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TitleStable isotope probing identifies uncultured Planctomycetes as primary degraders of a complex heteropolysaccharide in soil
AuthorWang, X; Sharp, C; Jones, G; Grasby, S E; Brady, A; Dunfield, P
SourceApplied and Environmental Microbiology vol. 81, no. 14, 2015 p. 4607-4615,
Alt SeriesEarth Sciences Sector, Contribution Series 20150046
PublisherAmerican Society for Microbiology
Mediapaper; on-line; digital
File formatpdf
Subjectsstable isotope studies; soil studies; Beijerinckia indica; Planctomycetes; exopolysaccharides; bacteria; heteropolysaccharide; cellulose-degrading bacteria
Illustrationstables; graphs; diagrams
ProgramShale Reservoir Characterization, Geoscience for New Energy Supply (GNES)
Exopolysaccharides (EPS) produced by some bacteria are potential growth substrates for other bacteria in soil. We used stable isotope probing (SIP) to identify aerobic soil bacteria that assimilated carbon from cellulose produced by Gluconacetobacter xylinus, or from EPS produced by Beijerinckia indica. The latter is a heteropolysaccharide comprised primarily of L-guluronic acid, D-glucose, and D-glycero-D-mannoheptose. 13C-labeled EPS and 13C-labeled cellulose were purified from bacterial cultures grown on 13C-glucose. Two soils were incubated with these substrates, and bacteria actively assimilating them were identified via pyrosequencing of 16S rRNA genes recovered from 13C-labeled DNA. Cellulose-C was assimilated primarily by soil bacteria closely related (93-100% 16S rRNA gene sequence identities) to known cellulose-degrading bacteria. However, B. indica EPS was assimilated primarily by bacteria with low identities (80-95%) to known species, particularly by different members of the phylum Planctomycetes. In one incubation Planctomycetes made up >60% of all reads in the labeled DNA and were only distantly related (<85% identity) to any described species. Although it is impossible with SIP to completely distinguish primary polysaccharide hydrolysers from bacteria growing on produced oligo- or monosaccharides, the predominance of Planctomycetes suggested that they were primary degraders of EPS. Other bacteria assimilating B. ndica EPS included members of the Verrucomicrobia, candidate division OD1, and Armatimonadetes. The results indicate that some uncultured bacteria in soils may be adapted to using complex heteropolysaccharides for growth, and suggest that use of these substrates may provide a means for culturing new species.
Summary(Plain Language Summary, not published)
Research on microbes that degrade organic matter in rock is hampered by the difficulty of cultivating and growing them in a laboratory environment. A novel method of 'stable isotope probing' allows separation of microbes from a sample based on their selective incorporation of heavy isotopes of carbon into their cell. These can then be selectively run for DNA analyses to identify specific species responsible for organic matter degradation. These new methods allow enhanced understanding of microbial processes in organic-rich rocks.