Carbon fixation by soil autotrophic microbes is an overlooked process in organic carbon anabolism,which is potentially affected by biochar.In this study,we quantified the abundance of functional genes cbbL and cbbM,ke...Carbon fixation by soil autotrophic microbes is an overlooked process in organic carbon anabolism,which is potentially affected by biochar.In this study,we quantified the abundance of functional genes cbbL and cbbM,key components of the widely distributed Calvin cycle,and combined this with Ribulose-1,5-bisphosphate carboxylase/oxygenase(RubisCO)enzyme activity assays and high-throughput sequencing of cbbL-and cbbM-harboring microbial communities to investigate the carbon fixation potential,activity,and community structure under biochar application in paddy and upland soils.Results showed that cbbL consistently dominated over cbbM in both paddy and upland soils,with higher abundances in paddy soils,driven by biochar amendment,rice growth stage,and rhizosphere effects.The rhizosphere acted as a hotspot for cbbL and cbbM genes and RubisCO activity in paddy soil.In upland soils,nitrogen availability(NH_(₄)^(+),dissolved organic nitrogen-DON),microbial biomass carbon,and labile carbon and nitrogen pools(dissolved organic carbon,N-acetyl-β-D-glucosaminidase)were consistently associated with cbbL abundance,underscoring their ecological role in soil CO_(2)fixation.In paddy soils,inorganic nitrogen(NH_(₄)^(+),NO_(3)^(⁻),NO_(2)^(⁻)),redox potential(Eh),and urease activity were the main predictors of cbbL abundance and the cbbL/16S ratio,while pH and nitrogen availability(NO_(2)^(⁻),DON)was mostly associated with cbbM/16S ratio.Biochar was the primary driver reshaping the structure of autotrophic microbial communities harboring cbbL and cbbM genes across different soil compartments,including surface soil,rhizosphere,and bulk soil.Pseudomonadota,Cyanobacteriota,Actinomycetota and Chloroflexota were dominant cbbL carriers,while Pseudomonadota,Actinomycetota and Myxococcota predominated in cbbM assemblages across soils.Biochar induced functional differentiation of facultative autotrophic taxa under different RubisCO forms by enhancing the abundance of Rhodopseudomonas in cbbM-bearing communities while decreasing it in cbbL-bearing ones.Furthermore,Calvin cycle-mediated CO_(2)fixation was found to couple with pathways including methylotrophy,methanotrophy,iron oxidation and respiration,nitrogen fixation and reduction,and arsenate reduction and detoxification.Collectively,the results of this study emphasize the importance of soil type,micro-environmental conditions,nitrogen status and the impact of biochar in shaping microbial carbon assimilation via the Calvin cycle pathway and the cbbL and cbbM-harboring microbial community.展开更多
Phosphoribulokinase （PRK）, a nuclear-encoded plastid-localized enzyme unique to the photosynthetic carbon reduction （Calvin） cycle, was cloned and characterized from the stramenopile alga Vaucheria litorea. This a...Phosphoribulokinase （PRK）, a nuclear-encoded plastid-localized enzyme unique to the photosynthetic carbon reduction （Calvin） cycle, was cloned and characterized from the stramenopile alga Vaucheria litorea. This alga is the source of plastids for the mollusc （sea slug） Elysia chlorotica which enable the animal to survive for months solely by photoautotrophic CO2 fixation. The 1633-bp V. litorea prk gene was cloned and the coding region, found to be interrupted by four introns, encodes a 405-amino acid protein. This protein contains the typical bipartite target sequence expected of nuclearencoded proteins that are directed to complex （i.e. four membrane-bound） algal plastids. De novo synthesis of PRK and enzyme activity were detected in E. chlorotica in spite of having been starved of V. litorea for several months. Unlike the algal enzyme, PRK in the sea slug did not exhibit redox regulation. Two copies of partial PRK-encoding genes were isolated from both sea slug and aposymbiotic sea slug egg DNA using PCR. Each copy contains the nucleotide region spanning exon 1 and part of exon 2 of V litorea prk, including the bipartite targeting peptide. However, the larger prk fragment also includes intron 1. The exon and intron sequences of prk in E. chlorotica and V/itorea are nearly identical. These data suggest that PRK is differentially regulated in V. litorea and E. chlorotica and at least a portion of the V. litorea nuclear PRK gene is present in sea slugs that have been starved for several months.展开更多
Aerated drip irrigation(ADI)is an important practice for promoting soil fertility and crop productivity in greenhouse vegetable production,yet little research has comprehensively investigated its effects on the functi...Aerated drip irrigation(ADI)is an important practice for promoting soil fertility and crop productivity in greenhouse vegetable production,yet little research has comprehensively investigated its effects on the functional traits of carbon(C)-cycling microorganisms.In this study,we sought to assess the potential efficacy of ADI in increasing soil organic C(SOC)by changing soil microbial communities and the expressions of genes associated with C cycling.To this end,we adopted a metagenomic approach to compare the effects of ADI with three dissolved oxygen concentrations(10,15,and 20 mg L^(-1))during a three-season tomato cultivation experiment in northern China.The results revealed that the 10 mg L^(-1)treatment led to a significant increase in the abundance of korA/B genes(associated with the reductive tricarboxylic acid cycle)in the C fixation pathway,whereas the 15 mg L^(-1)treatment increased the abundances of cbbL/R and coxL/S genes associated with the Calvin cycle and carbon monoxide oxidation,respectively.In addition,based on a co-occurrence network analysis,we observed a positive correlation between cbbL and coxS.Interestingly,r-selected microorganisms,such as Proteobacteria and Actinobacteria,characterized by rapid cell multiplication and high biomass production,were identified as the primary contributors to C fixation and were the main predictors of SOC pools.In contrast,the 20 mg L^(-1)treatment was found to adversely influence C fixation,although the enhanced C degradation could be attributed to the extracellular enzymes secreted by K-selected microorganisms.Collectively,our findings indicate that ADI with dissolved oxygen concentrations 15 mg L^(-1)can promote SOC content by altering the life history strategies of r-selected microorganisms and genes associated with C fixation.These findings will provide valuable references for agroecosystem irrigation management,help improve soil fertility,and promote sustainable production.展开更多
Rethinking carbon fixation beyond the Calvin cycle.The Calvin-Benson-Bassham(CBB)cycle is the central pathway for CO_(2) fixation.However,its efficiency is limited by two major carbon losses.The first is the oxidative...Rethinking carbon fixation beyond the Calvin cycle.The Calvin-Benson-Bassham(CBB)cycle is the central pathway for CO_(2) fixation.However,its efficiency is limited by two major carbon losses.The first is the oxidative decarboxylation of pyruvate to acetyl-coenzyme A(CoA),which causes the loss of one out of every three fixed carbons.展开更多
基金the National Natural Science Foundation of China(Grant No.42177107,42307043,21607125)Natural Science Foundation of Anhui Province,China(Grant No.2108085MC85).
文摘Carbon fixation by soil autotrophic microbes is an overlooked process in organic carbon anabolism,which is potentially affected by biochar.In this study,we quantified the abundance of functional genes cbbL and cbbM,key components of the widely distributed Calvin cycle,and combined this with Ribulose-1,5-bisphosphate carboxylase/oxygenase(RubisCO)enzyme activity assays and high-throughput sequencing of cbbL-and cbbM-harboring microbial communities to investigate the carbon fixation potential,activity,and community structure under biochar application in paddy and upland soils.Results showed that cbbL consistently dominated over cbbM in both paddy and upland soils,with higher abundances in paddy soils,driven by biochar amendment,rice growth stage,and rhizosphere effects.The rhizosphere acted as a hotspot for cbbL and cbbM genes and RubisCO activity in paddy soil.In upland soils,nitrogen availability(NH_(₄)^(+),dissolved organic nitrogen-DON),microbial biomass carbon,and labile carbon and nitrogen pools(dissolved organic carbon,N-acetyl-β-D-glucosaminidase)were consistently associated with cbbL abundance,underscoring their ecological role in soil CO_(2)fixation.In paddy soils,inorganic nitrogen(NH_(₄)^(+),NO_(3)^(⁻),NO_(2)^(⁻)),redox potential(Eh),and urease activity were the main predictors of cbbL abundance and the cbbL/16S ratio,while pH and nitrogen availability(NO_(2)^(⁻),DON)was mostly associated with cbbM/16S ratio.Biochar was the primary driver reshaping the structure of autotrophic microbial communities harboring cbbL and cbbM genes across different soil compartments,including surface soil,rhizosphere,and bulk soil.Pseudomonadota,Cyanobacteriota,Actinomycetota and Chloroflexota were dominant cbbL carriers,while Pseudomonadota,Actinomycetota and Myxococcota predominated in cbbM assemblages across soils.Biochar induced functional differentiation of facultative autotrophic taxa under different RubisCO forms by enhancing the abundance of Rhodopseudomonas in cbbM-bearing communities while decreasing it in cbbL-bearing ones.Furthermore,Calvin cycle-mediated CO_(2)fixation was found to couple with pathways including methylotrophy,methanotrophy,iron oxidation and respiration,nitrogen fixation and reduction,and arsenate reduction and detoxification.Collectively,the results of this study emphasize the importance of soil type,micro-environmental conditions,nitrogen status and the impact of biochar in shaping microbial carbon assimilation via the Calvin cycle pathway and the cbbL and cbbM-harboring microbial community.
基金This research was supported by National Science Foundation grants IBN-9808904 （M,R. and J.M.） and IOS-0726178 （M.R. and M.T.） the American Society of Plant Biologists＇ Education Foundation （M.R. and M.T.）+1 种基金 Ministry for Food, Agriculture, Forestry, and Fisheries, Korean Government, Korea Research Foundation （J.L.） the National Institutes of Health （grant R01ES013679 to D.B.）, and the University of Maine （M.R.）. This is Maine Agricultural and Forest Experiment Station Publication Number 3079, Hatch Project no. ME08361-08MRF （NC 1168）.ACKNOWLEDGMENTS The authors thank Dr Michael Salvucci for providing antibodies to PRK and Dr Jorn Petersen for analyzing the genomic PRK sequence for introns. No conflict of interest declared.
文摘Phosphoribulokinase （PRK）, a nuclear-encoded plastid-localized enzyme unique to the photosynthetic carbon reduction （Calvin） cycle, was cloned and characterized from the stramenopile alga Vaucheria litorea. This alga is the source of plastids for the mollusc （sea slug） Elysia chlorotica which enable the animal to survive for months solely by photoautotrophic CO2 fixation. The 1633-bp V. litorea prk gene was cloned and the coding region, found to be interrupted by four introns, encodes a 405-amino acid protein. This protein contains the typical bipartite target sequence expected of nuclearencoded proteins that are directed to complex （i.e. four membrane-bound） algal plastids. De novo synthesis of PRK and enzyme activity were detected in E. chlorotica in spite of having been starved of V. litorea for several months. Unlike the algal enzyme, PRK in the sea slug did not exhibit redox regulation. Two copies of partial PRK-encoding genes were isolated from both sea slug and aposymbiotic sea slug egg DNA using PCR. Each copy contains the nucleotide region spanning exon 1 and part of exon 2 of V litorea prk, including the bipartite targeting peptide. However, the larger prk fragment also includes intron 1. The exon and intron sequences of prk in E. chlorotica and V/itorea are nearly identical. These data suggest that PRK is differentially regulated in V. litorea and E. chlorotica and at least a portion of the V. litorea nuclear PRK gene is present in sea slugs that have been starved for several months.
基金financially supported by the National Natural Science Foundation of China(Nos.52379048 and 52079112)the Key Research and Development Program of Shaanxi Province,China(No.2022ZDLNY03-03)the Major Science and Technology Engineering Innovation Project of Shandong Province,China(No.2020CXGC 010808)。
文摘Aerated drip irrigation(ADI)is an important practice for promoting soil fertility and crop productivity in greenhouse vegetable production,yet little research has comprehensively investigated its effects on the functional traits of carbon(C)-cycling microorganisms.In this study,we sought to assess the potential efficacy of ADI in increasing soil organic C(SOC)by changing soil microbial communities and the expressions of genes associated with C cycling.To this end,we adopted a metagenomic approach to compare the effects of ADI with three dissolved oxygen concentrations(10,15,and 20 mg L^(-1))during a three-season tomato cultivation experiment in northern China.The results revealed that the 10 mg L^(-1)treatment led to a significant increase in the abundance of korA/B genes(associated with the reductive tricarboxylic acid cycle)in the C fixation pathway,whereas the 15 mg L^(-1)treatment increased the abundances of cbbL/R and coxL/S genes associated with the Calvin cycle and carbon monoxide oxidation,respectively.In addition,based on a co-occurrence network analysis,we observed a positive correlation between cbbL and coxS.Interestingly,r-selected microorganisms,such as Proteobacteria and Actinobacteria,characterized by rapid cell multiplication and high biomass production,were identified as the primary contributors to C fixation and were the main predictors of SOC pools.In contrast,the 20 mg L^(-1)treatment was found to adversely influence C fixation,although the enhanced C degradation could be attributed to the extracellular enzymes secreted by K-selected microorganisms.Collectively,our findings indicate that ADI with dissolved oxygen concentrations 15 mg L^(-1)can promote SOC content by altering the life history strategies of r-selected microorganisms and genes associated with C fixation.These findings will provide valuable references for agroecosystem irrigation management,help improve soil fertility,and promote sustainable production.
基金supported by the National Key R&D Program of China(2025YFC3409200 and 2022YFC3401800)the Hundred Talents Program of the Chinese Academy of Sciences(E3J56201)+2 种基金the Director-Led Scientific Research and Innovation Fund Program(SZJJ2024-019 and SZJJ2024-032)the Beijing Life Science Academy(2023200CB0070 and 2023000CB0040)the Science and Technology Program of Tangshan(24150214C).
文摘Rethinking carbon fixation beyond the Calvin cycle.The Calvin-Benson-Bassham(CBB)cycle is the central pathway for CO_(2) fixation.However,its efficiency is limited by two major carbon losses.The first is the oxidative decarboxylation of pyruvate to acetyl-coenzyme A(CoA),which causes the loss of one out of every three fixed carbons.
