A comparative analysis of the codon usage bias was conducted in Methanosarcina mazei str. Goel and two related Euryarchaeota microorganisms （Picrophilus torridus str. DSM 9790 and Natronomonas pharaonis str. DSM 2160...A comparative analysis of the codon usage bias was conducted in Methanosarcina mazei str. Goel and two related Euryarchaeota microorganisms （Picrophilus torridus str. DSM 9790 and Natronomonas pharaonis str. DSM 2160）. Results revealed that synonymous codon usage in Methanosarcina mazei str. Goel was less biased, which was highly correlated with the GC3S value. And the codon usage patterns were phylogenetically conserved among those Euryarchaeota microorganisms. By employing a hierarchical clustering analysis, it can be seen that it is more the species than the gene function that determines their gene codon usage pattems. Considering that those microorganisms live in different environments where the pH conditions vary quite a lot, it can be presumed that their living environments, especially the pH conditions, play an important role in determining those microorganisms＇ codon usage pattems.展开更多
利用半人工光合系统(非光合微生物-纳米半导体生物杂化体系)将二氧化碳转化为高热值的甲烷有助于缓解全球温室效应和能源危机.作为生物杂化体系的关键组分,纳米半导体颗粒的结构及性质显著影响生物杂化体系的性能.本研究以油菜花粉为原...利用半人工光合系统(非光合微生物-纳米半导体生物杂化体系)将二氧化碳转化为高热值的甲烷有助于缓解全球温室效应和能源危机.作为生物杂化体系的关键组分,纳米半导体颗粒的结构及性质显著影响生物杂化体系的性能.本研究以油菜花粉为原料,成功构建Methanosarcina barkeri-天然碳基半导体生物杂化体系(M. barkeriNCS),并将其应用于二氧化碳还原产甲烷过程.结果表明,所制备的天然碳基半导体具有可见光响应好、孔体积大等优势.在可见光(1.0±0.2 mW/cm2)照射下, M. barkeri-NCS生物杂化体系具有良好的光电性能,其甲烷产量最高可达51±4.5μmol/g.实时荧光定量多聚合酶链式反应结果进一步显示, M. barkeri膜结合氢酶和细胞色素相关基因表达显著上调,尤其是EchB(2.47±0.25倍)和VhtC(2.83±0.15倍),这表明这些基因在生物杂化体系光生电子传递-捕获-利用过程中起着关键作用.该研究结果有望为构建高效的半人工光合系统提供理论支撑.展开更多
The anaerobic digestion（AD）and microbial electrolysis cell（MEC）coupled system has been proved to be a promising process for biomethane production.In this paper,it was found that by co-cultivating Geobacter with Me...The anaerobic digestion（AD）and microbial electrolysis cell（MEC）coupled system has been proved to be a promising process for biomethane production.In this paper,it was found that by co-cultivating Geobacter with Methanosarcina in an AD–MEC coupled system,methane yield was further increased by 24.1%,achieving to 360.2 m L/g-COD,which was comparable to the theoretical methane yield of an anaerobic digester.With the presence of Geobacter,the maximum chemical oxygen demand（COD）removal rate（216.8 mg COD/（L·hr））and current density（304.3 A/m3）were both increased by 1.3 and 1.8 fold compared to the previous study without Geobacter,resulting in overall energy efficiency reaching up to 74.6%.Community analysis demonstrated that Geobacter and Methanosarcina could coexist together in the biofilm,and the electrochemical activities of both were confirmed by cyclic voltammetry.Our study observed that the carbon dioxide content in total gas generated from the AD reactor with Geobacter was only half of that generated from the same reactor without Geobacter,suggesting that Methanosarcina may obtain the electron transferred from Geobacter for the reduction of carbon dioxide to methane.Taken together,Geobacter not only can improve the performance of the MEC system,but also can enhance methane production.展开更多
Direct interspecies electron transfer(DIET)may be most important in methanogenic environments,but mechanistic studies of DIET to date have primarily focused on cocultures in which fumarate was the terminal electron ac...Direct interspecies electron transfer(DIET)may be most important in methanogenic environments,but mechanistic studies of DIET to date have primarily focused on cocultures in which fumarate was the terminal electron acceptor.To better understand DIET with methanogens,the transcriptome of Geobacter metallireducens during DIET‐based growth with G.sulfurreducens reducing fumarate was compared with G.metallireducens grown in coculture with diverse Methanosarcina.The transcriptome of G.metallireducens cocultured with G.sulfurreducens was significantly different from those with Methanosarcina.Furthermore,the transcriptome of G.metallireducens grown with Methanosarcina barkeri,which lacks outer‐surface c‐type cytochromes,differed from those of G.metallireducens cocultured with M.acetivorans or M.subterranea,which have an outer‐surface c‐type cytochrome that serves as an electrical connect for DIET.Differences in G.metallireducens expression patterns for genes involved in extracellular electron transfer were particularly notable.Cocultures with c‐type cytochrome deletion mutant strains,ΔGmet_0930,ΔGmet_0557 andΔGmet_2896,never became established with G.sulfurreducens but adapted to grow with all three Methanosarcina.Two porin–cytochrome complexes,PccF and PccG,were important for DIET;however,PccG was more important for growth with Methanosarcina.Unlike cocultures with G.sulfurreducens and M.acetivorans,electrically conductive pili were not needed for growth with M.barkeri.Shewanella oneidensis,another electroactive microbe with abundant outer‐surface c‐type cytochromes,did not grow via DIET.The results demonstrate that the presence of outer‐surface c‐type cytochromes does not necessarily confer the capacity for DIET and emphasize the impact of the electron‐accepting partner on the physiology of the electron‐donating DIET partner.展开更多
文摘A comparative analysis of the codon usage bias was conducted in Methanosarcina mazei str. Goel and two related Euryarchaeota microorganisms （Picrophilus torridus str. DSM 9790 and Natronomonas pharaonis str. DSM 2160）. Results revealed that synonymous codon usage in Methanosarcina mazei str. Goel was less biased, which was highly correlated with the GC3S value. And the codon usage patterns were phylogenetically conserved among those Euryarchaeota microorganisms. By employing a hierarchical clustering analysis, it can be seen that it is more the species than the gene function that determines their gene codon usage pattems. Considering that those microorganisms live in different environments where the pH conditions vary quite a lot, it can be presumed that their living environments, especially the pH conditions, play an important role in determining those microorganisms＇ codon usage pattems.
文摘利用半人工光合系统(非光合微生物-纳米半导体生物杂化体系)将二氧化碳转化为高热值的甲烷有助于缓解全球温室效应和能源危机.作为生物杂化体系的关键组分,纳米半导体颗粒的结构及性质显著影响生物杂化体系的性能.本研究以油菜花粉为原料,成功构建Methanosarcina barkeri-天然碳基半导体生物杂化体系(M. barkeriNCS),并将其应用于二氧化碳还原产甲烷过程.结果表明,所制备的天然碳基半导体具有可见光响应好、孔体积大等优势.在可见光(1.0±0.2 mW/cm2)照射下, M. barkeri-NCS生物杂化体系具有良好的光电性能,其甲烷产量最高可达51±4.5μmol/g.实时荧光定量多聚合酶链式反应结果进一步显示, M. barkeri膜结合氢酶和细胞色素相关基因表达显著上调,尤其是EchB(2.47±0.25倍)和VhtC(2.83±0.15倍),这表明这些基因在生物杂化体系光生电子传递-捕获-利用过程中起着关键作用.该研究结果有望为构建高效的半人工光合系统提供理论支撑.
基金supported by the National Natural Science Foundation of China(Nos.31270166,31300116 and 51408580)the Chinese Academy of Sciences foundation(Nos.Y4C5011100 and KLCAS-2013-03)
文摘The anaerobic digestion（AD）and microbial electrolysis cell（MEC）coupled system has been proved to be a promising process for biomethane production.In this paper,it was found that by co-cultivating Geobacter with Methanosarcina in an AD–MEC coupled system,methane yield was further increased by 24.1%,achieving to 360.2 m L/g-COD,which was comparable to the theoretical methane yield of an anaerobic digester.With the presence of Geobacter,the maximum chemical oxygen demand（COD）removal rate（216.8 mg COD/（L·hr））and current density（304.3 A/m3）were both increased by 1.3 and 1.8 fold compared to the previous study without Geobacter,resulting in overall energy efficiency reaching up to 74.6%.Community analysis demonstrated that Geobacter and Methanosarcina could coexist together in the biofilm,and the electrochemical activities of both were confirmed by cyclic voltammetry.Our study observed that the carbon dioxide content in total gas generated from the AD reactor with Geobacter was only half of that generated from the same reactor without Geobacter,suggesting that Methanosarcina may obtain the electron transferred from Geobacter for the reduction of carbon dioxide to methane.Taken together,Geobacter not only can improve the performance of the MEC system,but also can enhance methane production.
基金This study was supported by the Army Research Office and was accomplished under grant number W911NF‐17‐1‐0345.
文摘Direct interspecies electron transfer(DIET)may be most important in methanogenic environments,but mechanistic studies of DIET to date have primarily focused on cocultures in which fumarate was the terminal electron acceptor.To better understand DIET with methanogens,the transcriptome of Geobacter metallireducens during DIET‐based growth with G.sulfurreducens reducing fumarate was compared with G.metallireducens grown in coculture with diverse Methanosarcina.The transcriptome of G.metallireducens cocultured with G.sulfurreducens was significantly different from those with Methanosarcina.Furthermore,the transcriptome of G.metallireducens grown with Methanosarcina barkeri,which lacks outer‐surface c‐type cytochromes,differed from those of G.metallireducens cocultured with M.acetivorans or M.subterranea,which have an outer‐surface c‐type cytochrome that serves as an electrical connect for DIET.Differences in G.metallireducens expression patterns for genes involved in extracellular electron transfer were particularly notable.Cocultures with c‐type cytochrome deletion mutant strains,ΔGmet_0930,ΔGmet_0557 andΔGmet_2896,never became established with G.sulfurreducens but adapted to grow with all three Methanosarcina.Two porin–cytochrome complexes,PccF and PccG,were important for DIET;however,PccG was more important for growth with Methanosarcina.Unlike cocultures with G.sulfurreducens and M.acetivorans,electrically conductive pili were not needed for growth with M.barkeri.Shewanella oneidensis,another electroactive microbe with abundant outer‐surface c‐type cytochromes,did not grow via DIET.The results demonstrate that the presence of outer‐surface c‐type cytochromes does not necessarily confer the capacity for DIET and emphasize the impact of the electron‐accepting partner on the physiology of the electron‐donating DIET partner.
