Corals influence microorganisms within the surrounding seawater,yet the diversities and functions of seawater bacteria and microeukaryotes in coral-reef systems have not been well addressed.We collected 40 seawater sa...Corals influence microorganisms within the surrounding seawater,yet the diversities and functions of seawater bacteria and microeukaryotes in coral-reef systems have not been well addressed.We collected 40 seawater samples in outer coral reef flats and semi-closed inner lagoons from the surface,middle and bottom layers in the pristine coral-reef system of Xisha Islands,South China Sea.We detected the abundance,composition and distribution of bacteria and microeukaryotes using flow cytometry,qPCR and high throughput sequencing techniques,and profiled the potential ecological roles based on the information of 16S and 18S rDNA sequencing.In terms of flow cytometry,Prochlorococcus dominated the autotrophs with cell abundance ranging from 5.8×10^(2)to 5.44×10^(3)cells mL−1 seawater.Based on qPCR,the 16S rDNA copies were much higher in coral reef flats than in lagoons(P=0.003).The bacterial communities held significantly lower diversity in bottom waters compared with surface and middle waters(P<0.05),which were dominated by SAR11,Flavobacteriales,and Synechococcus.Alveolata represented most of the microeukaryotic communities with Dinophyceae and Syndiniales well represented in all samples.Neither bacterial nor microeukaryotic community exhibited distinct layer or niche pattern,however,Haptophyta and Picozoa decreased with depth and SAR 86,MAST-3 and Picozoa were enriched in lagoons(P<0.05).To adapt the nutrient-poor and organic matter-rich environment,bacterial nitrogen fixation and assimilatory/dissimilatory nitrate reduction were active in the system,and mixotrophy was the most important trophic strategy among microeukaryotes.The study highlighted the ecological adaptability of seawater microbes to the unique coral-reef environments.展开更多
The productivity and health of seagrass depend on the combined inputs of nutrients from the water and sediments in which they grow and the microbiota with which they live intimately.However,little is known about the c...The productivity and health of seagrass depend on the combined inputs of nutrients from the water and sediments in which they grow and the microbiota with which they live intimately.However,little is known about the composition and diversity pattern of single-celled benthic eukaryotes in seagrass meadows.Here,we investigated how the structure and diversity of the benthic microeukaryotic community vary with respect to season,location,and seagrass colonization,by applying 18S rRNA gene amplicon sequencing for 96 surface sediment samples that were collected from three different seagrass habitats through four seasons.We found that benthic microeukaryotic communities associated with seagrass Zostera japonica exhibited remarkable spatial and seasonal variations,as well as differences between vegetated and unvegetated sediments.Diatoms and dinoflagellates predominated in the benthic microeukaryotic communities,but they were inversely correlated and displaced each other as the dominant microbial group in different seasons or habitats.Mucoromycota was more prevalent in vegetated sediments,whereas Lobulomycetales and Chytridiales had higher proportions in unvegetated sites.Total organic carbon and total organic nitrogen were the most important environmental factors in driving the microeukaryotic assemblages and diversity.Our study expands the available knowledge on the biogeographic distribution patterns and niche preferences for benthic microeukaryotes in seagrass systems.展开更多
Antibiotic pollution imposes urgent threats to public health and microbial-mediated ecological processes.Existing studies have primarily focused on bacterial responses to antibiotic pollution,but they ignored the micr...Antibiotic pollution imposes urgent threats to public health and microbial-mediated ecological processes.Existing studies have primarily focused on bacterial responses to antibiotic pollution,but they ignored the microeukaryotic counterpart,though microeukaryotes are functionally important(e.g.,predators and saprophytes)in microbial ecology.Herein,we explored how the assembly of sediment microeukaryotes was affected by increasing antibiotic pollution at the inlet(control)and across the outlet sites along a shrimpwastewater discharge channel.The structures of sedimentmicroeukaryotic community were substantially altered by the increasing nutrient and antibiotic pollutions,whichwere primarily controlled by the direct effects of phosphate and ammonium(−0.645 and 0.507,respectively).In addition,tetracyclines exerted a large effect(0.209),including direct effect(0.326)and indirect effect(−0.117),on the microeukaryotic assembly.On the contrary,the fungal subcommunity was relatively resistant to antibiotic pollution.Segmented analysis depicted nonlinear responses of microeukaryotic genera to the antibiotic pollution gradient,as supported by the significant tipping points.We screened 30 antibiotic concentration-discriminatory taxa of microeukaryotes,which can quantitatively and accurately predict(98.7%accuracy)the in-situ antibiotic concentration.Sediment microeukaryotic(except fungal)community is sensitive to antibiotic pollution,and the identified bioindicators could be used for antibiotic pollution diagnosis.展开更多
Microeukaryotes play a vital role in shaping marine ecosystems,especially in marine productivity,the microbial food web,and carbon cycle.The Indian Ocean is one of the largest oligotrophic areas in the world,but littl...Microeukaryotes play a vital role in shaping marine ecosystems,especially in marine productivity,the microbial food web,and carbon cycle.The Indian Ocean is one of the largest oligotrophic areas in the world,but little is known about the biodiversity of microeukaryotes in the area.The community composition and geographical distribution of microeukaryotes collected from the surface(SUR)and deep chlorophyll maximum(DCM)layers in the southwestern Indian Ocean were studied using high-throughput sequencing of the 18S rRNA gene.The metagenomic data helped quantify the impact of environmental factors on microeukaryotic communities.The relative abundance of different taxa groups exhibited distinct patterns between SUR and DCM layers,except for the most dominant Dinoflagellata that accounted for more than 40.6%abundance in each sample.Radiolaria was much more abundant in the nutrient-rich DCM layer than the SUR layer.The community similarity of microeukaryotes decreased with increasing of geographic distance,whereas the temperature and inorganic nitrogen were the most important environmental parameters to community structure.Abundant communities were more influenced by dispersal limitations and rare communities were more responsive to environmental factors.Correlation network analyses revealed strong biotic interactions indicative of parasitism,predation and competition,and their contribution to microeukaryotic population in diverse environments.Overall,this study provided insights into the biodiversity of microeukaryotes by characterizing the differences between water layers and identifying the driving factors in the ocean.展开更多
Background Bacteria,Archaea,and Microeukaryotes comprise taxonomic domains that interact in mediating biogeochemical cycles in coastal waters.Many studies have revealed contrasting biogeographic patterns of community ...Background Bacteria,Archaea,and Microeukaryotes comprise taxonomic domains that interact in mediating biogeochemical cycles in coastal waters.Many studies have revealed contrasting biogeographic patterns of community structure and assembly mechanisms in microbial communities from diferent domains in coastal ecosystems;however,knowledge of specifc biogeographic patterns on microbial co-occurrence relationships across complex coastal environmental gradients remains limited.Using a dense sampling scheme at the regional scale,SSU rRNA gene amplicon sequencing,and network analysis,we investigated intra-and inter-domain co-occurrence relationships and network topology-based biogeographic patterns from three microbial domains in coastal waters that show environmental gradients across the inshore-nearshore-ofshore continuum in the East China Sea.Results Overall,we found the highest complexity and connectivity in the bacterial network,the highest modularity in the archaeal network,and the lowest complexity,connectivity,and modularity in the microeukaryotic network.Although microbial co-occurrence networks from the three domains showed distinct topological features,they exhibited a consistent biogeographic pattern across the inshore-nearshore-ofshore continuum.Specifcally,the nearshore zones with intermediate levels of terrestrial impacts refected by multiple environmental factors(including water temperature,salinity,pH,dissolved oxygen,and nutrient-related parameters)had a higher intensity of microbial co-occurrence for all three domains.In contrast,the intensity of microbial co-occurrence was weaker in both the inshore and the ofshore zones at the two ends of the environmental gradients.Archaea occupied a central position in the microbial inter-domain co-occurrence network.In particular,members of the Thaumarchaeota Marine Group I(MGI,now placed within the Family Nitrosopumilaceae of the Phylum Thermoproteota)appeared to be the hubs in the biogeographic shift between inter-domain network modules across environmental gradients.Conclusions Our work ofers new insights into microbial biogeography by integrating network features into biogeographic patterns,towards a better understanding of the potential of microbial interactions in shaping biogeographic patterns of coastal marine microbiota.展开更多
Microeukaryotes and bacteria are key drivers of primary productivity and nutrient cycling in aquaculture ecosystems.Although their diversity and composition have been widely investigated in aquaculture systems,the co-...Microeukaryotes and bacteria are key drivers of primary productivity and nutrient cycling in aquaculture ecosystems.Although their diversity and composition have been widely investigated in aquaculture systems,the co-occurrence bipartite network between microeukaryotes and bacteria remains poorly understood.This study used the bipartite network analysis of high-throughput sequencing datasets to detect the co-occurrence relationships between microeukaryotes and bacteria in water and sediment from coastal aquaculture ponds.Chlorophyta and fungi were dominant phyla in the microeukaryotic–bacterial bipartite networks in water and sediment,respectively.Chlorophyta also had overrepresented links with bacteria in water.Most microeukaryotes and bacteria were classified as generalists,and tended to have symmetric positive and negative links with bacteria in both water and sediment.However,some microeukaryotes with high density of links showed asymmetric links with bacteria in water.Modularity detection in the bipartite network indicated that four microeukaryotes and twelve uncultured bacteria might be potential keystone taxa among the module connections.Moreover,the microeukaryotic–bacterial bipartite network in sediment harbored significantly more nestedness than that in water.The loss of microeukaryotes and generalists will more likely lead to the collapse of positive co-occurrence relationships between microeukaryotes and bacteria in both water and sediment.This study unveils the topology,dominant taxa,keystone species,and robustness in the microeukaryotic–bacterial bipartite networks in coastal aquaculture ecosystems.These species herein can be applied for further management of ecological services,and such knowledge may also be very useful for the regulation of other eutrophic ecosystems.展开更多
基金the National Key Research and Development Program of China(No.2018YF C1406501)the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDA23050303)+1 种基金the National Natural Science Foundation of China(Nos.41676154,41976115)the Key Research Program of Frontier Sciences of CAS(Nos.QYZDB-SSW-DQC013,QYZ DB-SSW-DQC041)。
文摘Corals influence microorganisms within the surrounding seawater,yet the diversities and functions of seawater bacteria and microeukaryotes in coral-reef systems have not been well addressed.We collected 40 seawater samples in outer coral reef flats and semi-closed inner lagoons from the surface,middle and bottom layers in the pristine coral-reef system of Xisha Islands,South China Sea.We detected the abundance,composition and distribution of bacteria and microeukaryotes using flow cytometry,qPCR and high throughput sequencing techniques,and profiled the potential ecological roles based on the information of 16S and 18S rDNA sequencing.In terms of flow cytometry,Prochlorococcus dominated the autotrophs with cell abundance ranging from 5.8×10^(2)to 5.44×10^(3)cells mL−1 seawater.Based on qPCR,the 16S rDNA copies were much higher in coral reef flats than in lagoons(P=0.003).The bacterial communities held significantly lower diversity in bottom waters compared with surface and middle waters(P<0.05),which were dominated by SAR11,Flavobacteriales,and Synechococcus.Alveolata represented most of the microeukaryotic communities with Dinophyceae and Syndiniales well represented in all samples.Neither bacterial nor microeukaryotic community exhibited distinct layer or niche pattern,however,Haptophyta and Picozoa decreased with depth and SAR 86,MAST-3 and Picozoa were enriched in lagoons(P<0.05).To adapt the nutrient-poor and organic matter-rich environment,bacterial nitrogen fixation and assimilatory/dissimilatory nitrate reduction were active in the system,and mixotrophy was the most important trophic strategy among microeukaryotes.The study highlighted the ecological adaptability of seawater microbes to the unique coral-reef environments.
基金The National Key Research and Development Program under contract No.2020YFD0901003the National Natural Science Foundation of China under contract Nos 92051119,42077305 and 32070112+2 种基金the Special National Project on Investigation of Basic Resources of China under contract No.2019FY100700the Key Research Project of Frontier Science of Chinese Academy of Sciences under contract No.QYZDB-SSW-DQC041the Taishan Scholar Project Special Funding under contract No.Tspd20210317。
文摘The productivity and health of seagrass depend on the combined inputs of nutrients from the water and sediments in which they grow and the microbiota with which they live intimately.However,little is known about the composition and diversity pattern of single-celled benthic eukaryotes in seagrass meadows.Here,we investigated how the structure and diversity of the benthic microeukaryotic community vary with respect to season,location,and seagrass colonization,by applying 18S rRNA gene amplicon sequencing for 96 surface sediment samples that were collected from three different seagrass habitats through four seasons.We found that benthic microeukaryotic communities associated with seagrass Zostera japonica exhibited remarkable spatial and seasonal variations,as well as differences between vegetated and unvegetated sediments.Diatoms and dinoflagellates predominated in the benthic microeukaryotic communities,but they were inversely correlated and displaced each other as the dominant microbial group in different seasons or habitats.Mucoromycota was more prevalent in vegetated sediments,whereas Lobulomycetales and Chytridiales had higher proportions in unvegetated sites.Total organic carbon and total organic nitrogen were the most important environmental factors in driving the microeukaryotic assemblages and diversity.Our study expands the available knowledge on the biogeographic distribution patterns and niche preferences for benthic microeukaryotes in seagrass systems.
基金supported by the Natural Science Fund for Distinguished Young Scholars of Zhejiang Province (No. LR19C030001)the National Natural Science Foundation of China (Nos. 31872693, 32071549)+1 种基金the Key Public Welfare Technology Application Research Project of Ningbo (No. 202002N3032)the K.C. Wong Magna Fund in Ningbo University
文摘Antibiotic pollution imposes urgent threats to public health and microbial-mediated ecological processes.Existing studies have primarily focused on bacterial responses to antibiotic pollution,but they ignored the microeukaryotic counterpart,though microeukaryotes are functionally important(e.g.,predators and saprophytes)in microbial ecology.Herein,we explored how the assembly of sediment microeukaryotes was affected by increasing antibiotic pollution at the inlet(control)and across the outlet sites along a shrimpwastewater discharge channel.The structures of sedimentmicroeukaryotic community were substantially altered by the increasing nutrient and antibiotic pollutions,whichwere primarily controlled by the direct effects of phosphate and ammonium(−0.645 and 0.507,respectively).In addition,tetracyclines exerted a large effect(0.209),including direct effect(0.326)and indirect effect(−0.117),on the microeukaryotic assembly.On the contrary,the fungal subcommunity was relatively resistant to antibiotic pollution.Segmented analysis depicted nonlinear responses of microeukaryotic genera to the antibiotic pollution gradient,as supported by the significant tipping points.We screened 30 antibiotic concentration-discriminatory taxa of microeukaryotes,which can quantitatively and accurately predict(98.7%accuracy)the in-situ antibiotic concentration.Sediment microeukaryotic(except fungal)community is sensitive to antibiotic pollution,and the identified bioindicators could be used for antibiotic pollution diagnosis.
基金Supported by the China Ocean Mineral Resources R&D Association(Nos.DY135-E2-4-04,DY135-E2-4-06)the Global Change and AirSea Interaction Program(Nos.GASI-03-01-03-03,GASI-02-IND-STSspr)。
文摘Microeukaryotes play a vital role in shaping marine ecosystems,especially in marine productivity,the microbial food web,and carbon cycle.The Indian Ocean is one of the largest oligotrophic areas in the world,but little is known about the biodiversity of microeukaryotes in the area.The community composition and geographical distribution of microeukaryotes collected from the surface(SUR)and deep chlorophyll maximum(DCM)layers in the southwestern Indian Ocean were studied using high-throughput sequencing of the 18S rRNA gene.The metagenomic data helped quantify the impact of environmental factors on microeukaryotic communities.The relative abundance of different taxa groups exhibited distinct patterns between SUR and DCM layers,except for the most dominant Dinoflagellata that accounted for more than 40.6%abundance in each sample.Radiolaria was much more abundant in the nutrient-rich DCM layer than the SUR layer.The community similarity of microeukaryotes decreased with increasing of geographic distance,whereas the temperature and inorganic nitrogen were the most important environmental parameters to community structure.Abundant communities were more influenced by dispersal limitations and rare communities were more responsive to environmental factors.Correlation network analyses revealed strong biotic interactions indicative of parasitism,predation and competition,and their contribution to microeukaryotic population in diverse environments.Overall,this study provided insights into the biodiversity of microeukaryotes by characterizing the differences between water layers and identifying the driving factors in the ocean.
基金supported by the National Natural Science Foundation of China(41977192)Zhejiang Provincial Natural Science Foundation of China(LY21D060004)+2 种基金Natural Science Foundation of Ningbo(2021J060 and 2019A610449)Fundamental Research Funds for the Provincial Universities of Zhejiang(SJLY2022001)K.C.Wong Magna Fund in Ningbo University
文摘Background Bacteria,Archaea,and Microeukaryotes comprise taxonomic domains that interact in mediating biogeochemical cycles in coastal waters.Many studies have revealed contrasting biogeographic patterns of community structure and assembly mechanisms in microbial communities from diferent domains in coastal ecosystems;however,knowledge of specifc biogeographic patterns on microbial co-occurrence relationships across complex coastal environmental gradients remains limited.Using a dense sampling scheme at the regional scale,SSU rRNA gene amplicon sequencing,and network analysis,we investigated intra-and inter-domain co-occurrence relationships and network topology-based biogeographic patterns from three microbial domains in coastal waters that show environmental gradients across the inshore-nearshore-ofshore continuum in the East China Sea.Results Overall,we found the highest complexity and connectivity in the bacterial network,the highest modularity in the archaeal network,and the lowest complexity,connectivity,and modularity in the microeukaryotic network.Although microbial co-occurrence networks from the three domains showed distinct topological features,they exhibited a consistent biogeographic pattern across the inshore-nearshore-ofshore continuum.Specifcally,the nearshore zones with intermediate levels of terrestrial impacts refected by multiple environmental factors(including water temperature,salinity,pH,dissolved oxygen,and nutrient-related parameters)had a higher intensity of microbial co-occurrence for all three domains.In contrast,the intensity of microbial co-occurrence was weaker in both the inshore and the ofshore zones at the two ends of the environmental gradients.Archaea occupied a central position in the microbial inter-domain co-occurrence network.In particular,members of the Thaumarchaeota Marine Group I(MGI,now placed within the Family Nitrosopumilaceae of the Phylum Thermoproteota)appeared to be the hubs in the biogeographic shift between inter-domain network modules across environmental gradients.Conclusions Our work ofers new insights into microbial biogeography by integrating network features into biogeographic patterns,towards a better understanding of the potential of microbial interactions in shaping biogeographic patterns of coastal marine microbiota.
基金This study was supported by the Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)(SML2021SP203,313022004)the National Natural Science Foundation of China(32102821,92051120)+4 种基金the Yongjiang Talent Introduction Programme,the Natural Science Foundation of Ningbo(2022J050)the Zhejiang Major Program of Science and Technology(2021C02069-5-4)the Key Research and Development Program of Zhejiang Province(2019C02054)the Key Research and Development Program of Ningbo(2022Z172)China Agriculture Research System of MOF and MARA.
文摘Microeukaryotes and bacteria are key drivers of primary productivity and nutrient cycling in aquaculture ecosystems.Although their diversity and composition have been widely investigated in aquaculture systems,the co-occurrence bipartite network between microeukaryotes and bacteria remains poorly understood.This study used the bipartite network analysis of high-throughput sequencing datasets to detect the co-occurrence relationships between microeukaryotes and bacteria in water and sediment from coastal aquaculture ponds.Chlorophyta and fungi were dominant phyla in the microeukaryotic–bacterial bipartite networks in water and sediment,respectively.Chlorophyta also had overrepresented links with bacteria in water.Most microeukaryotes and bacteria were classified as generalists,and tended to have symmetric positive and negative links with bacteria in both water and sediment.However,some microeukaryotes with high density of links showed asymmetric links with bacteria in water.Modularity detection in the bipartite network indicated that four microeukaryotes and twelve uncultured bacteria might be potential keystone taxa among the module connections.Moreover,the microeukaryotic–bacterial bipartite network in sediment harbored significantly more nestedness than that in water.The loss of microeukaryotes and generalists will more likely lead to the collapse of positive co-occurrence relationships between microeukaryotes and bacteria in both water and sediment.This study unveils the topology,dominant taxa,keystone species,and robustness in the microeukaryotic–bacterial bipartite networks in coastal aquaculture ecosystems.These species herein can be applied for further management of ecological services,and such knowledge may also be very useful for the regulation of other eutrophic ecosystems.
