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
Introduction:Biological soil crusts(BSCs)can dominate surface cover in dry lands worldwide,playing an integral role in arid land biogeochemistry,particularly in N fertilization through fixation and cycling.Nitrificati...Introduction:Biological soil crusts(BSCs)can dominate surface cover in dry lands worldwide,playing an integral role in arid land biogeochemistry,particularly in N fertilization through fixation and cycling.Nitrification is a characteristic and universal N transformation in BSCs that becomes important for the export of N beyond the microscopic bounds of the crust itself.The contribution of ammonia-oxidizing bacteria(AOB)in BSCs has been shown,but the role and extent of the recently discovered ammonia-oxidizing archaea(AOA)have not.Methods:We sampled various types of crusts in four desert regions across the western United States and characterized the composition and size of ammonia-oxidizing communities using clone libraries and quantitative PCR targeting the amoA gene,which codes for the ammonia monooxygenase enzyme,universally present in ammonia-oxidizing microbes.Results:All archaeal amoA sequences retrieved from BSCs belonged to the Thaumarchaeota(Nitrososphaera associated Group I.1b).Sequences from the Sonoran Desert,Colorado Plateau,and Great Basin were indistinguishable from each other but distinct from those of the Chihuahuan Desert.Based on amoA gene abundances,archaeal and bacterial ammonia oxidizers were ubiquitous in our survey,but the ratios of archaeal to bacterial ammonia oxidizers shifted from bacterially dominated in northern,cooler deserts to archaeally dominated in southern,warmer deserts.Conclusions:Archaea are shown to be potentially important biogeochemical agents of biological soil crust N cycling.Conditions associated with different types of BSCs and biogeographical factors reveal a niche differentiation between AOA and AOB,possibly driven by temperature.展开更多
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We thank Moria Nagy and G.S.N.Reddy for sharing their experiences with crust archaea.We are grateful to the staff of Sevilleta and Jornada LTER sites as well as the National Park Service(Canyonlands N.P.and Organ Pipe N.M.)for providing sampling permits,guidance,and hospitality.Finally,we thank Scott Bingham for assistance with qPCR and sequencing.This research was funded by an NSF grant from the Biodiversity Surveys and Inventories Program and by a USDA grant from the Soil Processes Program to FGP.
文摘Introduction:Biological soil crusts(BSCs)can dominate surface cover in dry lands worldwide,playing an integral role in arid land biogeochemistry,particularly in N fertilization through fixation and cycling.Nitrification is a characteristic and universal N transformation in BSCs that becomes important for the export of N beyond the microscopic bounds of the crust itself.The contribution of ammonia-oxidizing bacteria(AOB)in BSCs has been shown,but the role and extent of the recently discovered ammonia-oxidizing archaea(AOA)have not.Methods:We sampled various types of crusts in four desert regions across the western United States and characterized the composition and size of ammonia-oxidizing communities using clone libraries and quantitative PCR targeting the amoA gene,which codes for the ammonia monooxygenase enzyme,universally present in ammonia-oxidizing microbes.Results:All archaeal amoA sequences retrieved from BSCs belonged to the Thaumarchaeota(Nitrososphaera associated Group I.1b).Sequences from the Sonoran Desert,Colorado Plateau,and Great Basin were indistinguishable from each other but distinct from those of the Chihuahuan Desert.Based on amoA gene abundances,archaeal and bacterial ammonia oxidizers were ubiquitous in our survey,but the ratios of archaeal to bacterial ammonia oxidizers shifted from bacterially dominated in northern,cooler deserts to archaeally dominated in southern,warmer deserts.Conclusions:Archaea are shown to be potentially important biogeochemical agents of biological soil crust N cycling.Conditions associated with different types of BSCs and biogeographical factors reveal a niche differentiation between AOA and AOB,possibly driven by temperature.
