Phylogenetic and Metabolic Diversity of
            <i>Planctomycetes</i>
            from Anaerobic, Sulfide- and Sulfur-Rich Zodletone Spring, Oklahoma

Elshahed, Mostafa S.; Youssef, Noha H.; Luo, Qingwei; Najar, Fares Z.; Roe, Bruce A.; Sisk, Tracy M.; Bühring, Solveig I; Hinrichs, Kai‐Uwe; Krumholz, Lee R.

doi:10.1128/aem.00591-07

Cited by 125 publications

(90 citation statements)

References 77 publications

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“…Both Gemmata obscuriglobus (21) and our uncultured Planctomycetes-like representative show moderately high GϩC contents (57 and 60%, respectively) in the 135-to 228-bp region of the 16S gene (based on E. coli 16S structure) (23), which is similar to that of Isosphaera pallida. This is also consistent with previous findings indicating that Gemmata and Isosphaera isolates are the most closely related phylogenetic groups in the Planctomycetes phylum (14,21). In a Planctomycetes-focused study at Zodletone Spring, a mesophilic sulfide spring in Oklahoma (14) Conclusion.…”

Section: Roseiflexus Strain Rs-1 (Unpublished)supporting

confidence: 82%

Formation of Multilayered Photosynthetic Biofilms in an Alkaline Thermal Spring in Yellowstone National Park, Wyoming

Boomer

Noll²,

Geesey

et al. 2009

Appl Environ Microbiol

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In this study, glass rods suspended at the air-water interface in the runoff channel of Fairy Geyser, Yellowstone National Park, WY, were used as a substratum to promote the development of biofilms that resembled multilayered mat communities in the splash zone at the geyser's source. This approach enabled the establishment of the temporal relationship between the appearance of Cyanobacteria, which ultimately formed the outer green layer, and the development of a red underlayer containing Roseiflexus-like Chloroflexi. This is the first study to define time-dependent successional events involved in the development of differently colored layers within microbial mats associated with many thermal features in Yellowstone National Park. Initial (1-month) biofilms were localized below the air-water interface (60 to 70°C), and the majority of retrieved bacterial sequence types were similar to Synechococcus and Thermus isolates. Biofilms then shifted, becoming established at and above the air-water interface after 3 months. During winter sampling (6 to 8 months), distinct reddish orange microcolonies were observed, consistent with the appearance of Roseiflexus-like sequences and bacteriochlorophyll a pigment signatures. Additionally, populations of Cyanobacteria diversified to include both unicellular and filamentous cell and sequence types. Distinct green and red layers were observed at 13 months. Planctomycetes-like sequences were also retrieved in high abundance from final biofilm layers and winter samples. Finally, biomass associated with geyser vent water contained Roseiflexus-like sequence types, in addition to other high-abundance sequence types retrieved from biofilm samples, supporting the idea that geothermal water serves as an inoculum for these habitats.

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Section: Roseiflexus Strain Rs-1 (Unpublished)supporting

confidence: 82%

Formation of Multilayered Photosynthetic Biofilms in an Alkaline Thermal Spring in Yellowstone National Park, Wyoming

Boomer

Noll²,

Geesey

et al. 2009

Appl Environ Microbiol

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“…A recent study done in Lake Kivu suggested that a variety of ecological niches of heterotrophic bacteria can be supported by the diversity of molecules excreted by the phytoplankton community [64]. Detection of a low abundance of potentially active Planctomycetes-affiliated sequences in the anoxic zone supported the idea that members of this group have anaerobic metabolic abilities, as suggested by previous studies showing that they rely on carbohydrate fermentation and sulfur reduction for growth and survival under anaerobic conditions [65]. Furthermore, sequences affiliated to Chlorobi phylum were recovered from both nucleic acid pools of either oxic or anoxic waters and sampling campaigns.…”

Section: Discussionmentioning

confidence: 64%

Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu

et al. 2015

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The microbial community composition in meromictic Lake Kivu, with one of the largest CH 4 reservoirs, was studied using 16S rDNA and ribosomal RNA (rRNA) pyrosequencing during the dry and rainy seasons. Highly abundant taxa were shared in a high percentage between bulk (DNA-based) and active (RNA-based) bacterial communities, whereas a high proportion of rare species was detected only in either an active or bulk community, indicating the existence of a potentially active rare biosphere and the possible underestimation of diversity detected when using only one nucleic acid pool. Most taxa identified as generalists were abundant, and those identified as specialists were more likely to be rare in the bulk community. The overall number of environmental parameters that could explain the variation was higher for abundant taxa in comparison to rare taxa. Clustering analysis based on operational taxonomic units (OTUs at 0.03 cutoff) level revealed significant and systematic microbial community composition shifts with depth. In the oxic zone, Actinobacteria were found highly dominant in the bulk community but not in the metabolically active community. In the oxic-anoxic transition zone, highly abundant potentially active Nitrospira and Methylococcales were observed. The cooccurrence of potentially active sulfur-oxidizing and sulfatereducing bacteria in the anoxic zone may suggest the presence of an active yet cryptic sulfur cycle.

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“…Schlesner demonstrated that Planctomycetes species required low-carbon and -nitrogen sources compared with the fast overgrowth of other bacterial species of complex ecosystems using N-acetylglucosamine (171). Because of the absence of the peptidoglycan responsible for ␤-lactam resistance in Planctomycetes (172), the use of these antibiotics also facilitates the fight against fast-growing bacterial species, thus assisting in pure Planctomycetes culture (169,173 (175). Nevertheless, to the best of our knowledge, no Planctomycetes pure cultures from human samples have been achieved to date.…”

Section: From Environmental To Clinical Microbiologymentioning

confidence: 99%

The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota

et al. 2015

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SUMMARY Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a “dark matter” of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the “great plate count anomaly,” which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire.

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Phylogenetic and Metabolic Diversity of Planctomycetes from Anaerobic, Sulfide- and Sulfur-Rich Zodletone Spring, Oklahoma

Cited by 125 publications

References 77 publications

Formation of Multilayered Photosynthetic Biofilms in an Alkaline Thermal Spring in Yellowstone National Park, Wyoming

Formation of Multilayered Photosynthetic Biofilms in an Alkaline Thermal Spring in Yellowstone National Park, Wyoming

Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu

The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota

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