ArticleApplied and environmental microbiology2009
Extensive phylogenetic analysis of a soil bacterial community illustrates extreme taxon evenness and the effects of amplicon length, degree of coverage, and DNA fractionation on classification and ecological parameters.
Article in Applied and environmental microbiology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Effect of molybdenum supply on crop performance through rhizosphere soil microbial diversity and metabolite variation.Frontiers in plant science · 2024Article
- Dataset of 16S rRNA and alkB genes in hydrocarbon polluted soils of Kuwait as revealed by Pyrosequencing.Data in brief · 2022Article
- Tool and techniques study to plant microbiome current understanding and future needs: an overview.Communicative & integrative biology · 2022Review
- Biosynthesis of rhamnolipid by a Marinobacter species expands the paradigm of biosurfactant synthesis to a new genus of the marine microflora.Microbial cell factories · 2019Article
- Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes.Frontiers in microbiology · 2019Article
- Differential Modulation of Endophytic Microbiome of Ginger in the Presence of Beneficial Organisms, Pathogens and Both as Identified by DGGE Analysis.Current microbiology · 2018Article
- Age-Related Differences in the Gastrointestinal Microbiota of Chinstrap Penguins (Pygoscelis antarctica).PloS one · 2016Article
- Fine Spatial Scale Variation of Soil Microbial Communities under European Beech and Norway Spruce.Frontiers in microbiology · 2016Article
- Wastewater irrigation increases the abundance of potentially harmful gammaproteobacteria in soils in Mezquital Valley, Mexico.Applied and environmental microbiology · 2014Article
- Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates.The ISME journal · 2012Article
- Characterization of soil bacterial assemblies in Brazilian savanna-like vegetation reveals acidobacteria dominance.Microbial ecology · 2012Article
- Article
- Amplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities.PloS one · 2012Article
- Hydrocarbon-degrading bacteria and the bacterial community response in gulf of Mexico beach sands impacted by the deepwater horizon oil spill.Applied and environmental microbiology · 2011Article
- Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils.PloS one · 2011Article
- Accessing the soil metagenome for studies of microbial diversity.Applied and environmental microbiology · 2011Article
- Horizon-specific bacterial community composition of German grassland soils, as revealed by pyrosequencing-based analysis of 16S rRNA genes.Applied and environmental microbiology · 2010Article
- Microbial populations responsive to denitrification-inducing conditions in rice paddy soil, as revealed by comparative 16S rRNA gene analysis.Applied and environmental microbiology · 2009Article
- Habitat heterogeneity and associated microbial community structure in a small-scale floodplain hyporheic flow path.Microbial ecology · 2009Article
- Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale.Applied and environmental microbiology · 2009Article
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Authors and funding
4 authors.
Funding
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Abstract
To thoroughly investigate the bacterial community diversity present in a single composite sample from an agricultural soil and to examine potential biases resulting from data acquisition and analytical approaches, we examined the effects of percent G+C DNA fractionation, sequence length, and degree of coverage of bacterial diversity on several commonly used ecological parameters (species estimation, diversity indices, and evenness). We also examined variation in phylogenetic placement based on multiple commonly used approaches (ARB alignments and multiple RDP tools). The results demonstrate that this soil bacterial community is highly diverse, with 1,714 operational taxonomic units demonstrated and 3,555 estimated (based on the Chao1 richness estimation) at 97% sequence similarity using the 16S rRNA gene. The results also demonstrate a fundamental lack of dominance (i.e., a high degree of evenness), with 82% of phylotypes being encountered three times or less. The data also indicate that generally accepted cutoff values for phylum-level taxonomic classification might not be as applicable or as general as previously assumed and that such values likely vary between prokaryotic phyla or groups.
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