title: Isolation and partial characterization of bacterial strains on low organic carbon medium from soils fertilized with different organic amendments.
abstract: A total of 720 bacterial strains were isolated from soils with four different organic amendment regimes on a low organic carbon (low-C) agar medium (10 µg C ml(-1)) traditionally used for isolation of oligotrophs. Organic amendments in combination with field history resulted in differences in dissolved organic carbon contents in these soils. There were negative correlations between total and dissolved organic carbon content and the number of isolates on low-C agar medium, whereas these correlations were absent for bacterial strains isolated from the same soil on high-C agar medium (1,000 µg C ml(-1)). Repeated transfers (up to ten times) of the isolates from low-C agar medium to fresh low- and high-C agar media were done to test for exclusive growth under oligotrophic conditions. The number of isolates exclusively growing under oligotrophic conditions dropped after each subsequent transfer from 241 after the first to 98 after the third transfer step. Identification on the basis of partial 16S rRNA gene sequences revealed that most of the 241 isolates (as well as the subset of 98 isolates) belong to widespread genera such as Streptomyces, Rhizobium, Bradyrhizobium, and Mesorhizobium, and the taxonomic composition of dominant genera changed from the first transfer step to the third. A selected subset of 17 isolates were further identified and characterized for exclusive growth on low-C agar medium. Two isolates continued to grow only on low-C agar medium up to the tenth transfer step and matched most closely with Rhizobium sullae and an uncultured bacterium on the basis of the almost full-length 16S rRNA gene. It was concluded that the vast majority of strains which are isolated on low-C agar media belong to the trophic group of microorganisms adapted to a "broad range" of carbon concentrations, including well-known and widespread bacterial genera. Oligotrophy is a physiological, not a taxonomic property, and can only be identified by cultural means so far. We showed that true oligotrophs that are unable to grow on high carbon media are rare and belong to genera that also contain broad-range and copiotrophic strains.
authors.affiliation: Plant Research International BV, Wageningen University and Research Center, Wageningen, The Netherlands.
authors.forename: Ilya V
authors.initials: IV
authors.lastname: Senechkin
authors.forename: Adrianus G C L
authors.initials: AG
authors.lastname: Speksnijder
authors.forename: Alexander M
authors.initials: AM
authors.lastname: Semenov
authors.forename: Ariena H C
authors.initials: AH
authors.lastname: van Bruggen
authors.forename: Leonard S
authors.initials: LS
authors.lastname: van Overbeek
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D002244:Carbon / Q000378:metabolism*; D003470:Culture Media / Q000378:metabolism*; D004269:DNA, Bacterial / Q000235:genetics; D005308:Fertilizers / Q000032:analysis; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012987:Soil / Q000032:analysis; D012988:Soil Microbiology
chemical_list: D003470:Culture Media; D004269:DNA, Bacterial; D005308:Fertilizers; D012336:RNA, Ribosomal, 16S; D012987:Soil; D002244:Carbon