.. Table 4 Number of genes associated with the general COG functional categories useful site Acknowledgements We would like to gratefully acknowledge the help of Maren Schr?der (DSMZ) for the growth of C. nitroreducens cultures. This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle, and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1.

A representative genomic 16S rRNA sequence of strain IS1BT was compared using NCBI BLAST under default values (e.g., considering only the best 250 hits) with the most recent release of the Greengenes database [6] and the relative frequencies, weighted by BLAST scores, of taxa and keywords (reduced to their stem [7]) were determined. The five most frequent genera were Isosphaera (35.4%), Nostocoida (26.4%; a genus with Candidatus status [8]), Singulisphaera (20.4%), ‘Isophaera’ (15.9%; a misspelling of Isosphaera) and Planctomyces (1.9%). The species yielding the highest score was CandidatusNostocoida limicola [8]. The five most frequent keywords within the labels of environmental samples which yielded hits were ‘skin’ (3.9%), ‘soil’ (3.0%), ‘fossa’ (2.2%), ‘adult/zebrafish’ (2.2%) and ‘microbi’ (1.9%).

The two most frequent keywords within the labels of environmental samples which yielded hits of a higher score than the highest scoring species were ‘adult, zebrafish’ (10.0%) and ‘conventionally-rais, digest, gender, germ-fre, gut, habitat, host, mice, micro-biota, mix, pool, recipi, reciproc, select, tract, transplant’ (5.0%), i.e. many ties occurred, rendering it difficult to ecologically interpret this outcome. Figure 1 shows the phylogenetic neighborhood of I. pallida IS1BT in a 16S rRNA based tree. The sequences of the three copies in the genome do not differ from each other, and differ by two nucleotides from the previously published 16S rRNA sequence (“type”:”entrez-nucleotide”,”attrs”:”text”:”AJ231195″,”term_id”:”4775458″,”term_text”:”AJ231195″AJ231195). Figure 1 Phylogenetic tree highlighting the position of I.

pallida relative to the other type strains within the class family Planctomycetacia. Anacetrapib The tree was inferred from 1,362 aligned characters [9,10] of the 16S rRNA gene sequence under the maximum likelihood … Cells of strain IS1BT are spherical with 2.5 to 3 ��m in diameter (Figure 2 and Table 1), with cell growth and division occurring by intercalary budding, resulting in filaments [1]. The cells are salmon-colored (caused by carotenoids), contain gas vesicles and resemble Isocystis pallida Worochin 1927 [5].