The Chinese Monal(Lophophorus thuysii)is an alpine-obligate galliform species of global conservation priority.It has been listed as a first class protected wildlife species in China,requiring conservation actions duri...The Chinese Monal(Lophophorus thuysii)is an alpine-obligate galliform species of global conservation priority.It has been listed as a first class protected wildlife species in China,requiring conservation actions during the 14 th Five-Year Plan period.However,the diet composition of Chinese Monal and its seasonal variations have rarely been studied,constraining the effective conservation of the species.Here,we investigated the plant diet composition of the Chinese Monal and its seasonal variations using a DNA metabarcoding approach on fecal samples.We collected 190 fecal samples of the Chinese Monals from the central Qionglai Mountains located in China,and analyzed the plant diet of this species using a DNA metabarcoding approach.Taxonomic profiling of higher plants in the fecal samples was performed using the second internal transcribed spacer(ITS2)amplicon.Downstream analyses,including rarefaction curves,nonmetric multidimensional scaling(NMDS)and permutational multivariate analysis of variance(PERMANOVA),were used to explore the seasonal variations in diet composition.The Chinese Monal foraged a wide range of plant recipes composed of 35 families and 83 genera throughout the year,with Brassicaceae,Apiaceae,and Poaceae as the dominant families,and Cardamine as the dominant genus.The species consumed plants from 62 genera from 28 families during the breeding season(n=81)and 66 genera from 31 families during the non-breeding season(n=109).Further,the plant diet composition significantly varied between the breeding and non-breeding seasons,especially for the frequency of occurrence and relative read abundances at genus level.Our study analyzed the plant diet of the Chinese Monal at a high resolution for the first time,and the results revealed that the seasonal variations in its plant diet composition was adapted to plant phenology and foraging strategy.Fritillaria species,a previously confirmed important food resource for the Chinese Monal,were not detected in any fecal samples,potentially due to overharvesting of Fritillaria bulbs for Traditional Chinese Medicine.Therefore,we highly recommend further restriction of herb gathering in Chinese Monal habitats to facilitate the conservation of this endangered species.Altogether,our study enriches essential ecological information for the Chinese Monal and also provides insights into conservation management for this endangered species.展开更多
Objective: Angelicae Sinensis Radix(ASR, Danggui in Chinese), Cistanches Herba(CH, Roucongrong in Chinese), Ginseng Radix et Rhizoma(PG, Renshen in Chinese), and Panacis Quinquefolii Radix(PQ,Xiyangshen in Chinese), w...Objective: Angelicae Sinensis Radix(ASR, Danggui in Chinese), Cistanches Herba(CH, Roucongrong in Chinese), Ginseng Radix et Rhizoma(PG, Renshen in Chinese), and Panacis Quinquefolii Radix(PQ,Xiyangshen in Chinese), widely used as medicine and dietary supplement around the world, are susceptible to fungal and mycotoxin contamination. In this study, we aim to analyze their fungal community by DNA metabarcoding.Methods: A total of 12 root samples were collected from three main production areas in China. The samples were divided into four groups based on herb species, including ASR, CH, PG, and PQ groups. The fungal community on the surface of four root groups was investigated through DNA metabarcoding via targeting the internal transcribed spacer 2 region(ITS2).Results: All the 12 samples were detected with fungal contamination. Rhizopus(13.04%-74.03%),Aspergillus(1.76%-23.92%), and Fusarium(0.26%-15.27%) were the predominant genera. Ten important fungi were identified at the species level, including two potential toxigenic fungi(Penicillium citrinum and P. oxalicum) and eight human pathogenic fungi(Alternaria infectoria, Candida sake, Hyphopichia burtonii, Malassezia globosa, M. restricta, Rhizopus arrhizus, Rhodotorula mucilaginosa, and Ochroconis tshawytschae). Fungal community in ASR and CH groups was significantly different from other groups,while fungal community in PG and PQ groups was relatively similar.Conclusion: DNA metabarcoding revealed the fungal community in four important root herbs. This study provided an important reference for preventing root herbs against fungal and mycotoxin contamination.展开更多
Objective: Zingiberis Rhizoma(ZR, Ganjiang in Chinese), also known as dried ginger, is a popular spice and medicinal herb that has been used for several thousand years. However, ZR is easily contaminated by fungi and ...Objective: Zingiberis Rhizoma(ZR, Ganjiang in Chinese), also known as dried ginger, is a popular spice and medicinal herb that has been used for several thousand years. However, ZR is easily contaminated by fungi and mycotoxin under suitable conditions, and might be hazardous to the health and safety of consumers, thus concerns about the herb's safety have been raised. The aim of this study was to investigate the fungal community and the effects of collection areas and processing methods on the fungal community in ZR.Methods: A total of 18 ZR samples were collected from four provinces of China, and the samples were divided into four groups based on collecting sites. Meanwhile, the samples collected in Sichuan Province, China were divided into three groups based on the processing methods. We employed the Illumina Mi Seq PE300 platform and targeted the internal transcribed spacer 2(ITS2) sequences to investigate fungal contamination in ZR samples, and the difference in fungal community among the groups of different collection sites and processing methods.Results: All 18 samples were contaminated with fungi. Ascomycota was the dominant phyla, accounting for 34.46%-100% of the fungal reads. At the genus level, Candida, Diutina, and Aspergillus were the most dominant genera, with relative abundances of 0–98.37%, 0–99.82%, and 0–79.08%, respectively.Meanwhile, four potential toxigenic fungi and seven human pathogens were found. Furthermore, differences in the community composition of ZR samples from four collecting sites and three processing methods were observed.Conclusion: DNA metabarcoding provides a novel insight into fungal community diversity in ZR samples,providing references to ensure the sustainable utilization and quality research of ZR.展开更多
Global concerns have been paid to the potential hazard of traditional herbal medicinal products(THMPs). Substandard and counterfeit THMPs, including traditional Chinese patent medicine, health foods, dietary supplemen...Global concerns have been paid to the potential hazard of traditional herbal medicinal products(THMPs). Substandard and counterfeit THMPs, including traditional Chinese patent medicine, health foods, dietary supplements, etc. are potential threats to public health. Recent marketplace studies using DNA barcoding have determined that the current quality control methods are not sufficient for ensuring the presence of authentic herbal ingredients and detection of contaminants/adulterants. An efficient biomonitoring method for THMPs is of great needed. Herein, metabarcoding and single-molecule, realtime(SMRT) sequencing were used to detect the multiple ingredients in Jiuwei Qianghuo Wan(JWQHW), a classical herbal prescription widely used in China for the last 800 years. Reference experimental mixtures and commercial JWQHW products from the marketplace were used to confirm the method. Successful SMRT sequencing results recovered 5416 and 4342 circular-consensus sequencing(CCS) reads belonging to the ITS2 and psb A-trn H regions. The results suggest that with the combination of metabarcoding and SMRT sequencing, it is repeatable, reliable, and sensitive enough to detect species in the THMPs, and the error in SMRT sequencing did not affect the ability to identify multiple prescribed species and several adulterants/contaminants. It has the potential for becoming a valuable tool for the biomonitoring of multi-ingredient THMPs.展开更多
Accurate diet identification of top predators is crucial to fully understand their ecological roles.Compared to terrestrial animals,gathering dietary information from cetaceans is notoriously difficult.Here,we applied a...Accurate diet identification of top predators is crucial to fully understand their ecological roles.Compared to terrestrial animals,gathering dietary information from cetaceans is notoriously difficult.Here,we applied a multilocus metabarcoding approach to investigate the diet of vulnerable Indo-Pacific humpback dolphins and Indo-Pacificfinless porpoises from the Pearl River Estuary(PRE),China.Our analyses identified 21 preyfish species from the 42 humpback dolphin stomachs,as well as 10 species offish and 1 species of cephalopod from the 13finless porpoise stomachs.All of the taxa were assigned to the species level,highlighting that the multimarker approach could facilitate species identification.Most of the prey species were small-and medium-sizedfishes that primarily fed on zooplankton.The calculated similarity index revealed a moderated dietary overlap between the 2 cetaceans,presumably due to the feeding of the 2 predators in association withfishing vessels in the PRE.A more diverse diet was observed in humpback dolphins in the closedfishing season compared to thefishing season,implying the influence on the dolphin diet due to the availability of commercialfishery resources.However,according to the results of species rarefaction curves,ourfindings on the feeding habits of the 2 cetaceans are still limited by insufficient sample size and therefore should be interpreted with caution.This study represents afirst attempt to apply the multilocus DNA metabarcoding technique in the diet analysis of small cetaceans,although more efforts are needed to improve this type of analysis.展开更多
近些年基因测序技术的大量应用为沉积物中植物古DNA的分析提供了技术支撑,将古植被重建的技术发展到了分子层面。国内外相关研究表明,来源于沉积体系中的沉积植物古DNA(Sediment plant ancient DNA,aDNA)可作为古植被重建的有效工具。...近些年基因测序技术的大量应用为沉积物中植物古DNA的分析提供了技术支撑,将古植被重建的技术发展到了分子层面。国内外相关研究表明,来源于沉积体系中的沉积植物古DNA(Sediment plant ancient DNA,aDNA)可作为古植被重建的有效工具。从技术基础理论、文献计量统计、发展应用及实验操作几个方面对沉积植物aDNA技术进行了全面的介绍。沉积aDNA技术在植物群落分析上是一个新的补充方法,它可以提供更高的分辨率以及更精确的丰度估算,然而在实验体系及数据库方面还需要不断完善成熟,其在未来将成为古植被重建重要的辅助技术手段。展开更多
As the sole obligate symbiotic birds in Africa,oxpeckers offer a unique model for studying symbiotic relationships.Due to the multitrophic level they occupy and the context dependent foraging behavior they exhibit,the...As the sole obligate symbiotic birds in Africa,oxpeckers offer a unique model for studying symbiotic relationships.Due to the multitrophic level they occupy and the context dependent foraging behavior they exhibit,the type of symbiotic relationship can be variable.In addition to providing a cleaning service to the host by removing ticks,oxpeckers frequently feed on blood,mucus,and saliva,inflicting potential damage on the host.Here,we used DNA metabarcoding on faecal samples to analyze the taxonomic composition of the trophic interactions of the Yellow-billed Oxpecker(Buphagus africanus)and Red-billed Oxpecker(B.erythrorhynchus)in northeastern Namibia.In contrast to conventional methods,DNA metabarcoding allows for a detailed identification of dietary resources encompassing both mammal hosts and consumed arthropods within the same samples.With this information,we examined differences in the diet composition between oxpecker species and localities,as well as the co-occurrence between host and arthropod species.Our findings revealed that oxpeckers predominantly source their diet from mammals,ticks,and flies;however,ticks and flies rarely co-occur in the diet of an individual.We observed variability among individuals in their feeding ecology,which is strongly correlated with locality and,to a lesser extent,with the mammal host.We noted a high degree of mobility between hosts within relatively short periods,with 32%of the samples showing traces of at least two mammal hosts.This study illustrates the dynamic foraging behavior of these specialized symbiotic birds,shedding light on their potential role in pest control services and disease transmission.展开更多
Plant environmental DNA extracted from lacustrine sediments(sedimentary DNA,sedDNA)has been increasingly used to investigate past vegetation changes and human impacts at a high taxonomic resolution.However,the represe...Plant environmental DNA extracted from lacustrine sediments(sedimentary DNA,sedDNA)has been increasingly used to investigate past vegetation changes and human impacts at a high taxonomic resolution.However,the representation of vegetation communities surrounding the lake is still unclear.In this study,we compared plant sedDNA metabarcoding and pollen assemblages from 27 lake surface-sediment samples collected from alpine meadow on the central-eastern Tibetan Plateau to investigate the representation of sedDNA data.In general,the identified components of sedDNA are consistent with the counted pollen taxa and local plant communities.Relative to pollen identification,sedDNA data have higher taxonomic resolution,thus providing a potential approach for reconstructing past plant diversity.The sedDNA signal is strongly influenced by local plants while rarely affected by exogenous plants.Because of the overrepresentation of local plants and PCR bias,the abundance of sedDNA sequence types is very variable among sites,and should be treated with caution when investigating past vegetation cover and climate based on sedDNA data.Our finding suggests that sedDNA analysis can be a complementary approach for investigating the presence/absence of past plants and history of human land-use with higher taxonomic resolution.展开更多
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 ...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.展开更多
基金supported by Department of Wildlife Conservation,National Forestry and Grassland Administration of Chinathe National Natural Science Foundation of China(32000354)+1 种基金the Special Foundation for National Science and Technology Basic Research Program of China(2018FY100701)the Sichuan Science and Technology Program。
文摘The Chinese Monal(Lophophorus thuysii)is an alpine-obligate galliform species of global conservation priority.It has been listed as a first class protected wildlife species in China,requiring conservation actions during the 14 th Five-Year Plan period.However,the diet composition of Chinese Monal and its seasonal variations have rarely been studied,constraining the effective conservation of the species.Here,we investigated the plant diet composition of the Chinese Monal and its seasonal variations using a DNA metabarcoding approach on fecal samples.We collected 190 fecal samples of the Chinese Monals from the central Qionglai Mountains located in China,and analyzed the plant diet of this species using a DNA metabarcoding approach.Taxonomic profiling of higher plants in the fecal samples was performed using the second internal transcribed spacer(ITS2)amplicon.Downstream analyses,including rarefaction curves,nonmetric multidimensional scaling(NMDS)and permutational multivariate analysis of variance(PERMANOVA),were used to explore the seasonal variations in diet composition.The Chinese Monal foraged a wide range of plant recipes composed of 35 families and 83 genera throughout the year,with Brassicaceae,Apiaceae,and Poaceae as the dominant families,and Cardamine as the dominant genus.The species consumed plants from 62 genera from 28 families during the breeding season(n=81)and 66 genera from 31 families during the non-breeding season(n=109).Further,the plant diet composition significantly varied between the breeding and non-breeding seasons,especially for the frequency of occurrence and relative read abundances at genus level.Our study analyzed the plant diet of the Chinese Monal at a high resolution for the first time,and the results revealed that the seasonal variations in its plant diet composition was adapted to plant phenology and foraging strategy.Fritillaria species,a previously confirmed important food resource for the Chinese Monal,were not detected in any fecal samples,potentially due to overharvesting of Fritillaria bulbs for Traditional Chinese Medicine.Therefore,we highly recommend further restriction of herb gathering in Chinese Monal habitats to facilitate the conservation of this endangered species.Altogether,our study enriches essential ecological information for the Chinese Monal and also provides insights into conservation management for this endangered species.
基金supported by CAMS Innovation Fund for Medical Sciences(CIFMS)(No.2021-I2M-1-071).
文摘Objective: Angelicae Sinensis Radix(ASR, Danggui in Chinese), Cistanches Herba(CH, Roucongrong in Chinese), Ginseng Radix et Rhizoma(PG, Renshen in Chinese), and Panacis Quinquefolii Radix(PQ,Xiyangshen in Chinese), widely used as medicine and dietary supplement around the world, are susceptible to fungal and mycotoxin contamination. In this study, we aim to analyze their fungal community by DNA metabarcoding.Methods: A total of 12 root samples were collected from three main production areas in China. The samples were divided into four groups based on herb species, including ASR, CH, PG, and PQ groups. The fungal community on the surface of four root groups was investigated through DNA metabarcoding via targeting the internal transcribed spacer 2 region(ITS2).Results: All the 12 samples were detected with fungal contamination. Rhizopus(13.04%-74.03%),Aspergillus(1.76%-23.92%), and Fusarium(0.26%-15.27%) were the predominant genera. Ten important fungi were identified at the species level, including two potential toxigenic fungi(Penicillium citrinum and P. oxalicum) and eight human pathogenic fungi(Alternaria infectoria, Candida sake, Hyphopichia burtonii, Malassezia globosa, M. restricta, Rhizopus arrhizus, Rhodotorula mucilaginosa, and Ochroconis tshawytschae). Fungal community in ASR and CH groups was significantly different from other groups,while fungal community in PG and PQ groups was relatively similar.Conclusion: DNA metabarcoding revealed the fungal community in four important root herbs. This study provided an important reference for preventing root herbs against fungal and mycotoxin contamination.
基金supported by CAMS Innovation Fund for Medical Sciences (CIFMS) (No. 2021-I2M-1-071)。
文摘Objective: Zingiberis Rhizoma(ZR, Ganjiang in Chinese), also known as dried ginger, is a popular spice and medicinal herb that has been used for several thousand years. However, ZR is easily contaminated by fungi and mycotoxin under suitable conditions, and might be hazardous to the health and safety of consumers, thus concerns about the herb's safety have been raised. The aim of this study was to investigate the fungal community and the effects of collection areas and processing methods on the fungal community in ZR.Methods: A total of 18 ZR samples were collected from four provinces of China, and the samples were divided into four groups based on collecting sites. Meanwhile, the samples collected in Sichuan Province, China were divided into three groups based on the processing methods. We employed the Illumina Mi Seq PE300 platform and targeted the internal transcribed spacer 2(ITS2) sequences to investigate fungal contamination in ZR samples, and the difference in fungal community among the groups of different collection sites and processing methods.Results: All 18 samples were contaminated with fungi. Ascomycota was the dominant phyla, accounting for 34.46%-100% of the fungal reads. At the genus level, Candida, Diutina, and Aspergillus were the most dominant genera, with relative abundances of 0–98.37%, 0–99.82%, and 0–79.08%, respectively.Meanwhile, four potential toxigenic fungi and seven human pathogens were found. Furthermore, differences in the community composition of ZR samples from four collecting sites and three processing methods were observed.Conclusion: DNA metabarcoding provides a novel insight into fungal community diversity in ZR samples,providing references to ensure the sustainable utilization and quality research of ZR.
基金supported by the National Natural Science Foundation of China (Grant No. 81373922)Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (Grant No. CIFMS, 2016-I2M-3–016)
文摘Global concerns have been paid to the potential hazard of traditional herbal medicinal products(THMPs). Substandard and counterfeit THMPs, including traditional Chinese patent medicine, health foods, dietary supplements, etc. are potential threats to public health. Recent marketplace studies using DNA barcoding have determined that the current quality control methods are not sufficient for ensuring the presence of authentic herbal ingredients and detection of contaminants/adulterants. An efficient biomonitoring method for THMPs is of great needed. Herein, metabarcoding and single-molecule, realtime(SMRT) sequencing were used to detect the multiple ingredients in Jiuwei Qianghuo Wan(JWQHW), a classical herbal prescription widely used in China for the last 800 years. Reference experimental mixtures and commercial JWQHW products from the marketplace were used to confirm the method. Successful SMRT sequencing results recovered 5416 and 4342 circular-consensus sequencing(CCS) reads belonging to the ITS2 and psb A-trn H regions. The results suggest that with the combination of metabarcoding and SMRT sequencing, it is repeatable, reliable, and sensitive enough to detect species in the THMPs, and the error in SMRT sequencing did not affect the ability to identify multiple prescribed species and several adulterants/contaminants. It has the potential for becoming a valuable tool for the biomonitoring of multi-ingredient THMPs.
基金supported by the Natural Science Foundation of Guangdong Province(2017A030308005)in Chinathe National Natural Science Foundation of China(41576128,42007225)+4 种基金Guangdong Basic and Applied Basic Research Foundation(2020A1515010910)in ChinaChina Postdoctoral Science Foundation(2019M653153)Fundamental Research Funds for the Central Universities(19lgpy95)Ocean Park Conservation Foundation of Hong Kong(MM01.1718)Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)(311021004,311020003).
文摘Accurate diet identification of top predators is crucial to fully understand their ecological roles.Compared to terrestrial animals,gathering dietary information from cetaceans is notoriously difficult.Here,we applied a multilocus metabarcoding approach to investigate the diet of vulnerable Indo-Pacific humpback dolphins and Indo-Pacificfinless porpoises from the Pearl River Estuary(PRE),China.Our analyses identified 21 preyfish species from the 42 humpback dolphin stomachs,as well as 10 species offish and 1 species of cephalopod from the 13finless porpoise stomachs.All of the taxa were assigned to the species level,highlighting that the multimarker approach could facilitate species identification.Most of the prey species were small-and medium-sizedfishes that primarily fed on zooplankton.The calculated similarity index revealed a moderated dietary overlap between the 2 cetaceans,presumably due to the feeding of the 2 predators in association withfishing vessels in the PRE.A more diverse diet was observed in humpback dolphins in the closedfishing season compared to thefishing season,implying the influence on the dolphin diet due to the availability of commercialfishery resources.However,according to the results of species rarefaction curves,ourfindings on the feeding habits of the 2 cetaceans are still limited by insufficient sample size and therefore should be interpreted with caution.This study represents afirst attempt to apply the multilocus DNA metabarcoding technique in the diet analysis of small cetaceans,although more efforts are needed to improve this type of analysis.
文摘近些年基因测序技术的大量应用为沉积物中植物古DNA的分析提供了技术支撑,将古植被重建的技术发展到了分子层面。国内外相关研究表明,来源于沉积体系中的沉积植物古DNA(Sediment plant ancient DNA,aDNA)可作为古植被重建的有效工具。从技术基础理论、文献计量统计、发展应用及实验操作几个方面对沉积植物aDNA技术进行了全面的介绍。沉积aDNA技术在植物群落分析上是一个新的补充方法,它可以提供更高的分辨率以及更精确的丰度估算,然而在实验体系及数据库方面还需要不断完善成熟,其在未来将成为古植被重建重要的辅助技术手段。
基金partially supported by the Namibia Students Financial Assistance Fund(NSFAF)Kreditanstalt für Wiederaufbau(KfW)-University of Namibia(UNAM,BMZ Ref.2015.67.015)+2 种基金funded by the project TROPIBIO NORTE-01-0145-FEDER-000046supported by Norte Portugal Regional Operational Programme(NORTE2020)developed in the framework of the“Twin Lab CIBIO/UNAM”(UNESCO Chair Life on Land)。
文摘As the sole obligate symbiotic birds in Africa,oxpeckers offer a unique model for studying symbiotic relationships.Due to the multitrophic level they occupy and the context dependent foraging behavior they exhibit,the type of symbiotic relationship can be variable.In addition to providing a cleaning service to the host by removing ticks,oxpeckers frequently feed on blood,mucus,and saliva,inflicting potential damage on the host.Here,we used DNA metabarcoding on faecal samples to analyze the taxonomic composition of the trophic interactions of the Yellow-billed Oxpecker(Buphagus africanus)and Red-billed Oxpecker(B.erythrorhynchus)in northeastern Namibia.In contrast to conventional methods,DNA metabarcoding allows for a detailed identification of dietary resources encompassing both mammal hosts and consumed arthropods within the same samples.With this information,we examined differences in the diet composition between oxpecker species and localities,as well as the co-occurrence between host and arthropod species.Our findings revealed that oxpeckers predominantly source their diet from mammals,ticks,and flies;however,ticks and flies rarely co-occur in the diet of an individual.We observed variability among individuals in their feeding ecology,which is strongly correlated with locality and,to a lesser extent,with the mammal host.We noted a high degree of mobility between hosts within relatively short periods,with 32%of the samples showing traces of at least two mammal hosts.This study illustrates the dynamic foraging behavior of these specialized symbiotic birds,shedding light on their potential role in pest control services and disease transmission.
基金supported by the National Natural Science Foundation of China(Grant Nos.42071107 and 41877459)the Mobility program of the Sino-German Center for Research Promotion(No.M-0359)+1 种基金the CAS Pioneer Hundred Talents Program(Xianyong Cao)the Russian Science Foundation(No.20-17-00110).
文摘Plant environmental DNA extracted from lacustrine sediments(sedimentary DNA,sedDNA)has been increasingly used to investigate past vegetation changes and human impacts at a high taxonomic resolution.However,the representation of vegetation communities surrounding the lake is still unclear.In this study,we compared plant sedDNA metabarcoding and pollen assemblages from 27 lake surface-sediment samples collected from alpine meadow on the central-eastern Tibetan Plateau to investigate the representation of sedDNA data.In general,the identified components of sedDNA are consistent with the counted pollen taxa and local plant communities.Relative to pollen identification,sedDNA data have higher taxonomic resolution,thus providing a potential approach for reconstructing past plant diversity.The sedDNA signal is strongly influenced by local plants while rarely affected by exogenous plants.Because of the overrepresentation of local plants and PCR bias,the abundance of sedDNA sequence types is very variable among sites,and should be treated with caution when investigating past vegetation cover and climate based on sedDNA data.Our finding suggests that sedDNA analysis can be a complementary approach for investigating the presence/absence of past plants and history of human land-use with higher taxonomic resolution.
基金supported by the National Natural Science Foundation of China(Grant number 32001876).
文摘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.
