Internal Transcribed Spacer and 16S Amplicon Sequencing Identifies Microbial Species Associated with Asbestos in New Zealand

Our plain-English summary of Internal Transcribed Spacer and 16S Amplicon Sequencing Identifies Microbial Species Associated with Asbestos in New Zealand, by E. Doyle, D. Blanchon, S. Wells, et al (Genes, 2023).

The study

• Authors: E. Doyle, D. Blanchon, S. Wells, P. de Lange, P. Lockhart, N. Waipara, M. Manefield, S. Wallis, T.A. Berry
• Journal: Genes
• Published: 2023;14(3)
• Read it: PubMed · Publisher · Free full text

Abstract

Inhalation of asbestos fibres can cause lung inflammation and the later development of asbestosis, lung cancer, and mesothelioma, and the use of asbestos is banned in many countries. In most countries, large amounts of asbestos exists within building stock, buried in landfills, and in contaminated soil. Mechanical, thermal, and chemical treatment options do exist, but these are expensive, and they are not effective for contaminated soil, where only small numbers of asbestos fibres may be present in a large volume of soil. Research has been underway for the last 20 years into the potential use of microbial action to remove iron and other metal cations from the surface of asbestos fibres to reduce their toxicity. To access sufficient iron for metabolism, many bacteria and fungi produce organic acids, or iron-chelating siderophores, and in a growing number of experiments these have been found to degrade asbestos fibres in vitro. This paper uses the internal transcribed spacer (ITS) and 16S amplicon sequencing to investigate the fungal and bacterial diversity found on naturally-occurring asbestos minerals, asbestos-containing building materials, and asbestos-contaminated soils with a view to later selectively culturing promising species, screening them for siderophore production, and testing them with asbestos fibres in vitro. After filtering, 895 ITS and 1265 16S amplicon sequencing variants (ASVs) were detected across the 38 samples, corresponding to a range of fungal, bacteria, cyanobacterial, and lichenized fungal species. Samples from Auckland (North Island, New Zealand) asbestos cement, Auckland asbestos-contaminated soils, and raw asbestos rocks from Kahurangi National Park (South Island, New Zealand) were comprised of very different microbial communities. Five of the fungal species detected in this study are known to produce siderophores.

In plain English

This study used DNA sequencing (ITS sequencing for fungi, 16S sequencing for bacteria) to identify the fungi and bacteria whose DNA was found in biofilms on asbestos-bearing materials and in asbestos-contaminated soils in New Zealand. It studied microbes, not people or disease. The authors took ten spatially separated biofilm samples from chrysotile-bearing rocks at an asbestos mine in Kahurangi National Park (South Island) in February 2022. They also sampled asbestos cement building materials and asbestos-contaminated soils in Auckland. After filtering, the fungal dataset held 819 sequence variants across 36 samples and the bacterial dataset 1003 variants across 35 samples. Each of the three sample types carried a distinct microbial community. On the mine rocks, bacteria were dominated by cyanobacteria. On the building materials, bacteria were mainly actinomycetes such as Rubrobacter. In the soils, no lichen fungi or cyanobacteria were detected. Five fungal species found here had already been reported by others as producing siderophores, which are iron-binding compounds. This study did not test that ability. The authors plan to culture species, screen them for siderophores and test them with asbestos fibres. The article's sample and variant counts differ from its abstract.

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: Environmental DNA survey (ITS and 16S amplicon sequencing) of microbial communities on asbestos-bearing materials; no human or animal subjects
• Who was studied: Biofilm and soil samples: 10 spatially separated biofilm samples from an asbestos mine in Kahurangi National Park, South Island, New Zealand (February 2022), plus biofilms from asbestos cement building materials and soil samples from three sites in the Auckland region. The tables list 18 building-material, 10 raw asbestos and 8 (ITS) or 7 (16S) soil samples.
• Exposure: Asbestos-bearing substrates: chrysotile-bearing rocks in mine tailings, asbestos-containing building materials (cladding and Super 6 roofing), and asbestos-contaminated soil
• Main results:
  • Fungal (ITS) dataset after filtering: 490,663 reads belonging to 819 sequence variants across 36 samples
  • Bacterial (16S) dataset: 287,686 reads belonging to 1003 sequence variants. One soil sample (Soil02) gave no 16S reads, leaving 35 samples.
  • Fungal and bacterial communities separated distinctly by sample type (stress 0.14 for both datasets)
  • Mine tailings samples were the most similar to one another and the most different from the other sample types
  • In building-material (ACM) samples, 608 of 639 (95.15%) bacterial sequence variants were not found in the other sample types
  • In raw asbestos (mine) samples, 269 of 287 (93.73%) fungal sequence variants were not found in the other sample types
  • Bacteria in the raw asbestos fibre biofilms (Kahurangi mine) were dominated by cyanobacteria, mainly Chroococcidiopsis
  • Bacteria in the ACM biofilms were mainly actinomycetes, particularly the genus Rubrobacter
  • In asbestos-contaminated soil samples, no lichenized fungi and no cyanobacteria were detected
  • The authors suggested that two polypore fungi detected in the mine biofilms may reflect spores or other material from the surrounding forest being deposited in the biofilms
  • Five fungal species detected in this study (Cladosporium cladosporioides, E. nigrum, F. oxysporum, S. ruberrimus and Y. lipolytica) had been reported in other published work as producing siderophores in vitro. This study did not test siderophore production.
• The authors' conclusion: The authors concluded that the sampled asbestos-containing sites hold a diverse range of fungi and bacteria, five of which were previously reported to produce siderophores. They plan to culture these species, screen them for siderophore production and test them with asbestos fibres in vitro.
• Limitations the authors state:
  • The low bacterial diversity in the soil samples may reflect a lower total read count after filtering of lower-quality sequences, which may have given insufficient information for identification

Topics

Medical terms in this study, explained in our Lexicon: Inflammation, Lung Cancer, Mesothelioma, Cation, Asbestos, Asbestos-Cement.

Related studies

• Siderophore-mediated iron removal from chrysotile: Implications for asbestos toxicity reduction and bioremediation — S.K. Mohanty, C. Gonneau, et al. (2018)
• Engineering siderophore production in Pseudomonas to improve asbestos weathering — M. Lemare, H. Puja, et al. (2022)
• Iron removal from raw asbestos by siderophores-producing Pseudomonas — S.R. David, D. Ihiawakrim, et al. (2020)
• Biodeterioration of asbestos cement by siderophore-producing Pseudomonas — S.R. David, A. Jaouen, et al. (2021)
• RNA sequencing identifies fusion of the EWSR1 and YY1 genes in mesothelioma with t(14;22)(q32;q12) — I. Panagopoulos, J. Thorsen, et al. (2013)
• Next-generation sequencing informs diagnosis and identifies unexpected therapeutic targets in lung squamous cell carcinomas — J.M. Sands, T. Nguyen, et al. (2020)

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