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
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
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
Dissolved oxygen(DO)concentration is regarded as one of the crucial factors to influence partial nitrification process.However,achieving and keeping stable partial nitrification under different DO concentrations were ...Dissolved oxygen(DO)concentration is regarded as one of the crucial factors to influence partial nitrification process.However,achieving and keeping stable partial nitrification under different DO concentrations were widely reported.The mechanism of DO concentration influencing partial nitrification is still unclear.Therefore,in this study two same sequencing batch reactors(SBRs)cultivated same seeding sludge were built up with realtime control strategy.Different DO concentrations were controlled in SBRs to explore the effect of DO concentration on the long-term stability of partial nitrification process at room temperature.It was discovered that ammonium oxidation rate(AOR)was inhibited when DO concentration decreased from 2.5 to 0.5 mg/L.The abundance of Nitrospira increased from 1011.5 to 1013.7 copies/g DNA,and its relative percentage increased from 0.056%to 3.2%during 190 operational cycles,causing partial nitrification gradually turning into complete nitrification process.However,when DO was 2.5 mg/L the abundance of Nitrospira was stable and AOB was always kept at 1010.7 copies/g DNA.High AOR was maintained,and stable partial nitrification process was kept.Ammonia oxidizing bacteria(AOB)activity was significantly higher than nitrite oxidizing bacteria(NOB)activity at DO of 2.5 mg/L,which was crucial to maintain excellent nitrite accumulation performance.展开更多
Two sequencing batch reactors（SBRs） were operated for 100 days under aerobic conditions,with one being fed with unsterilized municipal wastewater（USBR）, and the other fed with sterilized municipal wastewater（SSBR...Two sequencing batch reactors（SBRs） were operated for 100 days under aerobic conditions,with one being fed with unsterilized municipal wastewater（USBR）, and the other fed with sterilized municipal wastewater（SSBR）. Respirometric assays and fluorescence in situ hybridization（FISH） results show that active nitrifiers were present in the unsterilized influent municipal wastewater. The maximum ammonia utilization rate（AUR） and nitrite utilization rate（NUR） of the unsterilized influent were 0.32 ± 0.12 mg NH4＋-N/（L·hr） and0.71 ± 0.18 mg NO2--N/（L·hr）. Based on the maximum utilization rates, the estimated seeding intensity for the ammonia oxidizing bacteria（AOB） and nitrite oxidizing bacteria（NOB） of the USBR was 0.08 g AOB/（g AOB·day） and 0.20 g NOB/（g NOB·day） respectively. The fraction of nitrifiers/total bacteria in the influent was 5.35% ± 2.1%, the dominant AOB was Nitrosomonas spp., Nitrosococcus mobilis hybridizated with Nsm156, and the dominant NOB was Nitrospira hybridizated with Ntspa662. The influent nitrifiers potentially seeded the activated sludge of the bioreactor and hence demonstrated a mitigation of the acclimatization times and instability during start-up and early operation. The AUR and NUR in the USBR was 15% and 13% higher than the SSBR respectively during the stable stage, FISH results showed that nitrifiers population especially the Nitrospira in the USBR was higher than that in the SSBR. These results indicate that the natural continuous immigration of nitrifiers from municipal influent streams may have some repercussions on the modeling and design of bioreactors.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.
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supported by the National Natural Science Foundation of China(No.51878011)
文摘Dissolved oxygen(DO)concentration is regarded as one of the crucial factors to influence partial nitrification process.However,achieving and keeping stable partial nitrification under different DO concentrations were widely reported.The mechanism of DO concentration influencing partial nitrification is still unclear.Therefore,in this study two same sequencing batch reactors(SBRs)cultivated same seeding sludge were built up with realtime control strategy.Different DO concentrations were controlled in SBRs to explore the effect of DO concentration on the long-term stability of partial nitrification process at room temperature.It was discovered that ammonium oxidation rate(AOR)was inhibited when DO concentration decreased from 2.5 to 0.5 mg/L.The abundance of Nitrospira increased from 1011.5 to 1013.7 copies/g DNA,and its relative percentage increased from 0.056%to 3.2%during 190 operational cycles,causing partial nitrification gradually turning into complete nitrification process.However,when DO was 2.5 mg/L the abundance of Nitrospira was stable and AOB was always kept at 1010.7 copies/g DNA.High AOR was maintained,and stable partial nitrification process was kept.Ammonia oxidizing bacteria(AOB)activity was significantly higher than nitrite oxidizing bacteria(NOB)activity at DO of 2.5 mg/L,which was crucial to maintain excellent nitrite accumulation performance.
基金supported by the National Natural Science Foundation for Young Scholars of China(No.51208414)the Education Department of Shaanxi Province Special Scientific Research(No.12JK0650)
文摘Two sequencing batch reactors（SBRs） were operated for 100 days under aerobic conditions,with one being fed with unsterilized municipal wastewater（USBR）, and the other fed with sterilized municipal wastewater（SSBR）. Respirometric assays and fluorescence in situ hybridization（FISH） results show that active nitrifiers were present in the unsterilized influent municipal wastewater. The maximum ammonia utilization rate（AUR） and nitrite utilization rate（NUR） of the unsterilized influent were 0.32 ± 0.12 mg NH4＋-N/（L·hr） and0.71 ± 0.18 mg NO2--N/（L·hr）. Based on the maximum utilization rates, the estimated seeding intensity for the ammonia oxidizing bacteria（AOB） and nitrite oxidizing bacteria（NOB） of the USBR was 0.08 g AOB/（g AOB·day） and 0.20 g NOB/（g NOB·day） respectively. The fraction of nitrifiers/total bacteria in the influent was 5.35% ± 2.1%, the dominant AOB was Nitrosomonas spp., Nitrosococcus mobilis hybridizated with Nsm156, and the dominant NOB was Nitrospira hybridizated with Ntspa662. The influent nitrifiers potentially seeded the activated sludge of the bioreactor and hence demonstrated a mitigation of the acclimatization times and instability during start-up and early operation. The AUR and NUR in the USBR was 15% and 13% higher than the SSBR respectively during the stable stage, FISH results showed that nitrifiers population especially the Nitrospira in the USBR was higher than that in the SSBR. These results indicate that the natural continuous immigration of nitrifiers from municipal influent streams may have some repercussions on the modeling and design of bioreactors.
