Pub Date : 2018-09-11DOI: 10.2136/SSSABOOKSER5.2.C46
W. Ghiorse
Microbial oxidation and reduction of Fe and Mn are of wide-ranging importance to soil scientists (Alexander, 1977; Paul & Clark, 1989). Indeed, knowledge of the distribution, abundance, identity, and activity of Feand Mn-transforming microbes in soils and sediments can greatly enhance studies on such diverse agricultural and environmental problems as Fe and Mn availability to plants, metal accumulation, toxicity and mobility of metals and pesticides, and clogging in wells and wetland drainage systems. Knowledge of the biology of Feand Mn-transforming microorganisms may allow for future applications in which the metal mobilization and immobilization activities of these microorganisms are exploited for economic and environmental benefit (Ehrlich & Brierley, 1990). Except for the morphologically recognizable "iron bacteria," relatively little is known of the occurrence of Fe-Mn-transforming organisms in nature. Even less is known of their function in natural systems or the factors controlling their in situ activities. On the other hand, several model organisms have been isolated and characterized taxonomically (e.g., Thiobacillus ferrooxidans, Leptothrix discophora, Shewanella putrefaciens, and Geobacter metallireducens (Lovley et aI., 1993)). In some cases, the biochemical mechanisms underlying their Feand Mn-transforming abilities have been investigated. (For reviews, see Ghiorse 1984, 1988; Ehrlich, 1987, 1990; Lovley, 1987, 1991; Nealson et aI., 1988, 1989; Myers & Nealson, 1990; Ehrlich et aI., 1991; Nealson & Myers, 1992). A persistent problem has been the difficulty of distinguishing abiotic from biologically mediated (biotic) transformations, especially in environments like soil where microbial activity may alter the redox chemistry of the microenvironment, causing Fe and Mn redox changes to occur by direct or indirect mechanism (Ehrlich, 1990). These problems also apply to microbial growth media which, in some instances, may be altered by growthinduced changes in pH or Eh or metabolic products that cause chemical oxidation or reduction of Fe and Mn. These possibilities are taken into
{"title":"Iron and Manganese Oxidation and Reduction","authors":"W. Ghiorse","doi":"10.2136/SSSABOOKSER5.2.C46","DOIUrl":"https://doi.org/10.2136/SSSABOOKSER5.2.C46","url":null,"abstract":"Microbial oxidation and reduction of Fe and Mn are of wide-ranging importance to soil scientists (Alexander, 1977; Paul & Clark, 1989). Indeed, knowledge of the distribution, abundance, identity, and activity of Feand Mn-transforming microbes in soils and sediments can greatly enhance studies on such diverse agricultural and environmental problems as Fe and Mn availability to plants, metal accumulation, toxicity and mobility of metals and pesticides, and clogging in wells and wetland drainage systems. Knowledge of the biology of Feand Mn-transforming microorganisms may allow for future applications in which the metal mobilization and immobilization activities of these microorganisms are exploited for economic and environmental benefit (Ehrlich & Brierley, 1990). Except for the morphologically recognizable \"iron bacteria,\" relatively little is known of the occurrence of Fe-Mn-transforming organisms in nature. Even less is known of their function in natural systems or the factors controlling their in situ activities. On the other hand, several model organisms have been isolated and characterized taxonomically (e.g., Thiobacillus ferrooxidans, Leptothrix discophora, Shewanella putrefaciens, and Geobacter metallireducens (Lovley et aI., 1993)). In some cases, the biochemical mechanisms underlying their Feand Mn-transforming abilities have been investigated. (For reviews, see Ghiorse 1984, 1988; Ehrlich, 1987, 1990; Lovley, 1987, 1991; Nealson et aI., 1988, 1989; Myers & Nealson, 1990; Ehrlich et aI., 1991; Nealson & Myers, 1992). A persistent problem has been the difficulty of distinguishing abiotic from biologically mediated (biotic) transformations, especially in environments like soil where microbial activity may alter the redox chemistry of the microenvironment, causing Fe and Mn redox changes to occur by direct or indirect mechanism (Ehrlich, 1990). These problems also apply to microbial growth media which, in some instances, may be altered by growthinduced changes in pH or Eh or metabolic products that cause chemical oxidation or reduction of Fe and Mn. These possibilities are taken into","PeriodicalId":21966,"journal":{"name":"SSSA Book Series","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85371579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-09-11DOI: 10.2136/SSSABOOKSER8.C15
D. Suarez
{"title":"Chemistry of Salt-Affected Soils","authors":"D. Suarez","doi":"10.2136/SSSABOOKSER8.C15","DOIUrl":"https://doi.org/10.2136/SSSABOOKSER8.C15","url":null,"abstract":"","PeriodicalId":21966,"journal":{"name":"SSSA Book Series","volume":"54 6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80762165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-09-11DOI: 10.2136/SSSABOOKSER5.3.C10
C. Johnston, Y. Aochi
{"title":"Fourier Transform Infrared and Raman Spectroscopy","authors":"C. Johnston, Y. Aochi","doi":"10.2136/SSSABOOKSER5.3.C10","DOIUrl":"https://doi.org/10.2136/SSSABOOKSER5.3.C10","url":null,"abstract":"","PeriodicalId":21966,"journal":{"name":"SSSA Book Series","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83091401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-09-11DOI: 10.2136/SSSABOOKSER5.3.C31
W. Frankenberger, M. Tabatabai, D. Adriano, H. Doner
{"title":"Bromine, Chlorine, & Fluorine","authors":"W. Frankenberger, M. Tabatabai, D. Adriano, H. Doner","doi":"10.2136/SSSABOOKSER5.3.C31","DOIUrl":"https://doi.org/10.2136/SSSABOOKSER5.3.C31","url":null,"abstract":"","PeriodicalId":21966,"journal":{"name":"SSSA Book Series","volume":"41 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83161705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-09-11DOI: 10.2136/SSSABOOKSER5.3.C43
D. Sparks, S. Fendorf, C. V. Toner, T. H. Carski
{"title":"Kinetic Methods and Measurements","authors":"D. Sparks, S. Fendorf, C. V. Toner, T. H. Carski","doi":"10.2136/SSSABOOKSER5.3.C43","DOIUrl":"https://doi.org/10.2136/SSSABOOKSER5.3.C43","url":null,"abstract":"","PeriodicalId":21966,"journal":{"name":"SSSA Book Series","volume":"78 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83237816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-09-11DOI: 10.2136/SSSABOOKSER5.2.C2
T. Parkin, J. A. Robinson
{"title":"Statistical Treatment of Microbial Data","authors":"T. Parkin, J. A. Robinson","doi":"10.2136/SSSABOOKSER5.2.C2","DOIUrl":"https://doi.org/10.2136/SSSABOOKSER5.2.C2","url":null,"abstract":"","PeriodicalId":21966,"journal":{"name":"SSSA Book Series","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82251273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-09-11DOI: 10.2136/SSSABOOKSER5.2.C31
M. Sadowsky
DNA fingerprinting and restriction fragment length polymorphism (RFLP) analyses have proven extremely useful for strain identification, epidemiological studies, and the taxonomic analysis of prokaryotic and eukaryotic organisms. Both techniques require the isolation of relatively high-molecular-weight genomic or plasmid DNA, enzymatic cleavage of the isolated nucleic acids using restriction endonucleases, and electrophoretic separation of the resulting DNA fragments. The two techniques differ with respect to the means of examining the resultant restriction fragments: DNA fingerprinting uses ethidium bromide staining and visualizes all restriction fragments, whereas RFLP analysis used DNA or RNA probes that selectively bind (hybridize) to a few restriction fragments. In either case, the resulting banding patterns are generally unique to one or a few strains of a particular microbe and as such, can serve as a "fingerprint" for strain identification. Figure 31-1 shows the general scheme for DNA fingerprinting and RFLP analysis of bacterial genomic DNA. While DNA fingerprinting is relatively rapid, routine, and inexpensive to perform, RFLP analysis is more complex, expensive, and time consuming. However, RFLP analysis can show small differences between the genomic DNAs of organisms that is not evidenced by DNA fingerprinting techniques. In addition, RFLP analyses can also be useful for the construction of genetic maps and for map-based cloning in eukaryotic organisms (Young, 1990). More recently, it has been shown that DNA primers corresponding to repetitive extragenic palindromic (REP) and enterobacterial repetitive intergenic consensus (ERIC) sequences,coupled with the polymerase chain reaction (peR) technique can be used to fingerprint the genomes of a large number of different gram-negative soil bacteria (de Bruijn, 1992; Hulton et aI., 1991; Judd et aI., 1993; Stem et aI., 1984; Versalovic et aI., 1991).
DNA指纹图谱和限制性片段长度多态性(RFLP)分析已被证明对菌株鉴定、流行病学研究以及原核和真核生物的分类分析非常有用。这两种技术都需要分离相对高分子量的基因组或质粒DNA，使用限制性内切酶对分离的核酸进行酶切，并对所得DNA片段进行电泳分离。这两种技术在检测限制性内切酶片段的方法上有所不同:DNA指纹鉴定使用溴化乙啶染色并可视化所有限制性内切酶片段，而RFLP分析使用DNA或RNA探针选择性地结合(杂交)到少数限制性内切酶片段。在任何一种情况下，所得到的条带模式通常是特定微生物的一个或几个菌株所独有的，因此，可以作为菌株鉴定的“指纹”。图31-1显示了细菌基因组DNA指纹和RFLP分析的一般方案。虽然DNA指纹识别相对快速、常规且成本低廉，但RFLP分析更复杂、昂贵且耗时。然而，RFLP分析可以显示生物体基因组DNA之间的微小差异，这是DNA指纹技术无法证明的。此外，RFLP分析也可用于构建遗传图谱和真核生物的基于图谱的克隆(Young, 1990)。最近，研究表明，与重复基因外回文(REP)和肠杆菌重复基因间共识(ERIC)序列相对应的DNA引物，加上聚合酶链反应(peR)技术，可用于大量不同革兰氏阴性土壤细菌的基因组指纹(de Bruijn, 1992;霍尔顿等。, 1991;贾德和艾。, 1993;Stem et aI。, 1984;Versalovic等。, 1991)。
{"title":"DNA Fingerprinting and Restriction Fragment Length Polymorphism Analysis","authors":"M. Sadowsky","doi":"10.2136/SSSABOOKSER5.2.C31","DOIUrl":"https://doi.org/10.2136/SSSABOOKSER5.2.C31","url":null,"abstract":"DNA fingerprinting and restriction fragment length polymorphism (RFLP) analyses have proven extremely useful for strain identification, epidemiological studies, and the taxonomic analysis of prokaryotic and eukaryotic organisms. Both techniques require the isolation of relatively high-molecular-weight genomic or plasmid DNA, enzymatic cleavage of the isolated nucleic acids using restriction endonucleases, and electrophoretic separation of the resulting DNA fragments. The two techniques differ with respect to the means of examining the resultant restriction fragments: DNA fingerprinting uses ethidium bromide staining and visualizes all restriction fragments, whereas RFLP analysis used DNA or RNA probes that selectively bind (hybridize) to a few restriction fragments. In either case, the resulting banding patterns are generally unique to one or a few strains of a particular microbe and as such, can serve as a \"fingerprint\" for strain identification. Figure 31-1 shows the general scheme for DNA fingerprinting and RFLP analysis of bacterial genomic DNA. While DNA fingerprinting is relatively rapid, routine, and inexpensive to perform, RFLP analysis is more complex, expensive, and time consuming. However, RFLP analysis can show small differences between the genomic DNAs of organisms that is not evidenced by DNA fingerprinting techniques. In addition, RFLP analyses can also be useful for the construction of genetic maps and for map-based cloning in eukaryotic organisms (Young, 1990). More recently, it has been shown that DNA primers corresponding to repetitive extragenic palindromic (REP) and enterobacterial repetitive intergenic consensus (ERIC) sequences,coupled with the polymerase chain reaction (peR) technique can be used to fingerprint the genomes of a large number of different gram-negative soil bacteria (de Bruijn, 1992; Hulton et aI., 1991; Judd et aI., 1993; Stem et aI., 1984; Versalovic et aI., 1991).","PeriodicalId":21966,"journal":{"name":"SSSA Book Series","volume":"74 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80897170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2018-09-11DOI: 10.2136/SSSABOOKSER5.4.C48
K. McInnes
Back in Physics 9A, the idea of thermal energy first arose in the context of energy conservation. We concluded that work done by non-conservative forces would convert mechanical energy into this form of energy, which became internal to the system, and didn't spontaneously return to mechanical form. We know intuitively that this form of energy reveals itself to our senses through temperature. We also can intuit that two objects at different temperatures that are brought into contact can exchange energy an change their temperatures (cold milk added to hot coffee both cools the coffee and warms the milk).
{"title":"5.1 Temperature","authors":"K. McInnes","doi":"10.2136/SSSABOOKSER5.4.C48","DOIUrl":"https://doi.org/10.2136/SSSABOOKSER5.4.C48","url":null,"abstract":"Back in Physics 9A, the idea of thermal energy first arose in the context of energy conservation. We concluded that work done by non-conservative forces would convert mechanical energy into this form of energy, which became internal to the system, and didn't spontaneously return to mechanical form. We know intuitively that this form of energy reveals itself to our senses through temperature. We also can intuit that two objects at different temperatures that are brought into contact can exchange energy an change their temperatures (cold milk added to hot coffee both cools the coffee and warms the milk).","PeriodicalId":21966,"journal":{"name":"SSSA Book Series","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90791376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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