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
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
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
[Objective]Implementation of the Ten-Year Fishing Ban policy may alter fish diversity and niche characteristics of dominant species in spawning grounds within the National Nature Reserve for Rare and Endemic Fish in t...[Objective]Implementation of the Ten-Year Fishing Ban policy may alter fish diversity and niche characteristics of dominant species in spawning grounds within the National Nature Reserve for Rare and Endemic Fish in the Upper Yangtze River.This study initiated continuous monitoring of natural spawning habitats from February 2022 to assess these ecological changes.[Methods]Environmental DNA(eDNA)metabarcoding was employed to analyze fish species composition,biodiversity patterns,and niche parameters of dominant species.Water sampling followed the CEN/TS 19461 standard across five monitoring transects(ZT1-ZT5).[Results]The eDNA analysis detected 45 species of fish belonging to 38 genera,13 families,and 3 orders were detected through environmental DNA(eDNA)in this survey,including 10 species endemic to the upper reaches of the Yangtze River,such as Procypris rabaudi and Myxocyprinus asiaticus.The fish community was mainly composed of bottom-dwelling,settling ovum-producing,omnivorous fish.The variation ranges of the Chao1 index,ACE index,Shannon index,and Simpson index are 736~996,719~965,1.58~3.23,and 0.83~0.99,respectively,indicating that fish species in spawning sites are abundant and community distribution uniformity is high.All indexes are highest at ZT1 monitoring points.Cluster analysis showed that,at a certain similarity level,fish community types in spawning sites could be basically divided into two groups:ZT1,ZT3,and ZT5 clustered together,and ZT2 and ZT4 clustered together,indicating similar fish community habitats.There are 9 dominant fish species in typical deep pool habitats in the reserve,with niche widths(Bi)ranging from 1.13 to 3.87.The dominant fish species are broad and medium niche fish,such as Cyprinus carpio and Hemiculter tchangi,with the niche overlap index(Oik)of some dominant fish species reaching more than 0.95.This indicates fierce competition for resources among the fish in this spawning ground.[Conclusion]The Zhutuo spawning ground demonstrates high species richness with homogeneous community structure and intense resource competition.This study establishes an eDNA-based monitoring framework that enhances conventional survey method,providing critical baseline data for adaptive management under the fishing moratorium regime.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
Fish diversity of the Yarlung Zangbo River is very sensitive and vulnerable to biological invasion,anthropogenic activities and climate change,especially in the upper and middle reaches where several endemic fishes ha...Fish diversity of the Yarlung Zangbo River is very sensitive and vulnerable to biological invasion,anthropogenic activities and climate change,especially in the upper and middle reaches where several endemic fishes have become endangered and nearly ten invasive fishes have been established.Here,we used environmental DNA(eDNA)metabarcoding to monitor rare and invasive fishes,and to assess diversity in 25 sites from two wetlands(Lalu and Chabalang)and the main channel(YT),within the upper and middle reaches.To obtain a species-level resolution,we evaluated species discrimination potentials of three mitochondrial markers and found Cytb had the highest average genetic distance at each taxonomic level followed by COI and 12S.The 12S was unqualified for species assignment,as two species shared identical haplotypes.The newly designed Cytb primers used for metabarcoding showed an average mismatch of 0.28 and amplified well across species.In total,8942 operational taxonomic units(OTUs)were obtained based on a 100%identity threshold,among which 98.1%were assigned to 24 fishes based on our custom-made database and the remaining were assigned to six fishes based on the NCBI nt database.Almost all captured fishes were detected by the eDNA method except for two species.However,12 fishes detected by the eDNA method were not listed in catch data for several sites,including one endangered species(Oxygymnocypris stewartii),four previously recorded non-native species and two unrecorded non-native species(Monopterus albus and Siniperca chuatsi).The alpha diversities estimated by eDNA and capture-based methods were correlated for sites at Lalu.Both methods revealed significant differences in community composition between YT and the wetlands.Our results provide both basic information for conservation and management of rare and invasive fishes in the Yarlung Zangbo River and a framework of fish eDNA metabarcoding with a species-level resolution.展开更多
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 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(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.
文摘[Objective]Implementation of the Ten-Year Fishing Ban policy may alter fish diversity and niche characteristics of dominant species in spawning grounds within the National Nature Reserve for Rare and Endemic Fish in the Upper Yangtze River.This study initiated continuous monitoring of natural spawning habitats from February 2022 to assess these ecological changes.[Methods]Environmental DNA(eDNA)metabarcoding was employed to analyze fish species composition,biodiversity patterns,and niche parameters of dominant species.Water sampling followed the CEN/TS 19461 standard across five monitoring transects(ZT1-ZT5).[Results]The eDNA analysis detected 45 species of fish belonging to 38 genera,13 families,and 3 orders were detected through environmental DNA(eDNA)in this survey,including 10 species endemic to the upper reaches of the Yangtze River,such as Procypris rabaudi and Myxocyprinus asiaticus.The fish community was mainly composed of bottom-dwelling,settling ovum-producing,omnivorous fish.The variation ranges of the Chao1 index,ACE index,Shannon index,and Simpson index are 736~996,719~965,1.58~3.23,and 0.83~0.99,respectively,indicating that fish species in spawning sites are abundant and community distribution uniformity is high.All indexes are highest at ZT1 monitoring points.Cluster analysis showed that,at a certain similarity level,fish community types in spawning sites could be basically divided into two groups:ZT1,ZT3,and ZT5 clustered together,and ZT2 and ZT4 clustered together,indicating similar fish community habitats.There are 9 dominant fish species in typical deep pool habitats in the reserve,with niche widths(Bi)ranging from 1.13 to 3.87.The dominant fish species are broad and medium niche fish,such as Cyprinus carpio and Hemiculter tchangi,with the niche overlap index(Oik)of some dominant fish species reaching more than 0.95.This indicates fierce competition for resources among the fish in this spawning ground.[Conclusion]The Zhutuo spawning ground demonstrates high species richness with homogeneous community structure and intense resource competition.This study establishes an eDNA-based monitoring framework that enhances conventional survey method,providing critical baseline data for adaptive management under the fishing moratorium regime.
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supported by the Second Tibetan Plateau Scientific Expedition and Research(STEP)program(2019QZKK0304 and 2019QZKK0501)the National Natural Science Foundation of China(31601844)and the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA20050204).
文摘Fish diversity of the Yarlung Zangbo River is very sensitive and vulnerable to biological invasion,anthropogenic activities and climate change,especially in the upper and middle reaches where several endemic fishes have become endangered and nearly ten invasive fishes have been established.Here,we used environmental DNA(eDNA)metabarcoding to monitor rare and invasive fishes,and to assess diversity in 25 sites from two wetlands(Lalu and Chabalang)and the main channel(YT),within the upper and middle reaches.To obtain a species-level resolution,we evaluated species discrimination potentials of three mitochondrial markers and found Cytb had the highest average genetic distance at each taxonomic level followed by COI and 12S.The 12S was unqualified for species assignment,as two species shared identical haplotypes.The newly designed Cytb primers used for metabarcoding showed an average mismatch of 0.28 and amplified well across species.In total,8942 operational taxonomic units(OTUs)were obtained based on a 100%identity threshold,among which 98.1%were assigned to 24 fishes based on our custom-made database and the remaining were assigned to six fishes based on the NCBI nt database.Almost all captured fishes were detected by the eDNA method except for two species.However,12 fishes detected by the eDNA method were not listed in catch data for several sites,including one endangered species(Oxygymnocypris stewartii),four previously recorded non-native species and two unrecorded non-native species(Monopterus albus and Siniperca chuatsi).The alpha diversities estimated by eDNA and capture-based methods were correlated for sites at Lalu.Both methods revealed significant differences in community composition between YT and the wetlands.Our results provide both basic information for conservation and management of rare and invasive fishes in the Yarlung Zangbo River and a framework of fish eDNA metabarcoding with a species-level resolution.
