ArticleApplied and environmental microbiology2012
Novel high-rank phylogenetic lineages within a sulfur spring (Zodletone Spring, Oklahoma), revealed using a combined pyrosequencing-sanger approach.
Article in Applied and environmental microbiology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Phylogenetic diversity and community structure ofFrontiers in microbiology · 2025Article
- Metal-oxide precipitation influences microbiome structure in hyporheic zones receiving acid rock drainage.Applied and environmental microbiology · 2024Article
- Polar lake microbiomes have distinct evolutionary histories.Science advances · 2023Article
- Terabase-Scale Coassembly of a Tropical Soil Microbiome.Microbiology spectrum · 2023Article
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- Diversity and Abundance of Microbial Communities in UASB Reactors during Methane Production from Hydrolyzed Wheat Straw and Lucerne.Microorganisms · 2020Article
- Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere.The ISME journal · 2020Article
- Design of targeted primers based on 16S rRNA sequences in meta-transcriptomic datasets and identification of a novel taxonomic group in the Asgard archaea.BMC microbiology · 2020Article
- The Link Between the Ecology of the Prokaryotic Rare Biosphere and Its Biotechnological Potential.Frontiers in microbiology · 2020Review
- Diversity and functional profile of bacterial communities at Lancaster acid mine drainage dam, South Africa as revealed by 16S rRNA gene high-throughput sequencing analysis.Extremophiles : life under extreme conditions · 2019Article
- Genomic Characterization of Candidate Division LCP-89 Reveals an Atypical Cell Wall Structure, Microcompartment Production, and Dual Respiratory and Fermentative Capacities.Applied and environmental microbiology · 2019Article
- Bioreactor microbial ecosystems with differentiated methanogenic phenol biodegradation and competitive metabolic pathways unraveled with genome-resolved metagenomics.Biotechnology for biofuels · 2018Article
- Microbial Communities and Diversities in Mudflat Sediments Analyzed Using a Modified Metatranscriptomic Method.Frontiers in microbiology · 2018Article
- Modified RNA-seq method for microbial community and diversity analysis using rRNA in different types of environmental samples.PloS one · 2017Article
- Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage.Molecular biology and evolution · 2016Article
- Assessing the global phylum level diversity within the bacterial domain: A review.Journal of advanced research · 2015Review
- Ecology and exploration of the rare biosphere.Nature reviews. Microbiology · 2015Review
- Article
- Anaerobic degradation of cyclohexane by sulfate-reducing bacteria from hydrocarbon-contaminated marine sediments.Frontiers in microbiology · 2015Article
- Global patterns of abundance, diversity and community structure of the Aminicenantes (candidate phylum OP8).PloS one · 2014Article
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The utilization of high-throughput sequencing technologies in 16S rRNA gene-based diversity surveys has indicated that within most ecosystems, a significant fraction of the community could not be assigned to known microbial phyla. Accurate determination of the phylogenetic affiliation of such sequences is difficult due to the short-read-length output of currently available high-throughput technologies. This fraction could harbor multiple novel phylogenetic lineages that have so far escaped detection. Here we describe our efforts in accurate assessment of the novelty and phylogenetic affiliation of selected unclassified lineages within a pyrosequencing data set generated from source sediments of Zodletone Spring, a sulfide- and sulfur-rich spring in southwestern Oklahoma. Lineage-specific forward primers were designed for 78 putatively novel lineages identified within the pyrosequencing data set, and representative nearly full-length small-subunit (SSU) rRNA gene sequences were obtained by pairing those primers with reverse universal bacterial primers. Of the 78 lineages tested, amplifiable products were obtained for 52, 32 of which had at least one nearly full-length sequence that was representative of the lineage targeted. Analysis of phylogenetic affiliation of the obtained Sanger sequences identified 5 novel candidate phyla and 10 novel candidate classes (within Fibrobacteres, Planctomycetes, and candidate phyla BRC1, GN12, TM6, TM7, LD1, WS2, and GN06) in the data set, in addition to multiple novel orders and families. The discovery of multiple novel phyla within a pilot study of a single ecosystem clearly shows the potential of the approach in identifying novel diversities within the rare biosphere.
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