Hadal trenches are characterized by enhanced and infrequent high-rate episodic sedimentation events that likely introduce not only labile organic carbon and key nutrients but also new microbes that significantly alter...Hadal trenches are characterized by enhanced and infrequent high-rate episodic sedimentation events that likely introduce not only labile organic carbon and key nutrients but also new microbes that significantly alter the subseafloor microbiosphere.Currently,the role of high-rate episodic sedimentation in controlling the composition of the hadal subseafloor microbiosphere is unknown.Here,analyses of carbon isotope composition in a~750 cm long sediment core from the Challenger Deep revealed noncontinuous deposition,with anomalous ^(14)C ages likely caused by seismically driven mass transport and the funneling effect of trench geomorphology.Microbial community composition and diverse enzyme activities in the upper~27 cm differed from those at lower depths,probably due to sudden sediment deposition and differences in redox condition and organic matter availability.At lower depths,microbial population numbers,and composition remained relatively constant,except at some discrete depths with altered enzyme activity and microbial phyla abundance,possibly due to additional sudden sedimentation events of different magnitude.Evidence is provided of a unique role for high-rate episodic sedimentation events in controlling the subsurface microbiosphere in Earth’s deepest ocean floor and highlight the need to perform thorough analysis over a large depth range to characterize hadal benthic populations.Such depositional processes are likely crucial in shaping deep-water geochemical environments and thereby the deep subseafloor biosphere.展开更多
The majority of marine ammonia oxidizers belong to Thaumarchaeota,a phylum of Archaea,which is distributed throughout the water column.Marine surface waters contain distinct thaumarchaeotal phylotypes compared to the ...The majority of marine ammonia oxidizers belong to Thaumarchaeota,a phylum of Archaea,which is distributed throughout the water column.Marine surface waters contain distinct thaumarchaeotal phylotypes compared to the deeper ocean,but spatial dynamics of the surface-associated lineages are largely unsolved.This study of 120 seawater samples from the eastern Chinese marginal seas identifed contrasting distribution and association patterns among thaumarchaeotal phylotypes across diferent dimensions.Horizontally,Nitrosopumilus-like and Nitrosopelagicus-like phylotypes dominated the surface water(3 m)of the Yellow Sea(YS)and East China Sea(ECS),respectively,along with increased abundance of total free-living Thaumarchaeota in ECS.Similar compositional changes were observed in the surface microlayer.The spatial heterogeneity of particle-attached Thaumarchaeota was less clear in surface microlayers than in surface waters.Vertically,the Nitrosopelagicus-like phylotype increased in abundance from surface to 90 m in ECS,which led to an increase in the proportion of Thaumarchaeota relative to total prokaryotes.This occurred mainly in the free-living fraction.These results indicate a clear size-fractionated niche partitioning,which is more pronounced at lower depths than in the surface water/surface microlayer.In addition,associations of Thaumarchaeota with other microbial taxa varied between phylotypes and size fractions.Our results show that a phylotype-resolved and size-fractionated spatial heterogeneity of the thaumarchaeotal community is present in surface oceanic waters and a vertical variation of the Nitrosopelagicus-like phylotype is present in shallow shelf waters.展开更多
The Mariana Trench is the deepest location on earth and harbors unique microbial communities as evidenced by 16S rRNA gene amplicon and metagenomic sequencing.Obtaining culturable microorganisms from the Mariana Trenc...The Mariana Trench is the deepest location on earth and harbors unique microbial communities as evidenced by 16S rRNA gene amplicon and metagenomic sequencing.Obtaining culturable microorganisms from the Mariana Trench will contribute to a further understanding of hadal biogeochemical processes and act as a unique microbial reservoir with potential applications.Here,825 bacterial strains,identified by 16S rRNA gene sequencing,were isolated from 12 water depths(0-10,400 m)of the Mariana Trench with 2216E and R2A media at 4℃ or 28℃ on four cruises during 2015-2017.These bacteria belong to four phyla,nine classes,27 orders,45 families and 108 genera.Alphaproteobacteria,Gammaproteobacteria,Actinobacteria_c,Bacilli and Flavobacteriia were the most abundant classes,accounting for 37.9%,33.0%,11.8%,8.6%and 8.0%of the total bacterial isolates,respectively.2216E and R2A media were found to have a better selectivity to Bacilli and Flavobacteriia,respectively.Fifty strains were potential novel bacterial species with a 16S rRNA gene similarity<98.65%,and a higher percentage of novel strains were obtained from R2A than 2216E medium.Additionally,301(150 species)out of 354 strains(178 species)selected from each depth could degrade at least one of the ten kinds of macromolecules tested.These results indicate that there is a high diversity of culturable bacteria in the Mariana Trench and they can produce a variety of extracellular enzymes.Our study provides a valuable resource of microorganisms for investigating their biogeochemical roles in the Mariana Trench and for industrial applications.展开更多
Microorganisms play crucial roles in maintaining ecosystem stability. The last two decades have witnessed an upsurge instudies on marine microbial community composition using high-throughput sequencing methods. Extens...Microorganisms play crucial roles in maintaining ecosystem stability. The last two decades have witnessed an upsurge instudies on marine microbial community composition using high-throughput sequencing methods. Extensive mining ofthe compositional data has provided exciting new insights into marine microbial ecology from a number of perspectives.Both deterministic and stochastic processes contribute to microbial community assembly but their relative importance instructuring subcommunities, that are categorized by traits such as abundance, functional type and activity, differs. Throughcorrelation-based network analysis, significant progress has been made in unraveling microbial co-occurrence patterns anddynamics in response to environmental changes. Prediction of ecosystem functioning, based on microbial data, is receivingincreasing attention, as closely related microbes often share similar ecological traits and microbial diversity often exhibitssignificant correlations to ecosystem functioning. The ecosystem functioning is likely executed not by the whole community,but rather by an active fraction of a community, which can be inferred from the marker gene transcription level of communitymembers. Furthermore, the huge amount of microbial community data has significantly expanded the tree of lifeand illuminated microbial phylogenetic divergence and evolutionary history. This review summarizes important findingsin microbial assembly, interaction, functioning, activity and diversification, highlighting the interacting roles of differentaspects, derived from community compositional data.展开更多
With the advantages of wide distribution,fast growth,and broad metabolic spectrum to organic carbon compounds,Vibrio may play an important role in organic carbon cycling.However,the ecological roles of Vibrio in many ...With the advantages of wide distribution,fast growth,and broad metabolic spectrum to organic carbon compounds,Vibrio may play an important role in organic carbon cycling.However,the ecological roles of Vibrio in many marine environments have not been explored.Here,the world's deepest'blue hole',the Sansha Yongle Blue Hole(SYBH)in the South China Sea,which is a geographically semi-enclosed environment featuring unique chemical characters,was investigated.The abundance,diversity and carbon source utilization capability of Vibrio were studied by quantification and high-throughput sequencing of Vibrio specific 16S rRNA genes and cultivation methods.The abundance of Vibrio in water column of the SYBH ranged from 3.78×10^4 to 7.35×10^616S rRNA gene copies L_1.Free-living Vibrio was more abundant than particle-associated Vibrio(~1.20×10^6 versus-2.68×10^5 gene copies L_1),indicating that Vibrio prefers a free-living life style.The Vibrio assemblages showed clear vertical stratification and could be divided into three groups:aerobic-transition,middle anaerobic and bottom anaerobic zones.Dissolved oxygen(DO),temperature,pH and salinity were the main environmental factors affecting the abundance and community composition.Cultivated Vibrio demonstrated a degrading capability to various macromolecular substrates,including starch,Tween 20/40/80,DNA,gelatin,alginate,casein,chitin,lecithin,K-carrageenan,mannan,xylan and hyaluronic acid.This suggests that Vibrio could produce a variety of highly active extracellular enzymes.Our study provides new insights into the distribution pattern and possible role in carbon cycle of Vibrio in the unique environment of a"blue hole'.展开更多
基金supported by the Laoshan laboratory(LSKJ202203206)National Natural Science Foundation of China(92051115 and 42230412)+1 种基金the Fundamental Research Funds for the Central Universities(202172002 and 202141009)the Shandong Province Natural Science Foundation(ZR2022YQ38).
文摘Hadal trenches are characterized by enhanced and infrequent high-rate episodic sedimentation events that likely introduce not only labile organic carbon and key nutrients but also new microbes that significantly alter the subseafloor microbiosphere.Currently,the role of high-rate episodic sedimentation in controlling the composition of the hadal subseafloor microbiosphere is unknown.Here,analyses of carbon isotope composition in a~750 cm long sediment core from the Challenger Deep revealed noncontinuous deposition,with anomalous ^(14)C ages likely caused by seismically driven mass transport and the funneling effect of trench geomorphology.Microbial community composition and diverse enzyme activities in the upper~27 cm differed from those at lower depths,probably due to sudden sediment deposition and differences in redox condition and organic matter availability.At lower depths,microbial population numbers,and composition remained relatively constant,except at some discrete depths with altered enzyme activity and microbial phyla abundance,possibly due to additional sudden sedimentation events of different magnitude.Evidence is provided of a unique role for high-rate episodic sedimentation events in controlling the subsurface microbiosphere in Earth’s deepest ocean floor and highlight the need to perform thorough analysis over a large depth range to characterize hadal benthic populations.Such depositional processes are likely crucial in shaping deep-water geochemical environments and thereby the deep subseafloor biosphere.
基金We thank the scientists and crews on the R/V Dongfanghong 2 for their assistance with sampling during the cruises.We thank Chunying Liu and Guipeng Yang both of the Ocean University of China for providing pH and DO data,respectively.This work was funded by the National Natural Science Foundation of China(92051115,41976101,92251303 and 41730530)the Scientifc and Technological Innovation Project of Laoshan Laboratory(LSKJ202203206 and LSKJ202203201)+2 种基金the Shandong Provincial Natural Science Foundation(ZR2022YQ38)the National Key Research and Development Program of China(2018YFE0124100)the Fundamental Research Funds for the Central Universities(202141009 and 202172002).
文摘The majority of marine ammonia oxidizers belong to Thaumarchaeota,a phylum of Archaea,which is distributed throughout the water column.Marine surface waters contain distinct thaumarchaeotal phylotypes compared to the deeper ocean,but spatial dynamics of the surface-associated lineages are largely unsolved.This study of 120 seawater samples from the eastern Chinese marginal seas identifed contrasting distribution and association patterns among thaumarchaeotal phylotypes across diferent dimensions.Horizontally,Nitrosopumilus-like and Nitrosopelagicus-like phylotypes dominated the surface water(3 m)of the Yellow Sea(YS)and East China Sea(ECS),respectively,along with increased abundance of total free-living Thaumarchaeota in ECS.Similar compositional changes were observed in the surface microlayer.The spatial heterogeneity of particle-attached Thaumarchaeota was less clear in surface microlayers than in surface waters.Vertically,the Nitrosopelagicus-like phylotype increased in abundance from surface to 90 m in ECS,which led to an increase in the proportion of Thaumarchaeota relative to total prokaryotes.This occurred mainly in the free-living fraction.These results indicate a clear size-fractionated niche partitioning,which is more pronounced at lower depths than in the surface water/surface microlayer.In addition,associations of Thaumarchaeota with other microbial taxa varied between phylotypes and size fractions.Our results show that a phylotype-resolved and size-fractionated spatial heterogeneity of the thaumarchaeotal community is present in surface oceanic waters and a vertical variation of the Nitrosopelagicus-like phylotype is present in shallow shelf waters.
基金funded by the National Natural Science Foundation of China(Nos.91751202,41976101 and 41730530)Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology(Qingdao)(No.2018SDKJ0406-4).
文摘The Mariana Trench is the deepest location on earth and harbors unique microbial communities as evidenced by 16S rRNA gene amplicon and metagenomic sequencing.Obtaining culturable microorganisms from the Mariana Trench will contribute to a further understanding of hadal biogeochemical processes and act as a unique microbial reservoir with potential applications.Here,825 bacterial strains,identified by 16S rRNA gene sequencing,were isolated from 12 water depths(0-10,400 m)of the Mariana Trench with 2216E and R2A media at 4℃ or 28℃ on four cruises during 2015-2017.These bacteria belong to four phyla,nine classes,27 orders,45 families and 108 genera.Alphaproteobacteria,Gammaproteobacteria,Actinobacteria_c,Bacilli and Flavobacteriia were the most abundant classes,accounting for 37.9%,33.0%,11.8%,8.6%and 8.0%of the total bacterial isolates,respectively.2216E and R2A media were found to have a better selectivity to Bacilli and Flavobacteriia,respectively.Fifty strains were potential novel bacterial species with a 16S rRNA gene similarity<98.65%,and a higher percentage of novel strains were obtained from R2A than 2216E medium.Additionally,301(150 species)out of 354 strains(178 species)selected from each depth could degrade at least one of the ten kinds of macromolecules tested.These results indicate that there is a high diversity of culturable bacteria in the Mariana Trench and they can produce a variety of extracellular enzymes.Our study provides a valuable resource of microorganisms for investigating their biogeochemical roles in the Mariana Trench and for industrial applications.
基金supported by the National NaturalScience Foundation of China (Grants Nos. 41976101, 41506154 and41730530)the Fundamental Research Funds for the Central Universities(Grants No. 201762017).
文摘Microorganisms play crucial roles in maintaining ecosystem stability. The last two decades have witnessed an upsurge instudies on marine microbial community composition using high-throughput sequencing methods. Extensive mining ofthe compositional data has provided exciting new insights into marine microbial ecology from a number of perspectives.Both deterministic and stochastic processes contribute to microbial community assembly but their relative importance instructuring subcommunities, that are categorized by traits such as abundance, functional type and activity, differs. Throughcorrelation-based network analysis, significant progress has been made in unraveling microbial co-occurrence patterns anddynamics in response to environmental changes. Prediction of ecosystem functioning, based on microbial data, is receivingincreasing attention, as closely related microbes often share similar ecological traits and microbial diversity often exhibitssignificant correlations to ecosystem functioning. The ecosystem functioning is likely executed not by the whole community,but rather by an active fraction of a community, which can be inferred from the marker gene transcription level of communitymembers. Furthermore, the huge amount of microbial community data has significantly expanded the tree of lifeand illuminated microbial phylogenetic divergence and evolutionary history. This review summarizes important findingsin microbial assembly, interaction, functioning, activity and diversification, highlighting the interacting roles of differentaspects, derived from community compositional data.
基金This work was supported by the National Natural Science Foundation of China(Grants nos.41730530,91751202 and 41476112).
文摘With the advantages of wide distribution,fast growth,and broad metabolic spectrum to organic carbon compounds,Vibrio may play an important role in organic carbon cycling.However,the ecological roles of Vibrio in many marine environments have not been explored.Here,the world's deepest'blue hole',the Sansha Yongle Blue Hole(SYBH)in the South China Sea,which is a geographically semi-enclosed environment featuring unique chemical characters,was investigated.The abundance,diversity and carbon source utilization capability of Vibrio were studied by quantification and high-throughput sequencing of Vibrio specific 16S rRNA genes and cultivation methods.The abundance of Vibrio in water column of the SYBH ranged from 3.78×10^4 to 7.35×10^616S rRNA gene copies L_1.Free-living Vibrio was more abundant than particle-associated Vibrio(~1.20×10^6 versus-2.68×10^5 gene copies L_1),indicating that Vibrio prefers a free-living life style.The Vibrio assemblages showed clear vertical stratification and could be divided into three groups:aerobic-transition,middle anaerobic and bottom anaerobic zones.Dissolved oxygen(DO),temperature,pH and salinity were the main environmental factors affecting the abundance and community composition.Cultivated Vibrio demonstrated a degrading capability to various macromolecular substrates,including starch,Tween 20/40/80,DNA,gelatin,alginate,casein,chitin,lecithin,K-carrageenan,mannan,xylan and hyaluronic acid.This suggests that Vibrio could produce a variety of highly active extracellular enzymes.Our study provides new insights into the distribution pattern and possible role in carbon cycle of Vibrio in the unique environment of a"blue hole'.