ArticleApplied and environmental microbiology1999
Comparative phylogenetic assignment of environmental sequences of genes encoding 16S rRNA and numerically abundant culturable bacteria from an anoxic rice paddy soil.
Article in Applied and environmental microbiology, 1999. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
37 citing papers in PubMed.
- The potential of soil microbial communities to transform deoxynivalenol in agricultural soils-a soil microcosm study.Mycotoxin research · 2024Article
- Review
- Microbial diversity and functional response to the redox dynamics of pyrite-rich sediment and the impact of preload surcharge.Environmental monitoring and assessment · 2020Article
- Anaerobic pyrite oxidation in a naturally occurring pyrite-rich sediment under preload surcharge.Environmental monitoring and assessment · 2019Article
- Biochemical and structural features of diverse bacterial glucuronoyl esterases facilitating recalcitrant biomass conversion.Biotechnology for biofuels · 2018Article
- Denitrification versus respiratory ammonification: environmental controls of two competing dissimilatory NO3(-)/NO2(-) reduction pathways in Shewanella loihica strain PV-4.The ISME journal · 2015Article
- Depth-dependent geochemical and microbiological gradients in Fe(III) deposits resulting from coal mine-derived acid mine drainage.Frontiers in microbiology · 2014Article
- Identification of bacteria in enrichment cultures of sulfate reducers in the Cariaco Basin water column employing Denaturing Gradient Gel Electrophoresis of 16S ribosomal RNA gene fragments.Aquatic biosystems · 2013Article
- Diversity of cultivable methane-oxidizing bacteria in microsites of a rice paddy field: investigation by cultivation method and fluorescence in situ hybridization (FISH).Microbes and environments · 2012Article
- Microbial diversity in Tunisian geothermal springs as detected by molecular and culture-based approaches.Extremophiles : life under extreme conditions · 2010Article
- Bacterial community analysis of the water surface layer from a rice-planted and an unplanted flooded field.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2010Article
- Endophytic bacterial diversity in grapevine (Vitis vinifera L.) leaves described by 16S rRNA gene sequence analysis and length heterogeneity-PCR.Journal of microbiology (Seoul, Korea) · 2009Article
- Succession of bacterial populations during plant residue decomposition in rice field soil.Applied and environmental microbiology · 2009Article
- Prevalence of betaproteobacterial sequences in nifH gene pools associated with roots of modern rice cultivars.Microbial ecology · 2009Article
- Worlds within worlds: evolution of the vertebrate gut microbiota.Nature reviews. Microbiology · 2008Review
- Phylogenetic analysis and fluorescence in situ hybridization detection of archaeal and bacterial endosymbionts in the anaerobic ciliate trimyema compressum.Microbial ecology · 2007Article
- Microbial sulfate reduction and metal attenuation in pH 4 acid mine water.Geochemical transactions · 2007Article
- Global patterns in bacterial diversity.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- Identification of acetate-assimilating microorganisms under methanogenic conditions in anoxic rice field soil by comparative stable isotope probing of RNA.Applied and environmental microbiology · 2007Article
- Stable-isotope probing of microorganisms thriving at thermodynamic limits: syntrophic propionate oxidation in flooded soil.Applied and environmental microbiology · 2004Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We used both cultivation and direct recovery of bacterial 16S rRNA gene (rDNA) sequences to investigate the structure of the bacterial community in anoxic rice paddy soil. Isolation and phenotypic characterization of 19 saccharolytic and cellulolytic strains are described in the accompanying paper (K.-J. Chin, D. Hahn, U. Hengstmann, W. Liesack, and P. H. Janssen, Appl. Environ. Microbiol. 65:5042-5049, 1999). Here we describe the phylogenetic positions of these strains in relation to 57 environmental 16S rDNA clone sequences. Close matches between the two data sets were obtained for isolates from the culturable populations determined by the most-probable-number counting method to be large (3 x 10(7) to 2.5 x 10(8) cells per g [dry weight] of soil). This included matches with 16S rDNA similarity values greater than 98% within distinct lineages of the division Verrucomicrobia (strain PB90-1) and the Cytophaga-Flavobacterium-Bacteroides group (strains XB45 and PB90-2), as well as matches with similarity values greater than 95% within distinct lines of descent of clostridial cluster XIVa (strain XB90) and the family Bacillaceae (strain SB45). In addition, close matches with similarity values greater than 95% were obtained for cloned 16S rDNA sequences and bacteria (strains DR1/8 and RPec1) isolated from the same type of rice paddy soil during previous investigations. The correspondence between culture methods and direct recovery of environmental 16S rDNA suggests that the isolates obtained are representative geno- and phenotypes of predominant bacterial groups which account for 5 to 52% of the total cells in the anoxic rice paddy soil. Furthermore, our findings clearly indicate that a dual approach results in a more objective view of the structural and functional composition of a soil bacterial community than either cultivation or direct recovery of 16S rDNA sequences alone.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.