We investigated the changes in communities of bacteria,ammonia-oxidizing bacteria,and Nitrospira during the operation of a pufferfish Takifugu rubripes recirculating aquaculture system by using high-throughput DNA seq...We investigated the changes in communities of bacteria,ammonia-oxidizing bacteria,and Nitrospira during the operation of a pufferfish Takifugu rubripes recirculating aquaculture system by using high-throughput DNA sequencing.Differences in bacterial communities were observed at days 1-32,47-62 and 78-93 of biofilm development by using 16S rRNA gene pyrosequencing.The relative abundance of Proteobacteria(Gammaproteobacteria)increased,while that of Bacteroidetes(Flavobacteria)decreased.The proportions of Nitrosomonas and Nitrospina ranged from 0.02%to 0.30%and from 0.02%to 0.83%,respectively.Ammonia monooxygenase gene pyrosequencing revealed that the top three operational taxonomic units were related to Nitrosomonas aestuarii(17.5%-61.1%),uncultured beta proteobacterium clone B67S-54(1.9%-45.2%),and uncultured bacterium clone AZPa8(3.6%-24.7%).Nitrite oxidoreductase gene pyrosequencing revealed that the relative abundance of the dominant strain Nitrospira sp.Ecomares 2.1 increased,but that of the abundant species Nitrospira marina decreased.Our results demonstrated that the communities of bacteria,ammonia-oxidizing bacteria,and Nitrospira were changing during the operation of the pufferfish recirculating aquaculture system.展开更多
The identification of complete ammonia oxidizers(comammox)within the nitriteoxidizing bacteria(NOB)genus Nitrospira,capable of oxidizing ammonia directly to nitrite and nitrate,represents a pivotal advancement in eluc...The identification of complete ammonia oxidizers(comammox)within the nitriteoxidizing bacteria(NOB)genus Nitrospira,capable of oxidizing ammonia directly to nitrite and nitrate,represents a pivotal advancement in elucidating the microbial and metabolic pathways underlying nitrification in the global nitrogen cycle.Although comammox Nitrospira have been consistently identified across diverse environmental habitats,their rapid enrichment from complex activated sludge systems remains challenging owing to their intrinsically low growth rates and the restricted availability of cultured isolates.In this study,Candidatus Nitrospira inopinata(Ca.N.inopinata)was successfully enriched from anammox-inoculated sludge within 70 d under low ammonia concentrations(~4.88 mg/L),ambient temperatures(21.6-28.4℃),and minimal aeration(0-0.01 mg/L),facilitated by the application of kanamycin(KAN).By employing 16S rRNA gene amplicon sequencing and quantitative polymerase chain reaction(qPCR)targeting the functional marker gene amoA,Ca.N.inopinata was identified as the dominant ammonia oxidizer,achieving a relative abundance of 95.22% in the nitrifying community.Kanamycin was shown to exert significant selective pressure,further enhancing the enrichment of Ca.N.inopinata.These findings demonstrate the feasibility of establishing comammox Nitrospira through direct inoculation of anammox pellets coupled with kanamycin,offering a robust and efficient strategy for rapid enrichment of comammox Nitrospira for biotechnological applications,while underscoring the energy-efficient advantages of comammox-driven ammonia oxidation processes.展开更多
Comammox Nitrospira clade A and B showed contrasting responses to citrus planting.54d9-like AOA and Nitrobacter-NOB dominated in the 5Y and 10Y soils.Nitrososphaera-like AOA and Nitrospira-like NOB dominated in the 20...Comammox Nitrospira clade A and B showed contrasting responses to citrus planting.54d9-like AOA and Nitrobacter-NOB dominated in the 5Y and 10Y soils.Nitrososphaera-like AOA and Nitrospira-like NOB dominated in the 20Y and 30Y soils.Soil pH and P content were the major factors shaping nitrifying communities.展开更多
Magnetotactic bacteria （MTB）, a group of phylogeneti- cally diverse organisms that use their unique intracellular magnetosome organelles to swim along the Earth＇s magnetic field, play important roles in the biogeoc...Magnetotactic bacteria （MTB）, a group of phylogeneti- cally diverse organisms that use their unique intracellular magnetosome organelles to swim along the Earth＇s magnetic field, play important roles in the biogeochemical cycles of iron and sulfur. Previous studies have revealed that the bacterial actin protein MamK plays essential roles in the linear arrangement of magnetosomes in MTB cells belonging to the Proteobacteria phylum. However, the molecular mechanisms of multi- ple-magnetosome-chain arrangements in MTB remain largely unknown. Here, we report that the MamK filaments from the uncultivated ＇Candidatus Magnetobacterium casensis＇ （Mcas） within the phylum Nitrospirae polymerized in the presence of ATP alone and were stable without obvious ATP hydrolysis-mediated disassembly. MamK in Mcas can convert NTP to NDP and NDP to NMP, showing the highest preference to ATP. Unlike its Magnetospirillum counterparts, which form a single magnetosome chain, or other bacterial actins such as MreB and ParM, the polymerized MamK from Mcas is independent of metal ions and nucleotides except for ATP, and is assembled into well-ordered filamentous bundles consisted of multiple filaments. Our results suggest a dynamically stable assembly of MamK from the uncultivated Nitrospirae MTB that synthesizes multiple magnetosome chains per cell, These findings further improve the current knowledge of biomineralization and organelle biogenesis in prokaryotic systems.展开更多
基金This research was supported by the National Key R&D Program of China(No.2017YFD0701700)the National Natural Science Foundation of China(Nos.31472312 and 31672673).
文摘We investigated the changes in communities of bacteria,ammonia-oxidizing bacteria,and Nitrospira during the operation of a pufferfish Takifugu rubripes recirculating aquaculture system by using high-throughput DNA sequencing.Differences in bacterial communities were observed at days 1-32,47-62 and 78-93 of biofilm development by using 16S rRNA gene pyrosequencing.The relative abundance of Proteobacteria(Gammaproteobacteria)increased,while that of Bacteroidetes(Flavobacteria)decreased.The proportions of Nitrosomonas and Nitrospina ranged from 0.02%to 0.30%and from 0.02%to 0.83%,respectively.Ammonia monooxygenase gene pyrosequencing revealed that the top three operational taxonomic units were related to Nitrosomonas aestuarii(17.5%-61.1%),uncultured beta proteobacterium clone B67S-54(1.9%-45.2%),and uncultured bacterium clone AZPa8(3.6%-24.7%).Nitrite oxidoreductase gene pyrosequencing revealed that the relative abundance of the dominant strain Nitrospira sp.Ecomares 2.1 increased,but that of the abundant species Nitrospira marina decreased.Our results demonstrated that the communities of bacteria,ammonia-oxidizing bacteria,and Nitrospira were changing during the operation of the pufferfish recirculating aquaculture system.
基金supported by the Science and Technique Project of Yantai University(HJ19B92:1115/2219014)the Natural Science Foundation of Shandong Province(ZR2024ME069+2 种基金ZR202209150060)the Beijing Scholars Training Program Grants(BJXZ-2024-02)the Natural Science Foundation of Fujian Province(2022J01984).
文摘The identification of complete ammonia oxidizers(comammox)within the nitriteoxidizing bacteria(NOB)genus Nitrospira,capable of oxidizing ammonia directly to nitrite and nitrate,represents a pivotal advancement in elucidating the microbial and metabolic pathways underlying nitrification in the global nitrogen cycle.Although comammox Nitrospira have been consistently identified across diverse environmental habitats,their rapid enrichment from complex activated sludge systems remains challenging owing to their intrinsically low growth rates and the restricted availability of cultured isolates.In this study,Candidatus Nitrospira inopinata(Ca.N.inopinata)was successfully enriched from anammox-inoculated sludge within 70 d under low ammonia concentrations(~4.88 mg/L),ambient temperatures(21.6-28.4℃),and minimal aeration(0-0.01 mg/L),facilitated by the application of kanamycin(KAN).By employing 16S rRNA gene amplicon sequencing and quantitative polymerase chain reaction(qPCR)targeting the functional marker gene amoA,Ca.N.inopinata was identified as the dominant ammonia oxidizer,achieving a relative abundance of 95.22% in the nitrifying community.Kanamycin was shown to exert significant selective pressure,further enhancing the enrichment of Ca.N.inopinata.These findings demonstrate the feasibility of establishing comammox Nitrospira through direct inoculation of anammox pellets coupled with kanamycin,offering a robust and efficient strategy for rapid enrichment of comammox Nitrospira for biotechnological applications,while underscoring the energy-efficient advantages of comammox-driven ammonia oxidation processes.
基金supported by the National Key Research and Development Program of China(2021YFD1700900)the National Natural Science Foundation of China(42007033)+1 种基金the Scientific and Technological Key Projects of Henan Province(232102320117)the Natural Science Foundation of Henan Province(222300420464).
文摘Comammox Nitrospira clade A and B showed contrasting responses to citrus planting.54d9-like AOA and Nitrobacter-NOB dominated in the 5Y and 10Y soils.Nitrososphaera-like AOA and Nitrospira-like NOB dominated in the 20Y and 30Y soils.Soil pH and P content were the major factors shaping nitrifying communities.
基金ACKNOWLEDGEMENTS The authors would like to thank Rongcheng Han, Yabing Liu and Xiaolan Zhang for assistance with the fluorescence microscopy, and Jingnan Liang for assistance with transmission electron microscopy. This work was supported by the grants from the National Natural Science Foundation of China （Grants Nos. 31300065 and 41330104） and the Youth Innovation Promotion Association CAS.
文摘Magnetotactic bacteria （MTB）, a group of phylogeneti- cally diverse organisms that use their unique intracellular magnetosome organelles to swim along the Earth＇s magnetic field, play important roles in the biogeochemical cycles of iron and sulfur. Previous studies have revealed that the bacterial actin protein MamK plays essential roles in the linear arrangement of magnetosomes in MTB cells belonging to the Proteobacteria phylum. However, the molecular mechanisms of multi- ple-magnetosome-chain arrangements in MTB remain largely unknown. Here, we report that the MamK filaments from the uncultivated ＇Candidatus Magnetobacterium casensis＇ （Mcas） within the phylum Nitrospirae polymerized in the presence of ATP alone and were stable without obvious ATP hydrolysis-mediated disassembly. MamK in Mcas can convert NTP to NDP and NDP to NMP, showing the highest preference to ATP. Unlike its Magnetospirillum counterparts, which form a single magnetosome chain, or other bacterial actins such as MreB and ParM, the polymerized MamK from Mcas is independent of metal ions and nucleotides except for ATP, and is assembled into well-ordered filamentous bundles consisted of multiple filaments. Our results suggest a dynamically stable assembly of MamK from the uncultivated Nitrospirae MTB that synthesizes multiple magnetosome chains per cell, These findings further improve the current knowledge of biomineralization and organelle biogenesis in prokaryotic systems.
文摘土壤含水量和氮素水平是调控氨氧化微生物和硝化速率的重要因素。本研究以旱地红壤为对象,设置3个土壤含水量(40%WFPS、60%WFPS、80%WFPS,WFPS为土壤孔隙含水量)×4个氮添加水平(0、25、50和100 mg N·kg^(-1)),进行微宇宙培养试验,研究含水量和氮添加对土壤净硝化速率和氨氧化微生物功能基因丰度的影响。结果表明:土壤净硝化速率随土壤含水量和氮添加量的增加而增加。土壤含水量增加显著提高AOA和AOB amoA基因丰度,但降低完全氨氧化菌clade A amoA基因丰度,表明土壤含水量增加不利于完全氨氧化菌clade A生长。氮添加显著提高AOA和AOB amoA基因丰度,但对完全氨氧化菌clade A amoA基因丰度无显著影响。综上,土壤含水量增加不利于旱地农田红壤完全氨氧化菌生长,但氮添加对其丰度影响不显著。
