Molecular microbial diversity of an agricultural soil in Wisconsin.
A culture-independent survey of the soil microbial diversity in a clover-grass pasture in southern Wisconsin was conducted by sequence analysis of a universal clone library of genes coding for small-subunit rRNA (rDNA). A rapid and efficient method for extraction of DNA from soils which resulted in highly purified DNA with minimal shearing was developed. Universal small-subunit-rRNA primers were used to amplify DNA extracted from the pasture soil. The PCR products were cloned into pGEM-T, and either hypervariable or conserved regions were sequenced. The relationships of 124 sequences to those of cultured organisms of known phylogeny were determined. Of the 124 clones sequenced, 98.4% were from the domain Bacteria. Two of the rDNA sequences were derived from eukaryotic organelles. Two of the 124 sequences were of nuclear origin, one being fungal and the other a plant sequence. No sequences of the domain Archaea were found. Within the domain, Bacteria, three kingdoms were highly represented: the Proteobacteria (16.1%), the Cytophaga-Flexibacter-Bacteroides group (21.8%), and the low G+C-content gram-positive group (21.8%). Some kingdoms, such as the Thermotogales, the green nonsulfur group, Fusobacteria, and the Spirochaetes, were absent. A large number of the sequences (39.4%) were distributed among several clades that are not among the major taxa described by Olsen et al. (G.J. Olsen, C.R. Woese, and R. Overbeek, J. Bacteriol., 176:1-6, 1994). From the alignments of the sequence data, distance matrices were calculated to display the enormous microbial diversity found in this soil in two ways, as phylogenetic trees and as multidimensional-scaling plots.
Borneman
J
J
Department of Agronomy, University of Wisconsin-Madison 53706, USA.
Skroch
P W
PW
O'Sullivan
K M
KM
Palus
J A
JA
Rumjanek
N G
NG
Jansen
J L
JL
Nienhuis
J
J
Triplett
E W
EW
D001315:Australia; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D001483:Base Sequence; D002678:Chimera; D003001:Cloning, Molecular; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D004271:DNA, Fungal / Q000235:genetics / Q000302:isolation & purification; D004275:DNA, Ribosomal / Q000235:genetics / Q000302:isolation & purification; D017753:Ecosystem; D005658:Fungi / Q000235:genetics / Q000302:isolation & purification; D014644:Genetic Variation; D007564:Japan; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012988:Soil Microbiology; D014922:Wisconsin
D017931:DNA Primers; D004269:DNA, Bacterial; D004271:DNA, Fungal; D004275:DNA, Ribosomal