Characterization of large-insert DNA libraries from soil for environmental genomic studies of Archaea.
Complex genomic libraries are increasingly being used to retrieve complete genes, operons or large genomic fragments directly from environmental samples, without the need to cultivate the respective microorganisms. We report on the construction of three large-insert fosmid libraries in total covering 3 Gbp of community DNA from two different soil samples, a sandy ecosystem and a mixed forest soil. In a fosmid end sequencing approach including 5376 sequence tags of approximately 700 bp length, we show that mostly bacterial and, to a much lesser extent, archaeal and eukaryotic genome fragments (approximately 1% each) have been captured in our libraries. The diversity of putative protein-encoding genes, as reflected by their distribution into different COG clusters, was comparable to that encoded in complete genomes of cultivated microorganisms. A huge variety of genomic fragments has been captured in our libraries, as seen by comparison with sequences in the public databases and by the large variation in G+C contents. We dissect differences between the libraries, which relate to the different ecosystems analysed and to biases introduced by different DNA preparations. Furthermore, a range of taxonomic marker genes (other than 16S rRNA) has been identified that allows the assignment of genome fragments to specific lineages. The complete sequences of two genome fragments identified as being affiliated with Archaea, based on a gene encoding a CDC48 homologue and a thermosome subunit, respectively, are presented and discussed. We thereby extend the genomic information of uncultivated crenarchaeota from soil and offer hints to specific metabolic traits present in this group.
Treusch
Alexander H
AH
Institute of Microbiology and Genetics, Darmstadt University of Technology, Schnittspahnstrasse 10, 64287 Darmstadt, Germany.
Kletzin
Arnulf
A
Raddatz
Guenter
G
Ochsenreiter
Torsten
T
Quaiser
Achim
A
Meurer
Guido
G
Schuster
Stephan C
SC
Schleper
Christa
C
D000251:Adenosine Triphosphatases; D001105:Archaea / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics*; D001482:Base Composition; D001483:Base Sequence; D018797:Cell Cycle Proteins / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D017753:Ecosystem; D015723:Gene Library; D016680:Genome, Bacterial; D016013:Likelihood Functions; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D013045:Species Specificity; D000074405:Valosin Containing Protein
D001426:Bacterial Proteins; D018797:Cell Cycle Proteins; D004275:DNA, Ribosomal; D000251:Adenosine Triphosphatases; D000074405:Valosin Containing Protein