scholarly journals Potential of a 16S rRNA-Based Taxonomic Microarray for Analyzing the Rhizosphere Effects of Maize on Agrobacterium spp. and Bacterial Communities

2006 ◽  
Vol 72 (6) ◽  
pp. 4302-4312 ◽  
Author(s):  
Herv� Sanguin ◽  
Beno�t Remenant ◽  
Arnaud Dechesne ◽  
Jean Thioulouse ◽  
Timothy M. Vogel ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Diversity ◽  
Bacterial Community Composition ◽  
Perfect Match ◽  
Bulk Soil ◽  
New Taxon ◽  
Rhizosphere Effect ◽  
Soil Dna ◽  
Maize Rhizosphere ◽  
Probe Set

ABSTRACT Bacterial diversity is central to ecosystem sustainability and soil biological function, for which the role of roots is important. The high-throughput analysis potential of taxonomic microarray should match the breadth of bacterial diversity. Here, the power of this technology was evidenced through methodological verifications and analysis of maize rhizosphere effect based on a 16S rRNA-based microarray developed from the prototype of H. Sanguin et al. (Environ. Microbiol. 8:289-307, 2006). The current probe set was composed of 170 probes (41 new probes in this work) that targeted essentially the Proteobacteria. Cloning and sequencing of 16S rRNA amplicons were carried out on maize rhizosphere and bulk soil DNA. All tested clones that had a perfect match with corresponding probes were positive in the hybridization experiment. The hierarchically nested probes were reliable, but the level of taxonomic identification was variable, depending on the probe set specificity. The comparison of experimental and theoretical hybridizations revealed 0.91% false positives and 0.81% false negatives. The microarray detection threshold was estimated at 0.03% of a given DNA type based on DNA spiking experiments. A comparison of the maize rhizosphere and bulk soil hybridization results showed a significant rhizosphere effect, with a higher predominance of Agrobacterium spp. in the rhizosphere, as well as a lower prevalence of Acidobacteria, Bacteroidetes, Verrucomicrobia, and Planctomycetes, a new taxon of interest in soil. In addition, well-known taxonomic groups such as Sphingomonas spp., Rhizobiaceae, and Actinobacteria were identified in both microbial habitats with strong hybridization signals. The taxonomic microarray developed in the present study was able to discriminate and characterize bacterial community composition in related biological samples, offering extensive possibilities for systematic exploration of bacterial diversity in ecosystems.

scholarly journals Effects of Simulated Nitrogen Deposition on the Bacterial Community of Urban Green Spaces

2021 ◽  
Vol 11 (3) ◽  
pp. 918
Author(s):  
Lingzi Mo ◽  
Augusto Zanella ◽  
Xiaohua Chen ◽  
Bin Peng ◽  
Jiahui Lin ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Negative Impact ◽  
Bacterial Community Composition ◽  
N Deposition ◽  
Soil Bacterial Community ◽  
Rrna Gene ◽  
Soil Dna ◽  
Urban Green ◽  
Soil Bacterial

Continuing nitrogen (N) deposition has a wide-ranging impact on terrestrial ecosystems. To test the hypothesis that, under N deposition, bacterial communities could suffer a negative impact, and in a relatively short timeframe, an experiment was carried out for a year in an urban area featuring a cover of Bermuda grass (Cynodon dactylon) and simulating environmental N deposition. NH4NO3 was added as external N source, with four dosages (N0 = 0 kg N ha−2 y−1, N1 = 50 kg N ha−2 y−1, N2 = 100 kg N ha−2 y−1, N3 = 150 kg N ha−2 y−1). We analyzed the bacterial community composition after soil DNA extraction through the pyrosequencing of the 16S rRNA gene amplicons. N deposition resulted in soil bacterial community changes at a clear dosage-dependent rate. Soil bacterial diversity and evenness showed a clear trend of time-dependent decline under repeated N application. Ammonium nitrogen enrichment, either directly or in relation to pH decrease, resulted in the main environmental factor related to the shift of taxa proportions within the urban green space soil bacterial community and qualified as a putative important driver of bacterial diversity abatement. Such an impact on soil life induced by N deposition may pose a serious threat to urban soil ecosystem stability and surrounding areas.

scholarly journals Impacts of the rhizosphere effect and plant species on organic carbon mineralization rates and pathways, and bacterial community composition in a tidal marsh

2019 ◽  
Vol 95 (9) ◽  
Author(s):  
Yuxiu Liu ◽  
Min Luo ◽  
Rongzhong Ye ◽  
Jiafang Huang ◽  
Leilei Xiao ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Bacterial Community ◽  
Plant Species ◽  
Metabolic Pathways ◽  
Tidal Marsh ◽  
Bacterial Community Composition ◽  
Bulk Soil ◽  
Rhizosphere Effect ◽  
Total Bacteria ◽  
Soc Mineralization

ABSTRACT Despite the growing recognition regarding the carbon cycle in the rhizosphere of upland ecosystems, little is known regarding the rhizosphere effect on soil organic carbon (SOC) mineralization in tidal marsh soils. In the current study, in situ rhizobox experiments (including rhizosphere and inner and outer bulk soil) were conducted in an estuarine tidal marsh. Our results showed that a higher abundance of total bacteria, Geobacter, dsrA and mcrA and lower α-diversity were observed in the rhizosphere relative to the bulk soil. Rhizosphere effects shifted the partition of terminal metabolic pathways from sulfate reduction in the bulk soil to the co-dominance of microbial Fe(III) and sulfate reduction in the rhizosphere. Although the rhizosphere effect promoted the rates of three terminal metabolic pathways, it showed greater preference towards microbial Fe(III) reduction in the tidal marsh soils. Plant species had little impact on the partitioning of terminal metabolic pathways, but did affect the potential of total SOC mineralization together with the abundance and diversity of total bacteria. Both the rhizosphere effect and plant species influenced the bacterial community composition in the tidal marsh soils; however, plant species had a less pronounced impact on the bacterial community compared with that of the rhizosphere effect.

scholarly journals Novel Bacterial Lineages at the (Sub)Division Level as Detected by Signature Nucleotide-Targeted Recovery of 16S rRNA Genes from Bulk Soil and Rice Roots of Flooded Rice Microcosms

2001 ◽  
Vol 67 (2) ◽  
pp. 623-631 ◽  
Author(s):  
Manigee Derakshani ◽  
Thomas Lukow ◽  
Werner Liesack
Keyword(s):  
16S Rrna ◽  
Bacterial Diversity ◽  
16S Rdna ◽  
The Other ◽  
Bulk Soil ◽  
Rrna Genes ◽  
Pcr Assay ◽  
Rice Roots ◽  
Flooded Rice ◽  
Bacterial Lineages

ABSTRACT Using a newly developed 16S rRNA gene (rDNA)-targeted PCR assay with proposed group specificity for planctomycetes, we examined anoxic bulk soil of flooded rice microcosms for the presence of novel planctomycete-like diversity. For comparison, oxic rice roots were included as an additional sample in this investigation. The bacterial diversity detectable by this PCR assay was assessed by using a combined approach that included terminal restriction fragment length polymorphism (T-RFLP) analysis and comparative sequence analysis of cloned 16S rDNA. T-RFLP fingerprint patterns generated from rice roots contained 12 distinct terminal restriction fragments (T-RFs). In contrast, the T-RFLP fingerprint patterns obtained from the anoxic bulk soil contained 33 distinct T-RFs, a clearly higher level of complexity. A survey of 176 bulk soil 16S rDNA clone sequences permitted correlation of 20 T-RFs with phylogenetic information. The other 13 T-RFs remained unidentified. The predominant T-RFs obtained from rice roots could be assigned to members of the genus Pirellulawithin the Planctomycetales, while most of the T-RFs obtained from the bulk soil corresponded to novel lines of bacterial descent. Using a level of 16S rDNA sequence dissimilarity to cultured microorganisms of approximately 20% as a threshold value, we detected 11 distinct bacterial lineages for which pure-culture representatives are not known. Four of these lineages could be assigned to the orderPlanctomycetales, while one lineage was affiliated with the division Verrucomicrobia and one lineage was affiliated with the spirochetes. The other five lineages either could not be assigned to any of the main lines of bacterial descent or clearly expanded the known diversity of division level lineages WS3 and OP3. Our results indicate the presence of bacterial diversity at a subdivision and/or division level that has not been detected previously by the so-called universal 16S rDNA PCR assays.

Bacterial diversity in organic and conventional Minas Frescal cheese production using targeted 16S rRNA sequencing

2021 ◽  
pp. 105139
Author(s):  
Anderson Clayton da Silva Abreu ◽  
Marcelo Falsarella Carazzolle ◽  
Bruna Lourenço Crippa ◽  
Giovana Rueda Barboza ◽  
Vera Lúcia Mores Rall ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Diversity ◽  
16S Rrna Sequencing ◽  
Rrna Sequencing ◽  
Cheese Production

Exploring Bacterial Diversity of Endodontic Microbiota by Cloning and Sequencing 16S rRNA

2011 ◽  
Vol 37 (7) ◽  
pp. 922-926 ◽  
Author(s):  
Adriana C. Ribeiro ◽  
Flávia Matarazzo ◽  
Marcelo Faveri ◽  
Denise M. Zezell ◽  
Marcia P.A. Mayer
Keyword(s):  
16S Rrna ◽  
Bacterial Diversity ◽  
Cloning And Sequencing

scholarly journals Respiration of 13C-Labeled Substrates Added to Soil in the Field and Subsequent 16S rRNA Gene Analysis of 13C-Labeled Soil DNA

2003 ◽  
Vol 69 (3) ◽  
pp. 1614-1622 ◽  
Author(s):  
P. Padmanabhan ◽  
S. Padmanabhan ◽  
C. DeRito ◽  
A. Gray ◽  
D. Gannon ◽  
...  
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Gas Chromatography Mass Spectrometry ◽  
Rrna Gene ◽  
Labeled Compounds ◽  
Field Soil ◽  
Soil Dna

ABSTRACT Our goal was to develop a field soil biodegradation assay using 13C-labeled compounds and identify the active microorganisms by analyzing 16S rRNA genes in soil-derived 13C-labeled DNA. Our biodegradation approach sought to minimize microbiological artifacts caused by physical and/or nutritional disturbance of soil associated with sampling and laboratory incubation. The new field-based assay involved the release of 13C-labeled compounds (glucose, phenol, caffeine, and naphthalene) to soil plots, installation of open-bottom glass chambers that covered the soil, and analysis of samples of headspace gases for 13CO2 respiration by gas chromatography/mass spectrometry (GC/MS). We verified that the GC/MS procedure was capable of assessing respiration of the four substrates added (50 ppm) to 5 g of soil in sealed laboratory incubations. Next, we determined background levels of 13CO2 emitted from naturally occurring soil organic matter to chambers inserted into our field soil test plots. We found that the conservative tracer, SF6, that was injected into the headspace rapidly diffused out of the soil chamber and thus would be of little value for computing the efficiency of retaining respired 13CO2. Field respiration assays using all four compounds were completed. Background respiration from soil organic matter interfered with the documentation of in situ respiration of the slowly metabolized (caffeine) and sparingly soluble (naphthalene) compounds. Nonetheless, transient peaks of 13CO2 released in excess of background were found in glucose- and phenol-treated soil within 8 h. Cesium-chloride separation of 13C-labeled soil DNA was followed by PCR amplification and sequencing of 16S rRNA genes from microbial populations involved with 13C-substrate metabolism. A total of 29 full sequences revealed that active populations included relatives of Arthrobacter, Pseudomonas, Acinetobacter, Massilia, Flavobacterium, and Pedobacter spp. for glucose; Pseudomonas, Pantoea, Acinetobacter, Enterobacter, Stenotrophomonas, and Alcaligenes spp. for phenol; Pseudomonas, Acinetobacter, and Variovorax spp. for naphthalene; and Acinetobacter, Enterobacter, Stenotrophomonas, and Pantoea spp. for caffeine.

scholarly journals A Comparison of rpoB and 16S rRNA as Markers in Pyrosequencing Studies of Bacterial Diversity

PLoS ONE ◽  
2012 ◽  
Vol 7 (2) ◽  
pp. e30600 ◽  
Author(s):  
Michiel Vos ◽  
Christopher Quince ◽  
Agata S. Pijl ◽  
Mattias de Hollander ◽  
George A. Kowalchuk
Keyword(s):  
16S Rrna ◽  
Bacterial Diversity

scholarly journals Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by vineyard management

2016 ◽  
Vol 103 ◽  
pp. 337-348 ◽  
Author(s):  
Kayla N. Burns ◽  
Nicholas A. Bokulich ◽  
Dario Cantu ◽  
Rachel F. Greenhut ◽  
Daniel A. Kluepfel ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Soil Bacterial Diversity ◽  
Vineyard Soil ◽  
Soil Bacterial ◽  
Vineyard Management

scholarly journals Analysis of the Bacterial and Fungal Community Profiles in Bulk Soil and Rhizospheres of Three Mungbean [Vigna radiata (L.) R. Wilczek] Genotypes through PCR-DGGE

2020 ◽  
Vol 77 ◽  
pp. 1-26
Author(s):  
Anna Mae M. de los Reyes ◽  
Eureka Teresa M. Ocampo ◽  
Ma. Carmina C. Manuel ◽  
Bernadette C. Mendoza
Keyword(s):  
Plant Growth ◽  
Crop Production ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Diversity Index ◽  
Agricultural Practices ◽  
Fungal Communities ◽  
Bulk Soil ◽  
Initial Assessment ◽  
Rhizosphere Effect ◽  
Soil Microbial Diversity

Each plant species is regarded to substantially influence and thus, select for specific rhizosphere microbial populations. This is considered in the exploitation of soil microbial diversity associated with important crops, which has been of interest in modern agricultural practices for sustainable productivity. This study used PCR-DGGE (polymerase chain reaction - denaturing gradient gel electrophoresis) in order to obtain an initial assessment of the bacterial and fungal communities associated in bulk soil and rhizospheres of different mungbean genotypes under natural field conditions. Integrated use of multivariate analysis and diversity index showed plant growth stage as the primary driver of community shifts in both microbial groups while rhizosphere effect was found to be less discrete in fungal communities. On the other hand, genotype effect was not discerned but not inferred to be absent due to possible lack of manifestations of differences among genotypes based on tolerance to drought under non-stressed environment, and due to detection limits of DGGE. Sequence analysis of prominent members further revealed that Bacillus and Arthrobacter species were dominant in bacterial communities whereas members of Ascomycota and Basidiomycota were common in fungal communities of mungbean. Overall, fungal communities had higher estimated diversity and composition heterogeneity, and were more dynamic under plant growth influence, rhizosphere effect and natural environmental conditions during mungbean growth in upland field. These primary evaluations are prerequisite to understanding the interactions between plant and rhizosphere microorganisms with the intention of employing their potential use for sustainable crop production.

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