Leptothrix ochracea genotype
What’s new is old: resolving the identity of Leptothrix ochracea using single cell genomics, pyrosequencing and FISH
Pyrosequencing data used to determine the genotype of Leptothrix ochracea. The samples were obtained from from a freshwater iron mat during during the summer of 2008.  The full description of these reads and analysis are associated with a manuscript in PLOS One 2011 by  Fleming, EJ, AE Langdon M Martinez-Garcia, R Stepanauskas, N Poulton, D Masland and D Emerson
Leptothrix ochracea is a common inhabitant of freshwater iron seeps and iron rich wetlands. It’s defining characteristic is copious production of extracellular sheaths encrusted with iron oxyhydroxides. Surprisingly, over 90% of sheaths are empty, thus Leptothrix cells are only a minor fraction of the entire bacterial population in these ecosystems. Because L ochracea has proven difficult to cultivate, its identification is based solely on habitat preference and morphology. We utilized cultivation-independent techniques to resolve this long-standing enigma. By selecting the actively growing edge of a Leptothrix-containing iron mat, a conventional SSU rRNA gene clone library was obtained that had 29 clones (42% of the total library) related to the Leptothrix/Sphaerotilus group (=96% identical to cultured representatives). A pyrotagged library of the V4 hypervariable region constructed from the bulk mat showed that 7.2% of the total sequences also belonged to the Leptothrix/Sphaerotilus group. Sorting of individual L. ochracea sheaths, followed by whole genome amplification (WGA) identified a SSU rDNA PCR sequence that clustered closely with the putative Leptothrix clones and pyrotags. Using these data, a fluorescence in-situ hybridization (FISH) probe, Lepto175, was designed that bound to ensheathed cells. Quantitative use of this probe demonstrated that up to 35% of microbial cells in an actively accreting iron mat were L. ochracea. The SSU rRNA gene of L. ochracea shares 96% homology with its closet cultivated relative, L. cholodnii, This establishes that L. ochracea is indeed related to this group of morphologically similar, filamentous, sheathed microorganisms.