Abstract
Broad-scale approaches seek to integrate information on whole microbial communities. It is widely recognized that culture techniques are too selective and unrepresentative to allow a realistic assessment of the overall structure of microbial communities. Techniques based on fatty acid or metabolic profiles determine the phenotypic composition of the community. Complementary information about the genotypic structure of soil microbial communities necessitates analysis of community DNA. To determine broad-scale differences in soil microbial community structure (i.e., differences at the whole community level, rather than specific differences in species composition), we have applied a community hybridization technique to determine the similarity and relative diversity of two samples by cross hybridization. In previous studies this assay failed with whole-soil community DNA. Usable hybridization signals were obtained using whole-soil DNA, in this study, by digesting the DNA with restriction enzymes before the labeling with a random-primer reaction. The community hybridization technique was tested using a graded series of microbial fractions, increasing in complexity, all isolated from the same soil sample. This demonstrated that single bacterial species and a mixture of cultivable bacteria were less complex and only 5% similar to whole-community DNA or bacteria directly extracted from the soil. Extracted bacterial and whole-community DNA were 75% similar to each other and equally complex. When DNA was extracted from four different agricultural soils, their similarities ranged from 35 to 75%. The potential usefulness of community hybridization applied to soil microbial communities is discussed.
Similar content being viewed by others
References
Adriaenssens PI, Bixler CJ, Anderson W (1982) Isolation and quantification of DNA-bound benzo(a)-pyrene metabolites: comparison of hydroxyapatite and precipitation procedures. Anal Biochem 123:162–169
Amersham International (1994) Life science catalogue 1994. Amersham International, Amersham, UK.
Anderson MLM, Young BD (1985) Quantitative filter hybridization. In: Hames BD, Higgins SJ (eds) Nucleic acid hybridization. IRL Press, Oxford, England, pp 73–112
Bakken LIZ (1985) Separation and purification of bacteria from soil. Appl Environ Microbiol 49:1482–1487
Faegri A, Torsvik VL, Goksøyr J (1977) Bacterial and fungal activities in soil: separation of bacteria and fungi by a rapid fractionated centrifugation technique. Soil Biol Biochem 9: 105–112
Frosteg»rd A, Tunlid A, Bååth E (1993) Phospholipid fatty acid composition, biomass, and activity of microbial communities from two soil types experimentally exposed to different heavy metals. Appl Environ Microbiol 59:3605–3617
Garland JL, Mills AL (1991) Classification and characterisation of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source. Appl Environ Microbiol 57:2351–2359
Harris D (1994) Analysis of DNA extracted from microbial communities. In: Ritz K, Dighton J, Giller KE (eds) Beyond the biomass. John Wiley & Sons, Chichester, England, pp 111–118
Hicks RE, Amann RI, Stahl DA (1992) Dual staining of natural bacterioplankton with 4′,6-diamino-2-phenylindole and fluorescent oligonucleotide probes targeting Kingdom-level 16S rRNA sequences. Appl Environ Microbiol 58:2158–2163.
Hopkins DW O'Donnell AG, MacNaughton SJ (1991) Evaluation of a dispersion and elutriation technique for sampling microorganisms from soil. Soil Biol Biochem 23:227–232
Lee S, Fuhrman JA (1990) DNA hybridization to compare species compositions of natural bacterioplankton assemblages. Appl Environ Microbiol 56:739–746
Leser TD, Boye M, Hendriksen NB (1995) Survival and activity of Pseudomonas sp. Strain B13 (FR1) in a marine microcosm determined by quantitative PCR and an rRNA-targeting probe and its effect on the indigenous bacterioplankton. Appl Environ Microbiol 61:1201–1207
Lichtenstein C, Draper J (1985) Genetic engineering of plants. In: Glover DM (ed) DNA cloning, vol. 2, IRL Press, Oxford, England, pp 67–120
Maniatis T, Fritsch EF, Sambrook J (1982) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbour, New York
Odum EP (1971) Fundamentals of ecology, 3rd ed. WB Saunders, Philadelphia
Pitcher DG, Saunders NA, Owen RJ (1989) Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 8:151–156
Ritz K, Dighton J, Giller KE (eds) (1994) Beyond the biomass, compositional and functional analysis of soil microbial communities. John Wiley & Sons, Chichester, England
Ritz K, Griffiths BS (1994) Potential application of a community hybridization technique for assessing changes in the population structure of soil microbial communities. Soil Biol Biochem 26:963–971
Rose AH (1989) Influence of the environment on microbial lipid composition. In: Ratledge C, Wilkinson SG (eds) Microbial lipids, vol 2. Academic Press, London, pp 255–278
Sayler GS, Nikbakht K, Fleming IT, Packard J (1992) Application of molecular techniques soil biochemistry. In: Stotzky G, Bollag J-M (eds) Soil biochemistry, vol 7. Marcel Dekker, New York, pp 131–172
Steffan RJ, Goksøyr J, Bej AK, Atlas RM (1988) Recovery of DNA from soils and sediments. Appl Environ Microbiol 54:2908–2915
Tebbe C, Vahjen W (1993) Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast. Appl Environ Microbiol 59:2657–2665
Torsvik V, Goksøyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56:782–787
van Elsas JD, Waalwijk C (1991) Methods for the detection of specific bacteria and their genes in soil. Agri Ecosyst Environ 34:97–105
Wagner M, Amann R, Lemmer H, Schleifer K-H (1993) Probing activated sludge with oligonucleotides specific for proteobacteria: inadequacy of culture-dependent methods for describing microbial community structure. Appl Environ Microbiol 59:1520–1525
Ward DM, Weller R, Bateson MM (1990) 16S rRNA sequences reveal numerous uncultured inhabitants in a natural community. Nature (London) 345:63–65
Weller R, Weller JW, Ward DM (1991) 16S rRNA sequences of uncultivated hot spring cyanobacterial mat inhabitants retrieved as randomly primed cDNA. Appl Environ Microbiol 57:1146–1151
Winding A (1994) Fingerprinting bacterial soil communities using Biolog microtitre plates. In: Ritz K, Dighton J, Giller KE (eds) Beyond the biomass. John Wiley & Sons, Chichester, England, pp 85–94
Zelles L, Bai QY, Beese F (1992) Signature fatty acids in phospholipids and lipopolysaccharides as indicators of microbial biomass and community structure in agricultural soils. Soil Biol Biochem 24:317–323
Zwart KB, Brussaard L (1991) Soil fauna and cereal crops. In: Firbank LG, Carter N, Darbyshire JF, Potts GR (eds) The ecology of temperate cereal fields. The 32nd Symposium of the British Ecological Society with the Association of Applied Biologists, University of Cambridge. Blackwell Scientific, Oxford, England, pp 139–168
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Griffiths, B.S., Ritz, K. & Glover, L.A. Broad-scale approaches to the determination of soil microbial community structure: Application of the community DNA hybridization technique. Microb Ecol 31, 269–280 (1996). https://doi.org/10.1007/BF00171571
Received:
Revised:
Issue Date:
DOI: https://doi.org/10.1007/BF00171571