Biodiversity serves as the foundation for human survival and development.Marine fishes play a crucial role in supporting both global biodiversity and food sources.The conventional methods for fish diversity and fisher...Biodiversity serves as the foundation for human survival and development.Marine fishes play a crucial role in supporting both global biodiversity and food sources.The conventional methods for fish diversity and fishery resources survey are inadequate to meet the growing demand for large-scale and long-period surveys.The eDNA metabarcoding approach provides an effective and noninvasive monitoring revolution,and has been applied to identify fish diversities.This study conducted a comprehensive comparison of fish diversity in the East China Sea on a large scale both horizontally and vertically.The results showed a total of 81 fish species,which were classified into 20 orders,44 families and 72 genera.Although no statistically significant difference in fish diversity was found amongst the horizontal groups(east-middle-west,south-middle-north,and shallow-middle-deep)and the various sampling layers(surface-middle-bottom),discernible trends were obtained in this study.Fish diversity results revealed the orders of east>middle>west,middle>north>south and deep>shallow>middle in horizontal groups.Additionally,surface water exhibited a higher level of fish diversity than other water layers.Some fish species were only detected at specific vertical depths.The diverse composition of fish species across different water layers can be attributed to their distinct ecological types.The overall findings suggest that an increase of sampling stations and mixed samples should be collected in deeper water bodies for comprehensive understanding of fish diversity.This study can also provide the fundamental data and experimental design reference for future studies and fishery management.展开更多
Understanding the seasonal variations of the zooplankton community’s structure in the Western Pacific Warm Pool(WPWP)-the most stable open marine environment in the Pacific Ocean-is crucial to predict the impacts of ...Understanding the seasonal variations of the zooplankton community’s structure in the Western Pacific Warm Pool(WPWP)-the most stable open marine environment in the Pacific Ocean-is crucial to predict the impacts of climate change on the ecosystem.However,knowledge on these variations in this region down to the mesopelagic zone is insufficient.In this study,the environmental DNA(eDNA)metabarcoding method was used to investigate the zooplankton community during summer,autumn,and winter,from the surface to a depth of 1000 m spanning the epipelagic to mesopelagic zones.The zooplankton community structure exhibited seasonal fluctuations at multiple depths except for 200 and 1000 m.In addition,a stronger zooplankton seasonality was particularly recorded in the epipelagic zone than in the mesopelagic zone,which is consistent with the environmental changes.The studied zooplanktons are dominated by medusae and copepods that showed distinct seasonality.At all depths,medusae exhibited greater seasonal variations than the overall zooplankton community,whereas the copepods did not exhibit significant seasonality.The environmental features and the seasons exerted greater influences on the structure of the zooplankton communities than did the spatial factors.The results of this study indicate that eDNA metabarcoding can provide novel insights into zooplankton assemblages due to its ability to capture a rich variety of medusae,which are often underestimated by net collection.展开更多
Harmful algal blooms(HABs)have emerged as a critical global environmental and ecological concern.Timely and accurate monitoring of the prevalent bloom-forming genera is crucial for HABmanagement.Conventional microscop...Harmful algal blooms(HABs)have emerged as a critical global environmental and ecological concern.Timely and accurate monitoring of the prevalent bloom-forming genera is crucial for HABmanagement.Conventional microscope-based methods are time-consuming,laborintensive,and specialized expertise-dependent,often making them impractical for largescale surveillance.Molecular methods,such as metabarcoding,provide efficient technical solutions;however,the lack of competent PCR primers and further field validation present obstacles to their wide use.Here,we successfully developed Aphanizomenon-specific primers and validated the application of environmental DNA(eDNA)metabarcoding for field-based monitoring of Aphanizomenon in 37 sites across lentic and lotic freshwater ecosystems in Beijing.The sensitivity and specificity tests of newly developed primers demonstrated high performance-comprehensive recovery of biodiversity in Aphanizomenon communities and high ratios(>95%)of Aphanizomenon sequences in datasets.We observed significant correlations between the sequence abundance derived fromeDNAmetabarcoding and the total cell density determined through microscopic identification across all the sampling sites,both in the spring(r=0.8086,p<0.0001)and summer(r=0.7902,p<0.0001),thus validating the utility of eDNA metabarcoding based on the newly developed primers for monitoring in the field.Further,we identified key environmental variables that were primary drivers responsible for the spatiotemporal distribution of Aphanizomenon abundance.These variables included temperature,total nitrogen,and dissolved oxygen in lentic ecosystems,and total phosphorus in lotic ecosystems.The method developed and validated here offers an accurate,efficient,and high-throughput tool for the monitoring of Aphanizomenon blooms in freshwater ecosystems.展开更多
Coral reefs support a wide range of organisms in the world,including jellyfish and their benthic relatives.However,quantifying the biodiversity of these organisms in reefs is a challenge because of their uneven distri...Coral reefs support a wide range of organisms in the world,including jellyfish and their benthic relatives.However,quantifying the biodiversity of these organisms in reefs is a challenge because of their uneven distribution and cryptic early life stages,requiring the validation of alternative techniques for biodiversity assessment.Here,the biodiversity and spatial distribution patterns of jellyfish and their benthic relatives,from the Scyphozoa,Hydrozoa,and Ctenophora taxa(hereafter referred to as SHC),were investigated in the coral reefs of Xisha,China,using environmental DNA(eDNA)metabarcoding technology by collecting shallow seawater,mesophotic seawater,and sediment samples.One-hundred and eighty-eight SHC species spanning two phyla(Cnidaria and Ctenophora),three classes,11 orders,65 families,and 104 genera were identified,among which hydrozoans were the most dominant taxa,accounting for 89.81% of all SHC species.SHC species showed low connectivity between shallow and mesophotic habitats,presenting a clear vertical distribution pattern in coral reefs.In the mesophotic coral ecosystems(MCEs),140 SHC species(84.34%)were detected,of which 39.76% were exclusive to MCEs,with Zanclea sp.1,Orthopyxis integra,and Fabienna sphaerica being the dominant species.Additionally,although SHC diversity in seawater was higher than that in the sediment samples,22 species were identified only in the sediment samples,indicating that sediment eDNA may represent a valuable supplementary tool for the investigation of SHC communities in hot spots.In addition to revealing the vast diversity of SHC species occupying coral reef ecosystems in the Xisha Islands,our findings confirm the potential of eDNA metabarcoding as an advanced tool for monitoring the biodiversity of cryptic species.展开更多
Zooplankton,a crucial component of urban wetland,are one of the effective bioindicators for monitoring the feeding stocks of organisms at higher trophic levels and assessing the ecological quality of ecosystems.Howeve...Zooplankton,a crucial component of urban wetland,are one of the effective bioindicators for monitoring the feeding stocks of organisms at higher trophic levels and assessing the ecological quality of ecosystems.However,information about the characteristics of epiphytic zooplankton community structure resulted from traditional methods is limited and hindered by the large amount of detritus and sludge attached to the macrophytes.We investigated the epiphytic zooplankton communities associated with macrophytes(Vallisneria,Nymphaea,and Thalia dealbata)in a subtropical wetland using as DNA markers of the 18 S rRNA gene and the mitochondrial cytochrome c oxidase subunit I(COI)gene.A total of 241 OTUs of zooplankton were obtained from COI amplicons,including 194 OTUs of Rotifera,22 of Cladocera,and 25 of Copepoda,while only 62 OTUs of zooplankton were obtained from 18 S rDNA amplicons including 34 OTUs of Rotifera and 28 of Copepoda.The zooplankton communities associated with the three macrophytes were similar,but they differed significantly from those in the open waters.However,there were no significant temporal differences among the zooplankton communities.Epiphytic zooplankton communities were dominated by littoral zooplankton such as Testudinella,Lecane,and Philodina.Microzooplankton,especially littoral species,utilize macrophytes as food sources and as refuges against predation.This further led to an increase inαandβdiversity of zooplankton communities in urban wetlands.Our result suggests that the joint use of multiple molecular markers could improve the taxonomic resolution and generate a comprehensive biodiversity profile of zooplankton.展开更多
Environmental DNA(eDNA)integrated with metabarcoding is a promising and powerful tool for species composition and biodiversity assessment in aquatic ecosystems and is increasingly applied to evaluate fish diversity.To...Environmental DNA(eDNA)integrated with metabarcoding is a promising and powerful tool for species composition and biodiversity assessment in aquatic ecosystems and is increasingly applied to evaluate fish diversity.To date,however,no standardized eDNA-based protocol has been established to monitor fish diversity.In this study,we investigated and compared two filtration methods and three DNA extraction methods using three filtration water volumes to determine a suitable approach for eDNA-based fish diversity monitoring in the Pearl River Estuary(PRE),a highly anthropogenically disturbed estuarine ecosystem.Compared to filtration-based precipitation,direct filtration was a more suitable method for eDNA metabarcoding in the PRE.The combined use of DNeasy Blood and Tissue Kit(BT)and traditional phenol/chloroform(PC)extraction produced higher DNA yields,amplicon sequence variants(ASVs),and Shannon diversity indices,and generated more homogeneous and consistent community composition among replicates.Compared to the other combined protocols,the PC and BT methods obtained better species detection,higher fish diversity,and greater consistency for the filtration water volumes of 1000 and 2000 mL,respectively.All eDNA metabarcoding protocols were more sensitive than bottom trawling in the PRE fish surveys and combining two techniques yielded greater taxonomic diversity.Furthermore,combining traditional methods with eDNA analysis enhanced accuracy.These results indicate that methodological decisions related to eDNA metabarcoding should be made with caution for fish community monitoring in estuarine ecosystems.展开更多
Environmental DNA(eDNA)metabarcoding has emerged as a potentially powerful tool to monitor invasive fish species.As an alternative(or complementary)tool for biodiversity monitoring,e DNA metabarcoding had been used to...Environmental DNA(eDNA)metabarcoding has emerged as a potentially powerful tool to monitor invasive fish species.As an alternative(or complementary)tool for biodiversity monitoring,e DNA metabarcoding had been used to detect species in aquariums,which represents an important transit avenue for introducing non-indigenous species with high population densities.In this study,eDNA metabarcoding as well as morphological characterization were used to reveal the diversity of non-indigenous species in a large aquarium at Qingdao Underwater World.Environmental DNA metabarcoding of 14 water samples at five locations from the Big Water Tank detected 24 non-indigenous species and four putative non-indigenous operational taxonomic units(OTUs).In contrast,only 20 non-indigenous species were observed by morphological characterization.Some species undetected by morphological characterization,such as Oreochromis niloticus(Linnaeus,1758),are highly adaptable to various environments and/or have invaded preferred regions where they threaten native aquatic species.eDNA metabarcoding also detected seven local fishes that were not identified by morphological characterization.However,analysis of OTU diversity among stations and sample replications revealed that eDNA varied within and/or between stations.Increasing sampling effort as well as negative controls are required to increase the detection rate of species and to eliminate false-positive OTUs.展开更多
Due to the overexploitation of farming,as well as habitat destruction,the wild population of Chinese giant salamander(CGS)Andrias davidianus,a species with seven genetically distinct lineages,has decreased by over 80%...Due to the overexploitation of farming,as well as habitat destruction,the wild population of Chinese giant salamander(CGS)Andrias davidianus,a species with seven genetically distinct lineages,has decreased by over 80%in the past 70 years.Traditional survey methods have proven to be unsuitable for finding this rare and elusive species.We evaluated the efficacy of environmental DNA(eDNA)sampling to detect CGS indirectly from its aquatic environment.We developed several species-specific primer sets;validated their specificity and sensitivity;and assessed their utility in silico,in the laboratory,and at two field sites harboring released farm-bred CGS.We detected the presence of CGS DNA by using polymerase chain reaction and Sanger sequencing.We also sequenced an amplicon mixture of seven haplotype-represented samples using high-throughput sequencing.Our eDNA methods could detect the presence of CGS at moderate densities reported across its range,proving them as a cost-effective way to establish broad-scale patterns of occupancy for CGS.In addition,our primers enabled the detection of mitochondrial lineage mixture or introduced individuals from geographically isolated populations of CGS.展开更多
Seamount is a unique deep-sea ecosystem widely distributed in the world.Its biodiversity is vibrant due to its specific geographical and hydrological conditions.However,the diversity and features of foraminifera in su...Seamount is a unique deep-sea ecosystem widely distributed in the world.Its biodiversity is vibrant due to its specific geographical and hydrological conditions.However,the diversity and features of foraminifera in such an environment have rarely been studied.We extracted environmental DNA(eDNA)in sedime nts and amplified the partial small subunit ribo somal DNA(SSU rDNA)of fo raminife ra to understand the foraminiferal diversity from four sites in Magellan Seamount(Western Pacific Ocean).Partial S SU rDNA sequencing was conducted and 912979 foraminiferal reads were obtained and gathered into 266 operational taxonomic units(OTUs).In the available dataset,a high proportion of rare OTUs and low identity OTUs in each studied sample showed that the Magellan Seamount foraminiferal community might have a high genetic novelty.The relative abundance of foraminifera varied between replicates probably due to the existence of bias in amplification process and patchiness of the deep-sea floor.It showed that the Magellan Seamount has a relatively high benthic foraminiferal diversity characterized mainly by monothalamiids(76.37%of total reads)in association with rotaliids(19.03%of total reads),including planktic foraminiferal sequences(38.58%of rotaliids;7.36%of total reads).The remaining reads were assigned to miliolids(0.83%of total reads)and textulariids(0.66%of total reads),and 3.11%of total reads are unassigned to a specific family.The co mparative analysis with foraminiferal assemblage s from coastal and deep-sea environme nts indicated that seamounts could aggregate species from a nearby deep-sea.展开更多
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
eDNA metabarcoding is an advanced method formonitoring biodiversityproposed in recent years.By analyzing DNA in water,soil and sediment samples,the technology obtains species distribution and population quantity infor...eDNA metabarcoding is an advanced method formonitoring biodiversityproposed in recent years.By analyzing DNA in water,soil and sediment samples,the technology obtains species distribution and population quantity information.It was found that macrobarcode technology is more accurate than the traditional method in measuring the species richness of some groups.In Europe,America and South America,the relia bility of this technology in monitoring amphibian diversity in the wild was studied,and it was found to be better than traditional biodiversity monitoring methods in detecting species diversity.At present,amphibian monitoring mainly depends on various traditional methods,such as transects,drift fence traps,artificial shelters and mark-recapture.These monitoring techniques have many shortcomings,such as low accuracy and strong subjectivity of study results.These technologies have poor effects on rare,invasive and endangered species with strong concealment ability,low density and strong seasonality and are difficult to implement in sites inaccessible to people.Traditional monitoring technology also requires considerable investment of human and material resources,and the economic cost is relatively high,while eDNA metabarcoding ismore efficient and less costly,so it is important to use eDNA meta barcoding in amphibian monitoring in China.In this study,the eDNA meta barcoding and traditional line transect method(TLTM)were used to study the characteristics of the two methods in the Beijing-Tianjin-Hebeiregion.Repeated samplingwas conducted on 58 waterbodies in July 2019 and June 2020.After sequencing the samples using highthroughput sequencing technology,the differences between metabarcoding and commonly used TLTM surveys in detecting the diversity of four amphibians in North China were assessed.Our results showed that eDNA meta barcoding is more sensitive to the detection of the four amphibian species in the sampling area,and the combined use of eDNA metabarcoding and TLTM can improve the survey results of amphibians in the survey area to the greatest extent.In addition,in the process of species classification and identification of metabarcoding results,7 species of reptiles were detected,indicating that eDNA metabarcoding is also useful to detect reptiles.The results of this study indicate that metabarcoding in combination with TLTM can accurately estimate the diversityof amphibians in a short-term survey in North China and is also useful in reptile species detection.展开更多
基金funded by the National Key Research and Development Program of China(No.2023YFD2401903)the National Natural Science Foundation of China(No.41806180)+2 种基金the Science and Technology Project of Zhoushan(No.2022C41010)the Scientific Research Project of China Three Gorges Corporation(No.WWKY-2020-0079)the Shared Voyage Program of the National Natural Science Foundation of China in the East China Sea(No.NORC2019-02)。
文摘Biodiversity serves as the foundation for human survival and development.Marine fishes play a crucial role in supporting both global biodiversity and food sources.The conventional methods for fish diversity and fishery resources survey are inadequate to meet the growing demand for large-scale and long-period surveys.The eDNA metabarcoding approach provides an effective and noninvasive monitoring revolution,and has been applied to identify fish diversities.This study conducted a comprehensive comparison of fish diversity in the East China Sea on a large scale both horizontally and vertically.The results showed a total of 81 fish species,which were classified into 20 orders,44 families and 72 genera.Although no statistically significant difference in fish diversity was found amongst the horizontal groups(east-middle-west,south-middle-north,and shallow-middle-deep)and the various sampling layers(surface-middle-bottom),discernible trends were obtained in this study.Fish diversity results revealed the orders of east>middle>west,middle>north>south and deep>shallow>middle in horizontal groups.Additionally,surface water exhibited a higher level of fish diversity than other water layers.Some fish species were only detected at specific vertical depths.The diverse composition of fish species across different water layers can be attributed to their distinct ecological types.The overall findings suggest that an increase of sampling stations and mixed samples should be collected in deeper water bodies for comprehensive understanding of fish diversity.This study can also provide the fundamental data and experimental design reference for future studies and fishery management.
基金Supported by the National Key Research and Development Program of China(No.2022YFC2806805)the National Natural Science Foundation of China(Nos.42076122,42306130)the Digital Deep-sea Typical Habitats Program of China Deep Ocean Affairs Administration(No.DYXZ-02)。
文摘Understanding the seasonal variations of the zooplankton community’s structure in the Western Pacific Warm Pool(WPWP)-the most stable open marine environment in the Pacific Ocean-is crucial to predict the impacts of climate change on the ecosystem.However,knowledge on these variations in this region down to the mesopelagic zone is insufficient.In this study,the environmental DNA(eDNA)metabarcoding method was used to investigate the zooplankton community during summer,autumn,and winter,from the surface to a depth of 1000 m spanning the epipelagic to mesopelagic zones.The zooplankton community structure exhibited seasonal fluctuations at multiple depths except for 200 and 1000 m.In addition,a stronger zooplankton seasonality was particularly recorded in the epipelagic zone than in the mesopelagic zone,which is consistent with the environmental changes.The studied zooplanktons are dominated by medusae and copepods that showed distinct seasonality.At all depths,medusae exhibited greater seasonal variations than the overall zooplankton community,whereas the copepods did not exhibit significant seasonality.The environmental features and the seasons exerted greater influences on the structure of the zooplankton communities than did the spatial factors.The results of this study indicate that eDNA metabarcoding can provide novel insights into zooplankton assemblages due to its ability to capture a rich variety of medusae,which are often underestimated by net collection.
基金supported by the National Key R&D Program of China(No.2021YFC3200102)Yunnan Collaborative Innovation Center for Plateau Lake Ecology and Environmental Healththe Key Research and Development Project of Shandong Province(No.2020CXGC011202).
文摘Harmful algal blooms(HABs)have emerged as a critical global environmental and ecological concern.Timely and accurate monitoring of the prevalent bloom-forming genera is crucial for HABmanagement.Conventional microscope-based methods are time-consuming,laborintensive,and specialized expertise-dependent,often making them impractical for largescale surveillance.Molecular methods,such as metabarcoding,provide efficient technical solutions;however,the lack of competent PCR primers and further field validation present obstacles to their wide use.Here,we successfully developed Aphanizomenon-specific primers and validated the application of environmental DNA(eDNA)metabarcoding for field-based monitoring of Aphanizomenon in 37 sites across lentic and lotic freshwater ecosystems in Beijing.The sensitivity and specificity tests of newly developed primers demonstrated high performance-comprehensive recovery of biodiversity in Aphanizomenon communities and high ratios(>95%)of Aphanizomenon sequences in datasets.We observed significant correlations between the sequence abundance derived fromeDNAmetabarcoding and the total cell density determined through microscopic identification across all the sampling sites,both in the spring(r=0.8086,p<0.0001)and summer(r=0.7902,p<0.0001),thus validating the utility of eDNA metabarcoding based on the newly developed primers for monitoring in the field.Further,we identified key environmental variables that were primary drivers responsible for the spatiotemporal distribution of Aphanizomenon abundance.These variables included temperature,total nitrogen,and dissolved oxygen in lentic ecosystems,and total phosphorus in lotic ecosystems.The method developed and validated here offers an accurate,efficient,and high-throughput tool for the monitoring of Aphanizomenon blooms in freshwater ecosystems.
基金Supported by the National Science&Technology Fundamental Resources Investigation Program of China(No.2022FY100603)the Key Project of the NSFC-Shandong Joint Fund(No.U2106208)+1 种基金the National Key Research and Development Program of China(No.2023YFC3108200)the Taishan Scholars Program(No.tsqn202211263)。
文摘Coral reefs support a wide range of organisms in the world,including jellyfish and their benthic relatives.However,quantifying the biodiversity of these organisms in reefs is a challenge because of their uneven distribution and cryptic early life stages,requiring the validation of alternative techniques for biodiversity assessment.Here,the biodiversity and spatial distribution patterns of jellyfish and their benthic relatives,from the Scyphozoa,Hydrozoa,and Ctenophora taxa(hereafter referred to as SHC),were investigated in the coral reefs of Xisha,China,using environmental DNA(eDNA)metabarcoding technology by collecting shallow seawater,mesophotic seawater,and sediment samples.One-hundred and eighty-eight SHC species spanning two phyla(Cnidaria and Ctenophora),three classes,11 orders,65 families,and 104 genera were identified,among which hydrozoans were the most dominant taxa,accounting for 89.81% of all SHC species.SHC species showed low connectivity between shallow and mesophotic habitats,presenting a clear vertical distribution pattern in coral reefs.In the mesophotic coral ecosystems(MCEs),140 SHC species(84.34%)were detected,of which 39.76% were exclusive to MCEs,with Zanclea sp.1,Orthopyxis integra,and Fabienna sphaerica being the dominant species.Additionally,although SHC diversity in seawater was higher than that in the sediment samples,22 species were identified only in the sediment samples,indicating that sediment eDNA may represent a valuable supplementary tool for the investigation of SHC communities in hot spots.In addition to revealing the vast diversity of SHC species occupying coral reef ecosystems in the Xisha Islands,our findings confirm the potential of eDNA metabarcoding as an advanced tool for monitoring the biodiversity of cryptic species.
基金Supported by the Guangzhou Municipal Science and Technology Project(No.202201010592)the Fundamental Research Funds for the Central Public Welfare Research Institutes(No.PM-zx 703-202305-165)。
文摘Zooplankton,a crucial component of urban wetland,are one of the effective bioindicators for monitoring the feeding stocks of organisms at higher trophic levels and assessing the ecological quality of ecosystems.However,information about the characteristics of epiphytic zooplankton community structure resulted from traditional methods is limited and hindered by the large amount of detritus and sludge attached to the macrophytes.We investigated the epiphytic zooplankton communities associated with macrophytes(Vallisneria,Nymphaea,and Thalia dealbata)in a subtropical wetland using as DNA markers of the 18 S rRNA gene and the mitochondrial cytochrome c oxidase subunit I(COI)gene.A total of 241 OTUs of zooplankton were obtained from COI amplicons,including 194 OTUs of Rotifera,22 of Cladocera,and 25 of Copepoda,while only 62 OTUs of zooplankton were obtained from 18 S rDNA amplicons including 34 OTUs of Rotifera and 28 of Copepoda.The zooplankton communities associated with the three macrophytes were similar,but they differed significantly from those in the open waters.However,there were no significant temporal differences among the zooplankton communities.Epiphytic zooplankton communities were dominated by littoral zooplankton such as Testudinella,Lecane,and Philodina.Microzooplankton,especially littoral species,utilize macrophytes as food sources and as refuges against predation.This further led to an increase inαandβdiversity of zooplankton communities in urban wetlands.Our result suggests that the joint use of multiple molecular markers could improve the taxonomic resolution and generate a comprehensive biodiversity profile of zooplankton.
基金supported by the National Natural Science Foundation of China(32102793)National Key R&D Program of China(2018YFD0900802)+4 种基金Central Public-Interest Scientific Institution Basal Research FundSouth China Sea Fisheries Research Institute,CAFS(2019TS13,2021SD18)Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou)(GML2019ZD0605)Open Fund Project of Key Laboratory of Offshore Fishery Development of Ministry of Agriculture and Rural Affairs(LOF 2020-02)China-ASEAN Maritime Cooperation Fund(CAMC-2018F)。
文摘Environmental DNA(eDNA)integrated with metabarcoding is a promising and powerful tool for species composition and biodiversity assessment in aquatic ecosystems and is increasingly applied to evaluate fish diversity.To date,however,no standardized eDNA-based protocol has been established to monitor fish diversity.In this study,we investigated and compared two filtration methods and three DNA extraction methods using three filtration water volumes to determine a suitable approach for eDNA-based fish diversity monitoring in the Pearl River Estuary(PRE),a highly anthropogenically disturbed estuarine ecosystem.Compared to filtration-based precipitation,direct filtration was a more suitable method for eDNA metabarcoding in the PRE.The combined use of DNeasy Blood and Tissue Kit(BT)and traditional phenol/chloroform(PC)extraction produced higher DNA yields,amplicon sequence variants(ASVs),and Shannon diversity indices,and generated more homogeneous and consistent community composition among replicates.Compared to the other combined protocols,the PC and BT methods obtained better species detection,higher fish diversity,and greater consistency for the filtration water volumes of 1000 and 2000 mL,respectively.All eDNA metabarcoding protocols were more sensitive than bottom trawling in the PRE fish surveys and combining two techniques yielded greater taxonomic diversity.Furthermore,combining traditional methods with eDNA analysis enhanced accuracy.These results indicate that methodological decisions related to eDNA metabarcoding should be made with caution for fish community monitoring in estuarine ecosystems.
基金supported by the National Key R&D Program of China(Nos.2018YFD0900301,2019YFD0901301)the National Natural Science Foundation of China(No.41776171)。
文摘Environmental DNA(eDNA)metabarcoding has emerged as a potentially powerful tool to monitor invasive fish species.As an alternative(or complementary)tool for biodiversity monitoring,e DNA metabarcoding had been used to detect species in aquariums,which represents an important transit avenue for introducing non-indigenous species with high population densities.In this study,eDNA metabarcoding as well as morphological characterization were used to reveal the diversity of non-indigenous species in a large aquarium at Qingdao Underwater World.Environmental DNA metabarcoding of 14 water samples at five locations from the Big Water Tank detected 24 non-indigenous species and four putative non-indigenous operational taxonomic units(OTUs).In contrast,only 20 non-indigenous species were observed by morphological characterization.Some species undetected by morphological characterization,such as Oreochromis niloticus(Linnaeus,1758),are highly adaptable to various environments and/or have invaded preferred regions where they threaten native aquatic species.eDNA metabarcoding also detected seven local fishes that were not identified by morphological characterization.However,analysis of OTU diversity among stations and sample replications revealed that eDNA varied within and/or between stations.Increasing sampling effort as well as negative controls are required to increase the detection rate of species and to eliminate false-positive OTUs.
基金the National Key Program of Research and Development(2016YFC0503200)the National Natural Science Foundation of China(31570391,31200411)+2 种基金the Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment(2019HJ2096001006)the Construction of Basic Conditions Platform of Sichuan Science and Technology Department(2019JDPT0020)the China Biodiversity Observation Networks(Sino BON-Amphibian&Reptile).
文摘Due to the overexploitation of farming,as well as habitat destruction,the wild population of Chinese giant salamander(CGS)Andrias davidianus,a species with seven genetically distinct lineages,has decreased by over 80%in the past 70 years.Traditional survey methods have proven to be unsuitable for finding this rare and elusive species.We evaluated the efficacy of environmental DNA(eDNA)sampling to detect CGS indirectly from its aquatic environment.We developed several species-specific primer sets;validated their specificity and sensitivity;and assessed their utility in silico,in the laboratory,and at two field sites harboring released farm-bred CGS.We detected the presence of CGS DNA by using polymerase chain reaction and Sanger sequencing.We also sequenced an amplicon mixture of seven haplotype-represented samples using high-throughput sequencing.Our eDNA methods could detect the presence of CGS at moderate densities reported across its range,proving them as a cost-effective way to establish broad-scale patterns of occupancy for CGS.In addition,our primers enabled the detection of mitochondrial lineage mixture or introduced individuals from geographically isolated populations of CGS.
基金the Science&Technology Basic Resources Investigation Program of China(No.2017FY100804)the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDB42000000)+5 种基金the National Program on Global Change and Air-Sea Interaction(No.GASIGEOGE-04)the Key Program of National Natural Science Foundation of China(No.41930533)the Taishan Scholars Project Funding(No.TS20190963)the Senior User Project of R/V KexueCenter for Ocean Mega-Science,Chinese Academy of Sciences。
文摘Seamount is a unique deep-sea ecosystem widely distributed in the world.Its biodiversity is vibrant due to its specific geographical and hydrological conditions.However,the diversity and features of foraminifera in such an environment have rarely been studied.We extracted environmental DNA(eDNA)in sedime nts and amplified the partial small subunit ribo somal DNA(SSU rDNA)of fo raminife ra to understand the foraminiferal diversity from four sites in Magellan Seamount(Western Pacific Ocean).Partial S SU rDNA sequencing was conducted and 912979 foraminiferal reads were obtained and gathered into 266 operational taxonomic units(OTUs).In the available dataset,a high proportion of rare OTUs and low identity OTUs in each studied sample showed that the Magellan Seamount foraminiferal community might have a high genetic novelty.The relative abundance of foraminifera varied between replicates probably due to the existence of bias in amplification process and patchiness of the deep-sea floor.It showed that the Magellan Seamount has a relatively high benthic foraminiferal diversity characterized mainly by monothalamiids(76.37%of total reads)in association with rotaliids(19.03%of total reads),including planktic foraminiferal sequences(38.58%of rotaliids;7.36%of total reads).The remaining reads were assigned to miliolids(0.83%of total reads)and textulariids(0.66%of total reads),and 3.11%of total reads are unassigned to a specific family.The co mparative analysis with foraminiferal assemblage s from coastal and deep-sea environme nts indicated that seamounts could aggregate species from a nearby deep-sea.
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 grants from The Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China (2019HJ2096001006)National Natural Science Foundation of China (32030070)+2 种基金the High-Level Talents Research Start-Up Project of Hebei UniversityChina’s Biodiversity Observation Network (Sino-BON)Second Tibetan Plateau Scientific Expedition and Research (STEP) Program (2019QZKK0501)
文摘eDNA metabarcoding is an advanced method formonitoring biodiversityproposed in recent years.By analyzing DNA in water,soil and sediment samples,the technology obtains species distribution and population quantity information.It was found that macrobarcode technology is more accurate than the traditional method in measuring the species richness of some groups.In Europe,America and South America,the relia bility of this technology in monitoring amphibian diversity in the wild was studied,and it was found to be better than traditional biodiversity monitoring methods in detecting species diversity.At present,amphibian monitoring mainly depends on various traditional methods,such as transects,drift fence traps,artificial shelters and mark-recapture.These monitoring techniques have many shortcomings,such as low accuracy and strong subjectivity of study results.These technologies have poor effects on rare,invasive and endangered species with strong concealment ability,low density and strong seasonality and are difficult to implement in sites inaccessible to people.Traditional monitoring technology also requires considerable investment of human and material resources,and the economic cost is relatively high,while eDNA metabarcoding ismore efficient and less costly,so it is important to use eDNA meta barcoding in amphibian monitoring in China.In this study,the eDNA meta barcoding and traditional line transect method(TLTM)were used to study the characteristics of the two methods in the Beijing-Tianjin-Hebeiregion.Repeated samplingwas conducted on 58 waterbodies in July 2019 and June 2020.After sequencing the samples using highthroughput sequencing technology,the differences between metabarcoding and commonly used TLTM surveys in detecting the diversity of four amphibians in North China were assessed.Our results showed that eDNA meta barcoding is more sensitive to the detection of the four amphibian species in the sampling area,and the combined use of eDNA metabarcoding and TLTM can improve the survey results of amphibians in the survey area to the greatest extent.In addition,in the process of species classification and identification of metabarcoding results,7 species of reptiles were detected,indicating that eDNA metabarcoding is also useful to detect reptiles.The results of this study indicate that metabarcoding in combination with TLTM can accurately estimate the diversityof amphibians in a short-term survey in North China and is also useful in reptile species detection.
