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9 – Community Structure

K. Alef, G. Sparling
Published 1995 · Chemistry, Biology

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Publisher Summary The quantification of the microbial community in soil is complicated because microorganisms are commonly attached to soil minerals and organic matter, and they occur in consortia usually containing different physiological and morphological types. One way to study microbial community structure in soil is to inhibit selectively the metabolic activity of different microbial groups. Fungi play an important role in the decomposition of organic matter such as cellulose and lignin in soil. Most traditional methods developed for the detection of microorganisms in soil suffer from the lack of specificity or sensitivity, or require the isolation of the target organisms. Methods based on isolation and identification of the nucleic acids of target organisms overcome these problems. The chapter describes three methods based on direct extraction of DNA in soil. The method represents three different approaches aiming at the same goal: the highest yield of extracted DNA sufficiently pure to allow the identification of its genetic origin. All methods aim at getting a high yield of DNA that is pure enough for molecular analysis by the DNA–DNA hybridization, the restriction fragment length polymorphism analysis, or the amplification by the polymerase chain reaction. Before the characterization of the isolated soil DNA is started, its concentration should be evaluated. Soil DNA samples can be tested by dot blotting and Southern blotting, as is done in other DNA samples. Serological assays for the detection of target microorganisms are based on a reaction of one or more antigenic determinants, present on molecules of the target, with antibodies directed against these determinants.
This paper references
10.1016/0167-7012(84)90005-8
Determination of the gram-positive bacterial content of soils and sediments by analysis of teichoic acid components.
M. J. Gehron (1984)
10.1016/0167-7012(86)90008-4
Improvement of the selective respiratory inhibition technique to measure eukaryote:prokaryote ratios in soils
A. West (1986)
10.1139/M75-045
Measurement of bacterial and fungal contributions to respiration of selected agricultural and forest soils.
J. Anderson (1975)
10.1016/0038-0717(83)90095-0
The degradation of 14C-labelled phosphatidyl choline in soil
T. Tollefson (1983)
10.4319/LO.1980.25.2.0290
Sterols in decomposing Spartina alterniflora and the use of ergosterol in estimating the contribution of fungi to detrital nitrogen1
C. Lee (1980)
10.1002/JPLN.19871500410
Methoden zur relativen Quantifizierung der pilzlichen Biomasse im Boden
L. Zelles (1987)
10.1139/M70-054
Evidence for muramic acid in soil.
W. N. Millar (1970)
10.1016/0167-7012(85)90051-X
Precision and sensitivity of the measurement of 15N enrichment in D-alanine from bacterial cell walls using positive/negative ion mass spectrometry.
A. Tunlid (1985)
10.1111/j.1472-765X.1991.tb00559.x
DNA recovery and direct detection of Tn5 sequences from soil
S. Selenska (1991)
10.3109/10408417709102311
Lipids in Bacterial Taxonomy - A Taxonomist's View
Lechevalier Mp (1977)
10.1016/0167-7012(90)90056-C
Analysis of lipopolysaccharide (lipid A) fatty acids
H. Wollenweber (1990)
10.1016/0038-0717(92)90010-U
Specific detection of rhizobia in root nodules and soil using the polymerase chain reaction
S. Pillai (1992)
10.1139/M85-091
Quantitative determination of microbial activity and community nutritional status in estuarine sediments: evidence for a disturbance artifact.
R. Findlay (1985)
10.1002/JPLN.19871500411
Differenzierte Erfassung der Bioaktivität von Pilzen und Bakterien zweier Böden unter Fichte
L. Zelles (1987)
10.1016/0038-0717(91)90176-K
Microbial activity measured in soils stored under different temperature and humidity conditions
L. Zelles (1991)
10.1016/0038-0717(92)90025-S
Detection of Rhizobium galegae from one-gram soil samples by non-radioactive DNA-DNA-hybridization
A. Saano (1992)
10.2307/1310976
Lipid analysis in microbial ecology: quantitative approaches to the study of microbial communities.
J. Vestal (1989)
10.1139/X90-149
Comparison of ergosterol and chitin as quantitative estimates of mycorrhizal infection and Pinuscontorta seedling response to inoculation
B. N. Johnson (1990)
10.1016/0167-7012(86)90023-0
Determination of monosaturated fatty acid double-bond position and geometry for microbial monocultures and complex consortia by capillary GC-MS of their dimethyl disulphide adducts
P. Nichols (1986)
10.1139/M86-022
Quantitative characterization of microbial biomass and community structure in subsurface material: a prokaryotic consortium responsive to organic contamination
G. A. Smith (1986)
10.1016/0038-0717(92)90191-Y
Signature fatty acids in phospholipids and lipopolysaccharides as indicators of microbial biomass and community structure in agricultural soils
L. Zelles (1992)
10.1016/0003-2697(83)90398-6
An improved gas chromatographic method for measuring glucosamine and muramic acid concentrations.
R. E. Hicks (1983)
10.1094/PHYTO-79-322
Pathovar-specific monoclonal antibodies for Xanthomonas campestris pv. oryzae and for Xanthomonas campestris pv. oryzicola.
A. Benedict (1989)
10.1094/PHYTO-69-1202
Ergosterol as a Measure of Fungal Growth
L. M. Seitz (1979)
10.1016/0167-7012(86)90031-X
Measurement of ergosterol, diaminopimelic acid and glucosamine in soil: evaluation as indicators of microbial biomass
W. Grant (1986)
10.1016/0038-0717(93)90075-M
Fractionation of fatty acids derived from soil lipids by solid phase extraction and their quantitative analysis by GC-MS
L. Zelles (1993)
10.2307/3544405
A comparison of glucosamine and biovolume conversion factors for estimating fungal biomass
R. E. Hicks (1984)
10.1016/0038-0717(87)90106-4
Use of ergosterol, diaminopimelic acid and glucosamine contents of soils to monitor changes in microbial populations
A. West (1987)
10.1016/0038-0717(92)90201-8
Sensitive chemoluminescence-based immunological quantification of bacteria in soil extracts with monoclonal antibodies
M. Schloter (1992)
10.1016/B978-1-4831-9938-2.50008-X
Bacterial Lipids* *Issued as N.R.C. No. 8043.
M. Kates (1964)
10.1016/0038-0717(78)90030-5
A comparison of two methods for the estimation of mycelial biomass in leaf litter
J. C. Frankland (1978)
10.1007/BF00422226
Extraction, distribution and biodegradation of bacterial lipopolysaccharides in estuarine sediments
J. N. Saddler (2004)
10.1146/ANNUREV.MI.35.100181.001503
The bacterial glycocalyx in nature and disease.
J. Costerton (1981)
10.1016/0003-2697(91)90120-I
Fast and sensitive silver staining of DNA in polyacrylamide gels.
B. J. Bassam (1991)
10.1016/B978-0-12-024923-7.50007-8
Structure and Function of Sterols in Fungi
J. Weete (1989)
10.1016/S0146-6380(86)80004-3
Bacterial contribution to sedimentary organic matter. A comparative study of lipid moieties in bacteria and recent sediments
H. Goossens (1986)
10.1146/ANNUREV.MI.33.100179.001125
Biosynthesis of polysaccharides by prokaryotes.
S. J. Tonn (1979)
10.1126/SCIENCE.2448875
Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase.
R. Saiki (1988)
10.1146/ANNUREV.MI.22.100168.000511
Cell wall chemistry, morphogenesis, and taxonomy of fungi.
S. Bartnicki-García (1968)
10.1016/0038-0717(82)90105-5
Decomposition of 14C- and 15N-labelled microbial cells in soil
T. Marumoto (1982)
10.1016/0038-0717(92)90218-M
Evaluation of methods to extract ergosterol for quantitation of soil fungal biomass
M. W. Davis (1992)
10.1139/O59-099
A rapid method of total lipid extraction and purification.
E. Bligh (1959)
10.1126/science.175.4023.720
The Fluid Mosaic Model of the Structure of Cell Membranes
S. Singer (1972)
10.1111/J.1365-2672.1993.TB02999.X
Rapid DNA extraction protocol from soil for polymerase chain reaction‐mediated amplification
K. Smalla (1993)
10.1126/SCIENCE.2466341
Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells.
E. DeLong (1989)



This paper is referenced by
10.1080/03650340600915554
Soil microbial diversity of four German long-term field experiments
U. Langer (2006)
10.1080/02757540.2013.871271
The importance of different forms of Pb on diminishing biological activities in a calcareous soil
R. Zalaghi (2014)
10.1080/15320380903252903
Effects of Sterilization and Temperature on the Decrease Kinetic of Lead Bioavailability in Two Different Soil Groups
A. A. S. Sinegani (2009)
10.1080/00103624.2013.823985
Changes of Inorganic Active P Forms in Two Calcareous Soils and Maize Growth in Pot Culture in Sterile and Unsterile Conditions
A. A. S. Sinegani (2013)
10.1080/15324982.2013.806605
Survival of Pseudomonas fluorescens CHA0 in Soil; Impact of Calcium Carbonate and Temperature
M. Farhangi (2014)
10.1080/10256016.2013.826212
N2O emissions and source processes in snow-covered soils in the Swiss Alps
J. Mohn (2013)
10.1080/00103624.2013.736267
Soil Quality under Different Farming Systems in Santa Clara, Cuba
Y. Ruiz-Gonzalez (2013)
10.1080/03601234.2014.844600
A correlation between the fate and non-extractable residue formation of 14C-metalaxyl and enzymatic activities in soil
Jens Botterweck (2014)
10.1080/01490450701456834
Iron-Reducing Microorganisms in a Landfill Leachate-Polluted Aquifer: Complementing Culture-Independent Information with Enrichments and Isolations
B. Lin (2007)
10.1080/01448765.2014.1002537
Impact of ecological and conventional farming systems on chemical and biological soil quality indices in a cold mountain climate in Slovakia
L. Bobul'ská (2015)
10.1080/02757540.2016.1157172
Lead redistribution in a mine soil treated with three manures and incubated at two different temperatures
A. A. Safari Sinegani (2016)
10.1080/15287394.2010.491777
Microbiological Hazards Resulting from Application of Dairy Sewage Sludge: Effects on Occurrence of Pathogenic Microorganisms in Soil
S. Jezierska-Tys (2010)
10.1080/02571862.2006.10634739
Microbial community function and structure on coal mine discard under rehabilitation
S. Claassens (2006)
10.1080/00103624.2012.689399
Soil Carbon Dioxide Emissions from Sorghum–Sunflower Rotation in Rainfed Semi-arid Tropical Alfisols: Effects of Fertilization Rate and Legume Biomass Incorporation
V. Ramesh (2012)
10.1081/ESE-120037852
Identification of Recalcitrant Hydrocarbons Present in a Drilling Waste-Polluted Soil
J. M. Arce-Ortega (2004)
10.1080/00103624.2014.954286
Change in Soil Microbial and Enzyme Activities in Response to the Addition of Rock-Phosphate-Enriched Compost
Suelen Martins de Oliveira (2014)
10.1080/10889868.2014.933173
Establishing Correlations and Scale-Up Factor for Estimating the Petroleum Biodegradation Rate in Soil
A. Khan (2015)
10.1080/10406630008028542
Degradation of Benzo[a]Pyrene as Sole Carbon Source by a Non White Rot Fungus, Fusarium Solani
Rafin C. (2000)
10.1080/00103621003592325
Microbial Biomass, Community Diversity, and Enzyme Activities in Response to Urea Application in Tea Orchard Soils
Chaorong Ge (2010)
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