Characterization of Bacterial and Fungal Soil Communities by Automated Ribosomal Intergenic Spacer Analysis Fingerprints: Biological and Methodological Variability

Ranjard, Lionel; Poly, Franck; Lata, Jean‐Christophe; Mougel, Christophe; Thioulouse, Jean; Nazaret, Sylvie

doi:10.1128/aem.67.10.4479-4487.2001

Cited by 401 publications

(281 citation statements)

References 30 publications

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“…A preliminary step in the comparison of DNA meta-barcoding and fingerprinting approaches was to post-process the data according to molecular analysis steps specific to each method. For DNA fingerprinting, this was handled by setting a fixed number of OTU bin to be considered during the band profiles analysis (Ranjard et al, 2001(Ranjard et al, , 2013. For the NGS approach, methodological biases (for example, PCRs or sequencing errors), which might generate OTUs of low abundance and equally represented across samples, were removed by bioinformatic filters (Quince et al, 2011) and by two post-processing steps.…”

Section: Discussionmentioning

confidence: 99%

Improving soil bacterial taxa–area relationships assessment using DNA meta-barcoding

et al. 2014

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The evaluation of the taxa-area relationship (TAR) with molecular fingerprinting data demonstrated the spatial structuration of soil microorganisms and provided insights into the processes shaping their diversity. The increasing use of massive sequencing technologies in biodiversity investigations has now raised the question of the advantages of such technologies over the fingerprinting approach for elucidation of the determinism of soil microbial community assembly in broad-scale biogeographic studies. Our objectives in this study were to compare DNA fingerprinting and meta-barcoding approaches for evaluating soil bacterial TAR and the determinism of soil bacterial community assembly on a broad scale. This comparison was performed on 392 soil samples from four French geographic regions with different levels of environmental heterogeneity. Both molecular approaches demonstrated a TAR with a significant slope but, because of its more sensitive description of soil bacterial community richness, meta-barcoding provided significantly higher and more accurate estimates of turnover rates. Both approaches were useful in evidencing the processes shaping bacterial diversity variations on a broad scale. When different taxonomic resolutions were considered for meta-barcoding data, they significantly influenced the estimation of turnover rates but not the relative importance of each component process. Altogether, DNA meta-barcoding provides a more accurate evaluation of the TAR and may lead to re-examination of the processes shaping soil bacterial community assembly. This should provide new insights into soil microbial ecology in the context of sustainable use of soil resources.

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Section: Discussionmentioning

confidence: 99%

Improving soil bacterial taxa–area relationships assessment using DNA meta-barcoding

et al. 2014

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“…In Model I of this study, we concentrated on analysis of the amplified intergenic spacer of the rRNA gene, as have other researchers [46][47][48][49], because of greater variability in amplified intergenic spacer than 16S rRNA. The relative conservation of the 16S rRNA may not identify all the variation in microbial community structure, such as certain species-level variation [46].…”

Section: Model I Of Amazonian Agricultural System: the "Slash-and-burmentioning

confidence: 99%

A Molecular Survey of the Diversity of Microbial Communities in Different Amazonian Agricultural Model Systems

et al. 2010

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Abstract:The processes of land conversion and agricultural intensification are a significant cause of biodiversity loss, with consequent negative effects both on the environment and the sustainability of food production. The anthrosols associated with pre-Colombian settlements in the Amazonian region are examples of how anthropogenic activities may sustain the native populations against harsh tropical environments for human establishment, even without a previous intentionality of anthropic soil formation. In a case study (Model I-"Slash-andBurn") the community structures detected by automated ribosomal intergenic spacer analysis (ARISA) revealed that soil archaeal, bacterial and fungal communities are heterogeneous and each capable of responding differently to environmental characteristics. ARISA data evidenced considerable difference in structure existing between microbial communities in forest and agricultural soils. In a second study (Model II-"Anthropogenic Soil"), the bacterial community structures revealed by terminal restriction fragment length polymorphism (T-RFLP) differed among an Amazonian Dark Earth (ADE), black carbon (BC) and its adjacent non-anthropogenic oxisoil. The bacterial 16S rRNA gene (OTU) richness estimated by pyrosequencing was higher in ADE than BC. The most abundant bacterial phyla in ADE soils and BC were Proteobacteria-24% ADE, 15% BC; Acidobacteria-10% ADE, 21% BC; Actinobacteria-7% ADE, 12% BC; Verrucomicrobia, 8% ADE; 9% BC; Firmicutes-3% ADE, 8% BC. Overall, unclassified bacteria corresponded to 36% ADE, and 26% BC. Regardless of current land uses, our data suggest OPEN ACCESSDiversity 2010, 2 788 that soil microbial community structures may be strongly influenced by the historical soil management and that anthrosols in Amazonia, of anthropogenic origins, in addition to their capacity of enhancing crop yields, may also improve microbial diversity, with the support of the black carbon, which may sustain a particular and unique habitat for the microbes.

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“…Polymerase chain reaction (PCR) was performed using a PTC 100 thermal cycler (MJ Research Inc., Watertown, MA, USA). The ribosomal intergenic spacer region was amplified using primers 1522F (5 0 -TGCGGCTGGAT CCCCTCCTT-3 0 ) and 132R (5 0 -CCGGGTTTCCCCATT CGG-3 0 ) (Ranjard et al, 2001). The final 50 ml reaction mixture contained: 1 Â PCR buffer (Promega, Madison, WI, USA), 4 nmol deoxynucleoside triphosphates, 25 pmol forward and reverse primers, 1.25 units of Taq polymerase (Promega) and B1 ng of template DNA.…”

Section: Identification Of Resistant Bacterial Isolatesmentioning

confidence: 99%

The effects of subtherapeutic antibiotic use in farm animals on the proliferation and persistence of antibiotic resistance among soil bacteria

2007

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The use of antibiotics at subtherapeutic concentrations for agricultural applications is believed to be an important factor in the proliferation of antibiotic-resistant bacteria. The goal of this study was to determine if the application of manure onto agricultural land would result in the proliferation of antibiotic resistance among soil bacteria. Chlortetracycline-resistant bacteria were enumerated and characterized from soils exposed to the manure of animals fed subtherapeutic concentrations of antibiotics and compared to the chlortetracycline-resistant bacteria from soils at farms with restricted antibiotic use (dairy farms) and from non-agricultural soils. No significant differences were observed at nine different study sites with respect to the numbers and types of cultivated chlortetracycline-resistant bacteria. Genes encoding for tetracycline resistance were rarely detected in the resistant bacteria from these sites. In contrast, soils collected from a tenth farm, which allowed manure to indiscriminately accumulate outside the animal pen, had significantly higher chlortetracycline-resistance levels. These resistant bacteria frequently harbored one of 14 different genes encoding for tetracycline resistance, many of which (especially tet(A) and tet(L)) were detected in numerous different bacterial species. Subsequent bacterial enumerations at this site, following the cessation of farming activity, suggested that this farm remained a hotspot for antibiotic resistance. In conclusion, we speculate that excessive application of animal manure leads to the spread of resistance to soil bacteria (potentially by lateral gene transfer), which then serve as persistent reservoir of antibiotic resistance.

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Characterization of Bacterial and Fungal Soil Communities by Automated Ribosomal Intergenic Spacer Analysis Fingerprints: Biological and Methodological Variability

Cited by 401 publications

References 30 publications

Improving soil bacterial taxa–area relationships assessment using DNA meta-barcoding

Improving soil bacterial taxa–area relationships assessment using DNA meta-barcoding

A Molecular Survey of the Diversity of Microbial Communities in Different Amazonian Agricultural Model Systems

The effects of subtherapeutic antibiotic use in farm animals on the proliferation and persistence of antibiotic resistance among soil bacteria

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