PMC:3558958 / 4129-9661 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/3558958","sourcedb":"PMC","sourceid":"3558958","source_url":"http://www.ncbi.nlm.nih.gov/pmc/3558958","text":"Classification and features\nA phylogenetic tree was constructed to identify the family relationship of strain Y412MC10 (Figure 1). The tree was created using BLAST2Tree software [23]. The analysis was carried out using only type strains of validly-named organisms, and the analysis shows that Y412MC10 does not clade with known Geobacillus species. Rather, Y412MC10 clades in the Paenibacillus genus. Based on r16S analysis of validly-named organisms, Y412MC10 is most closely related to Paenibacillus lautus DSM 3055T (AB073188). The classification of the isolate was confirmed using the EzTaxon-e server [24], again on the basis of 16S rRNA sequence data. When compared to their entire r16S database, Y412MC10 was identified as being a strain of Paenibacillus lautus with 99.09% identity and 100% completeness to the r16S of the type strain, Paenibacillus lautus NRRL NRS-666 GenBank D78472.\nFigure 1 Phylogenetic tree highlighting the position of Paenibacillus lautus strain Y412MC10 and relative strains within the Bacillales. Strains used for the comparison (16S rRNA accession number) were (Paenibacillus Y412MC10); Paenibacillus lautus DSM 3035T (AB073188); Paenibacillus glucanolyticus DSM 5162T (AB073189); Paenibacillus illinoisensis DSM 11733T (AB073192); Paenibacillus chibensis DSM 11731T (AB073194); Paenibacillus ginsengisoli LMG 23406 T (AB245382); Paenibacillus macquariensis subsp defensor NCIB 14397 T (AB360546); Paenibacillus kribbensis KCTC 0766BP T (AF391123); Paenibacillus daejeonensis KCCM 41557 T (AF391124); Paenibacillus borealis DSM 13188 T (AJ011322); Paenibacillus odorifer DSM 15391 T (AJ223990); Paenibacillus cookie LMG 18419 T (AJ250317); Paenibacillus jamilae DSM 13815 T (AJ271157); Paenibacillus azoreducens DSM 13822 T (AJ272249); Paenibacillus stellifer DSM 14472 T (AJ316013); Paenibacillus peoriae DSM 8320 T (AJ320494); Paenibacillus cineris LMG 18349 T (AJ575658); Paenibacillus antarcticus LMG 22078 T (AJ605292); Paenibacillus favisporus LMG 20987 T (AY208751); Paenibacillus lactis DSM 15596 T (AY257868); Paenibacillus provencensis CIP 109358T (EF212893); Paenibacillus konsidanse KCTC 13165T (EU081509). Paenibacillus sp. Y412MC10 was one of a number of organisms isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA (44.6100594° latitude and -110.4388217° longitude) under a sampling permit from the National Park Service. The hot spring possesses a pH of 6.37 and a temperature range of 42-90°C. The organism was isolated from a sample of hot spring water by enrichment and plating on YTP-2 medium [25] (YTP-2 media contains (per liter) 2.0 g yeast extract, 2.0 g tryptone, 2.0 g sodium pyruvate, 1.0 g KCl, 2.0 g KNO3, 2.0 g Na2HPO4.7H2O, 0.1 g MgSO4, 0.03 g CaCl2, and 2.0 ml clarified tomato juice) at 50°C. Culture stocks were routinely maintained on YT (containing (per liter) 5.0 g yeast extract, 8.0 g tryptone, and 2.5 g NaCl) agar plates at 37°C. As part of the sequencing agreement with the Joint Genome Institute, the culture is available without restrictions from the authors. Lucigen, the National Park Service, and the Joint Genome Institute have placed no restrictions on the use of the culture or sequence data. Y412MC10 is a Gram-positive facultative anaerobe (Table 1) that grows well on a wide variety of standard lab media (YT, TB, LB). On plates, the organism grows as rods or chains of rods (Figure 2A). After growth for 6 days on plates, the cells still appear rod-shaped, but an extracellular matrix appears to surround and bind the individual cells together (light green background, Figure 2B). In liquid culture, the organism appears to also grow as a mixture of single cells and large clumps of cells surrounded by an extracellular matrix (Figure 2C). Prolonged growth on plates or in liquid culture results in sporulation of the culture; spores are subterminal with swollen sporangia.\nTable 1 Classification and general features of Paenibacillus strain Y412MC10 Evidence codes - IDA: Inferred from Direct Assay; TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project [41].\nFigure 2A Micrograph of Paenibacillus strain Y412MC10 cells showing individual cells and chains of cells. Cells were streaked on YT agar and incubated 18 hr. at 37°C. A colony was removed, re-suspended in sterile water and stained using a 5 μM solution of SYTO® 9 fluorescent stain in sterile water (Molecular Probes). Dark field fluorescence microscopy was performed using a Nikon Eclipse TE2000-S epifluorescence microscope at 2000× magnification using a high-pressure Hg light source and a 500 nm emission filter.\nFigure 2B Micrograph of same plate of Paenibacillus strain Y412MC10 cells showing individual cells and chains of cells. Same plate as Figure 2A, but incubated 6 days at 37°C.\nFigure 2C Micrograph of Paenibacillus strain Y412MC10 cells showing individual cells and clumps of cells. Cells were grown in YTP-2 media for 18 hours at 37°C and 200 rpm. An aliquot was removed and stained using a 5 μM solution of SYTO® 9 fluorescent stain in sterile water (Molecular Probes). Dark field fluorescence microscopy was performed using a Nikon Eclipse TE2000-S epifluorescence microscope at 200× magnification using a high-pressure Hg light source and 500 nm emission filter.\n\nG","divisions":[{"label":"Title","span":{"begin":0,"end":27}},{"label":"Figure caption","span":{"begin":894,"end":2156}},{"label":"Table caption","span":{"begin":3890,"end":4345}},{"label":"Title","span":{"begin":3899,"end":3967}},{"label":"Figure caption","span":{"begin":4345,"end":4864}},{"label":"Figure caption","span":{"begin":4863,"end":5040}},{"label":"Figure 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