web indices

Arbuscular mycorrhizal fungi reduce ammonia emissions under different land-use types in agro-pastoral areas

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Pedosphere 2024年第2期34卷 497-507页

作者： Huaisong WANG Rui GUO Yibo TIAN Nan CUI Xinxin WANG Lei WANG Zhongbao YANG Shuying LI Jixun GUO Lianxuan SHI Tao ZHANG Institute of grassland Science Northeast Normal UniversityKey Laboratory of Vegetation EcologyMinistry of EducationJilin Songnen Grassland Ecosystem National Observation and Research StationChangchun 130024China Institute of Environment and Sustainable Development in Agriculture Chinese Academy of Agricultural SciencesKey Laboratory of Dryland AgricultureMinistry of AgricultureBeijing 100081China Mountainous Area research Institute of Hebei Province Hebei Agricultural UniversityBaoding 071001China College of Agronomy Liaocheng UniversityLiaocheng 252059China The Key Laboratory of Plant Development and Environmental Adaptation Biology Ministry of EducationSchool of Life ScienceShandong UniversityQingdao 266237China Forestry and grassland Bureau of Aohan Banner Chifeng 024005China

Ammonia(NH3)emissions,the most important nitrogen(N)loss form,always induce a series of environmental problems such as increased frequency of regional haze pollution,accelerated N deposition,and N eutrophication.Arbuscular mycorrhizal(AM)fungi play key roles in N cycling.However,it is still unclear whether AM fungi can alleviate N losses by reducing NH3emissions.The potential mechanisms by which AM fungi reduce NH_(3)emissions in five land-use types(grazed grassland,mowed grassland,fenced grassland,artificial alfalfa grassland,and cropland)were explored in this study.Results showed that AM fungal inoculation significantly reduced NH3emissions,and the mycorrhizal responses of NH3emissions were determined by land-use type.Structural equation modeling(SEM)showed that AM fungi and land-use type directly affected NH_(3)emissions.In addition,the reduction in NH_(3)emissions was largely driven by the decline in soil NH_(4)^(+)-N and pH and the increases in abundances of ammonia-oxidizing archaea(AOA)amoA and bacteria(AOB)amoB genes,urease activity,and plant N uptake induced by AM fungal inoculation and land-use type.The present results highlight that reducing the negative influence of agricultural intensification caused by land-use type changes on AM fungi should be considered to reduce N losses in agriculture and grassland ecosystems.

关键词： agricultural intensification grassland management functional genes plant N uptake N leaching N loss