Our previously described environmental DNA extraction method has been widely used in environmental microbial community analysis.However,residual humic substances may remain with obtained environmental DNA,which interf...Our previously described environmental DNA extraction method has been widely used in environmental microbial community analysis.However,residual humic substances may remain with obtained environmental DNA,which interferes downstream molecular analyses.To remedy this situation,two DNA extraction buffers (PIPES and Tris-HCl) and four purification strategies including our new modified low melting point gel purification method and three commercial kits from QIAEX,Omega and Promega were evaluated with diverse soil samples.The PIPES buffer (pH 6.5) is found to be more effective for removing the humic substances,but it leads to lower DNA yield and causes more severe DNA shearing than using the Tris-HCl buffer (pH 8.0).Gel purification and the Promega purification kit achieve much higher DNA recoveries than QIAEX or Omega kit,and higher purity of DNA is obtained by gel purification than by the Promega kit with both DNA extraction buffers mentioned above.Considering all results together,two alternative methods for DNA extraction and purification are proposed:one uses Tris-HCl buffer extraction and gel purification as the primary approach when the amount of soil or biomass is not a major concern,and the other uses PIPES buffer extraction and the Promega kit purification when severe DNA shearing and/or limited biomass occurs.Purified DNA samples by both methods are amenable for use as templates for whole community genome amplifications and PCR amplifications of bacterial 16S rRNA genes.It is demonstrated that these two alternative methods could be applied to a wide variety of environmental samples.展开更多
Biofilm systems are effective for biosorption of metal ions. Shewanella oneidensis MR-1, a Gram-negative facultative anaerobe, is a natural pellicle-like biofilm former. The mechanisms of pellicle formation by S. onei...Biofilm systems are effective for biosorption of metal ions. Shewanella oneidensis MR-1, a Gram-negative facultative anaerobe, is a natural pellicle-like biofilm former. The mechanisms of pellicle formation by S. oneidensis MR-1 have not yet been understood. 17 S. oneidensis MR-1 deletion mutants, including 12 c-type cytochromes were generated and tested if they were involved in pellicle formation. The results show that △SO4666, △SO1777, △SO1782, △SO2361 and △SO2363 have varying deficiency in pellicle formation. The deletion mutant △SO4666 cannot form a pellicle under non-shake conditions, suggesting that it may play an important role in pellicle formation by S. oneidensis MR-1. Overall, these data suggest a very complex picture of aerobic respiration by S. oneidensis MR-1.展开更多
In plant cells, the accumulation of K^+ plays a primary role in osmotic regulation,and high-affinity K^+ uptake and transport systems have been investigated. InEscherichia coli, Hesse et aI.isolated a specific K^+ upt...In plant cells, the accumulation of K^+ plays a primary role in osmotic regulation,and high-affinity K^+ uptake and transport systems have been investigated. InEscherichia coli, Hesse et aI.isolated a specific K^+ uptake system known as Kdpwhich has a K_m of 2 μmol/L, and it was induced by osmotic stress. Its kdpABCgenes encode three membrane-binding proteins whose molecular weights are 47, 90 and22 kD, respectively, and kdpDE genes produce two regulatory factors. Gaber et al.展开更多
基金Project(51104189)supported by the National Natural Science Foundation of ChinaProject(2010CB630901)supported by the National Basic Research Program of China+1 种基金Project(1343-77341)supported by the Graduate Education Innovative Program of Central South University,ChinaProject(DOE-ER64125)supported by Department of Energy,Office of Science under the Environmental Remediation Science Program of the United States
文摘Our previously described environmental DNA extraction method has been widely used in environmental microbial community analysis.However,residual humic substances may remain with obtained environmental DNA,which interferes downstream molecular analyses.To remedy this situation,two DNA extraction buffers (PIPES and Tris-HCl) and four purification strategies including our new modified low melting point gel purification method and three commercial kits from QIAEX,Omega and Promega were evaluated with diverse soil samples.The PIPES buffer (pH 6.5) is found to be more effective for removing the humic substances,but it leads to lower DNA yield and causes more severe DNA shearing than using the Tris-HCl buffer (pH 8.0).Gel purification and the Promega purification kit achieve much higher DNA recoveries than QIAEX or Omega kit,and higher purity of DNA is obtained by gel purification than by the Promega kit with both DNA extraction buffers mentioned above.Considering all results together,two alternative methods for DNA extraction and purification are proposed:one uses Tris-HCl buffer extraction and gel purification as the primary approach when the amount of soil or biomass is not a major concern,and the other uses PIPES buffer extraction and the Promega kit purification when severe DNA shearing and/or limited biomass occurs.Purified DNA samples by both methods are amenable for use as templates for whole community genome amplifications and PCR amplifications of bacterial 16S rRNA genes.It is demonstrated that these two alternative methods could be applied to a wide variety of environmental samples.
基金Project(50321402) supported by Chinese Science Foundation for Distinguished GroupProject(30428014) supported by National Science Fund for Distinguished Young Scholars in Hong Kong and Abroad
文摘Biofilm systems are effective for biosorption of metal ions. Shewanella oneidensis MR-1, a Gram-negative facultative anaerobe, is a natural pellicle-like biofilm former. The mechanisms of pellicle formation by S. oneidensis MR-1 have not yet been understood. 17 S. oneidensis MR-1 deletion mutants, including 12 c-type cytochromes were generated and tested if they were involved in pellicle formation. The results show that △SO4666, △SO1777, △SO1782, △SO2361 and △SO2363 have varying deficiency in pellicle formation. The deletion mutant △SO4666 cannot form a pellicle under non-shake conditions, suggesting that it may play an important role in pellicle formation by S. oneidensis MR-1. Overall, these data suggest a very complex picture of aerobic respiration by S. oneidensis MR-1.
文摘In plant cells, the accumulation of K^+ plays a primary role in osmotic regulation,and high-affinity K^+ uptake and transport systems have been investigated. InEscherichia coli, Hesse et aI.isolated a specific K^+ uptake system known as Kdpwhich has a K_m of 2 μmol/L, and it was induced by osmotic stress. Its kdpABCgenes encode three membrane-binding proteins whose molecular weights are 47, 90 and22 kD, respectively, and kdpDE genes produce two regulatory factors. Gaber et al.
基金support from the National Natural Science Foundation of China (42141003, 91851210, 41876119, 42188102, 91751207, and 91951207)the National Key Research and Development Program of China (2018YFA06055800 and 2020YFA0607600)+9 种基金support by the Korean Ministry of Oceans and Fisheries (20220558)the National Research Foundation of Korea (NRF-2018R1A2B2006340)support by the German Academic Exchange service (Deutscher Akademischer Austauschdienst, Make Our Planet Great Again-German Research Initiative, 57429828)the German Federal Ministry of Education and Researchsupport by the joint National Natural Science Foundation of China-Israel Science Foundation (NSFC-ISF) Research Program (42161144006 and 3511/21, respectively)support by the Russian Foundation for Basic Research (20-05-00381-a)the Russian Fundamental Programs of Pacific Oceanological Institute (01201363041 and 01201353055)supported by the following provincial and municipal authorities of China: Southern Marine Science and Engineering Guangdong Laboratory (K19313901) (Guangzhou)Southern Marine Science and Engineering Guangdong Laboratory (SML2020SP004) (Zhuhai)Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology (ZDSYS201802081843490)。
