Comparison of 16S rRNA and 16S rDNA T-RFLP approaches to study bacterial communities in soil microcosms treated with chromate as perturbing agent

Our plain-English summary of Comparison of 16S rRNA and 16S rDNA T-RFLP approaches to study bacterial communities in soil microcosms treated with chromate as perturbing agent, by A. Mengoni, E. Tatti, F. Decorosi, et al (Microbial Ecology, 2005).

The study

• Authors: A. Mengoni, E. Tatti, F. Decorosi, C. Viti, M. Bazzicalupo, L. Giovannetti
• Journal: Microbial Ecology
• Published: 2005;50(3):375-84
• Cited by: 30 articles, as counted by NIH iCite
• Read it: PubMed · Publisher

Abstract

Transcripts of ribosomal RNA have been used for assessing the structure and dynamics of active bacterial populations; however, it remains unclear whether the information provided by community profiling derived from RNA is different from that derived from DNA, particularly when a selective pressure is applied on the bacterial community. In the present work, terminal-restriction fragment length polymorphism (T-RFLP) community profiles based on DNA and RNA extracted from soil microcosms treated with a toxic concentration of chromate were compared. Microcosms of a nonpolluted agricultural soil and of a heavy-metal-rich soil (serpentine) were treated with chromate and DNA and RNA were extracted. T-RFLP analysis was performed on amplified and retro-amplified 16SrRNA gene sequences, and band profiles obtained from samples of DNA and of RNA were compared. Some of the T-RFLP bands, identified as peculiar peaks in the profiles, were cloned and sequenced for taxonomic interpretation. Results indicated that: (1) community profiles derived from RNA and DNA were partly overlapping; (2) there was a strong correlation between the dynamics shown by RNA- and DNA-based T-RFLP profiles; (3) chromate addition exerted a clear effect on both agricultural and serpentine soil bacterial communities, either at the DNA and at the RNA level; however, the profiles derived from RNA showed sharper differences between treated and control samples than that of DNA-based profiles.

In plain English

This laboratory study was not about asbestos or human health. It examined soil bacteria exposed to chromate, a toxic form of chromium. The authors used two soils collected in May 2003: one from a heavy-metal-rich serpentine outcrop and one from agricultural land never treated with heavy metals. Part of each soil was treated with potassium chromate to 250 mg of Cr(VI) per kg of dry soil, and the controls received water. Samples were taken after 60 hours, 1 week and 2 weeks. The authors compared bacterial community fingerprints (T-RFLP) made from DNA with fingerprints made from RNA. The DNA-based and RNA-based profiles shared 56 to 58% of their fragments. Changes in the two kinds of profile were significantly correlated (r = 0.43 for serpentine soil, r = 0.58 for agricultural soil). In both soils, chromate-treated samples mostly grouped apart from controls, and RNA-based profiles separated them more clearly. The authors concluded that the two approaches may be complementary tools. They noted that technical biases from extraction and reverse transcription could not be excluded.

We wrote this plain-English summary from the full article with the help of AI, and a second AI model checked each sentence against the article. It is not the authors' wording; the abstract and the article are their own account.

What the study did and found

• Design: Laboratory soil microcosm experiment comparing DNA-based and RNA-based (16S rDNA and 16S rRNA) T-RFLP bacterial community profiles in chromate-treated and control soils
• Who was studied: Bacterial communities in two soils: a heavy-metal-rich serpentine soil (Galceti) and an agricultural soil never treated with heavy metals (Cerbaia). Both were collected in May 2003 from the upper 20 cm of soil.
• Exposure: Potassium chromate (K2CrO4) solution added to reach a final Cr(VI) concentration of 250 mg per kg of soil dry weight. Controls received deionized water. Sampling took place at 60 h, 1 week and 2 weeks.
• Main results:
  • A total of 72 different terminal-restriction fragments (TRFs) were scored in the agricultural soil microcosms and 79 in the serpentine soil microcosms.
  • In both soils, 56 to 58% of TRFs were shared between DNA- and RNA-based profiles. Agricultural soil: 40 shared (56%), 24 DNA-exclusive (33%), 8 RNA-exclusive (11%). Serpentine soil: 46 shared (58%), 18 DNA-exclusive (23%), 15 RNA-exclusive (19%).
  • Mantel's tests showed significant correlation between DNA- and RNA-based dynamics: r = 0.43, p less than 0.05 for serpentine soil microcosms; r = 0.58, p less than 0.005 for agricultural soil microcosms.
  • In principal component analysis, control samples from both soils mainly grouped apart from chromate-treated samples.
  • RNA-based profiles separated treated and untreated samples more clearly than DNA-based profiles. For the serpentine soil, separation of RNA-based profiles was more pronounced.
  • Fewer ribotypes were detected from RNA than from DNA only in the agricultural soil microcosms.
  • Of nine TRFs cloned and sequenced from serpentine soil samples taken 1 week after treatment, six were interpreted as possibly belonging to alpha-proteobacteria, especially Sphingomonadaceae.
• The authors' conclusion: The authors concluded that rRNA- and rDNA-based analyses may be considered complementary tools for studying bacterial community structure and dynamics.
• Limitations the authors state:
  • Technical biases from the extraction and reverse transcription steps cannot be excluded for real, more complex bacterial communities.
  • The differences seen between the two soil types cannot yet be fully explained.
  • More in-depth analyses are needed to interpret the lower RNA-based ribotype counts in agricultural soil.

Topics

The National Library of Medicine indexes this study under subjects our site covers: Chrysotile.

Medical terms in this study, explained in our Lexicon: Serpentine Group.

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