Fungal diversity is not determined by mineral and chemical differences in serpentine substrates

Our plain-English summary of Fungal diversity is not determined by mineral and chemical differences in serpentine substrates, by S. Daghino, C. Murat, E. Sizzano, et al (PloS One, 2012).

The study

• Authors: S. Daghino, C. Murat, E. Sizzano, M. Girlanda, S. Perotto
• Journal: PloS One
• Published: 2012;7(9):e44233
• Cited by: 13 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

The physico-chemical properties of serpentine soils lead to strong selection of plant species. Whereas many studies have described the serpentine flora, little information is available on the fungal communities dwelling in these sites. Asbestos minerals, often associated with serpentine rocks, can be weathered by serpentine-isolated fungi, suggesting an adaptation to this substrate. In this study, we have investigated whether serpentine substrates characterized by the presence of rocks with distinct mineral composition could select for different fungal communities. Both fungal isolation and 454 pyrosequencing of amplicons obtained from serpentine samples following direct DNA extraction revealed some fungal taxa shared by the four ophiolitic substrates, but also highlighted several substrate-specific taxa. Bootstrap analysis of 454 OTU abundances indicated weak clustering of fungal assemblages from the different substrates, which did not match substrate classification based on exchangeable macronutrients and metals. Intra-substrate variability, as assessed by DGGE profiles, was similar across the four serpentine substrates, and comparable to inter-substrate variability. These findings indicate the absence of a correlation between the substrate (mineral composition and available cations) and the diversity of the fungal community. Comparison of culture-based and culture-independent methods supports the higher taxonomic precision of the former, as complementation of the better performance of the latter.

In plain English

This was a field and laboratory study of fungi living on serpentine rock, not a study of human health. The authors collected 15 samples of rock debris, sometimes mixed with soil, from four sites in the Western Alps of Italy. Each site had different fibrous minerals: chrysotile with balangeroite at the disused Balangero asbestos mine, tremolite at Jouvenceaux, tremolite with antigorite at Mompantero, and chrysotile with carlosturanite at Confine. The authors grew fungi on plates, sequenced fungal DNA taken directly from the samples, and compared DNA fingerprint patterns. Some fungi were shared by all four sites and some were found at only one. Groupings of the fungal communities by site were weakly supported and did not match the sites' chemical differences. Variation within a site did not differ significantly from variation between sites. A fungus the authors had found abundant at Balangero in 2003, Verticillium leptobactrum, was not grown from Balangero samples this time. The authors concluded that fungal diversity and distribution were independent of substrate composition.

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 field survey with laboratory analysis: fungi were grown from samples on culture plates (dilution plate method), fungal DNA was extracted directly and sequenced (454 pyrosequencing of the ITS1 and ITS2 regions), DNA fingerprinting (DGGE) was done, and the samples were analysed chemically.
• Who was studied: 15 samples of rock fragments or debris, in some cases mixed with soil. Four samples each came from Balangero (BALA), Jouvenceaux (JOUV) and Confine in the Varaita Valley (VARA), and three from Mompantero (MOMP), all in the Western Alps, Italy. Two sites were disused asbestos mines and two were natural sites.
• Exposure: No human exposure was studied. The sites differed in their fibrous minerals: chrysotile with balangeroite (BALA), tremolite (JOUV), tremolite with antigorite, described as non-asbestos (MOMP), and chrysotile with carlosturanite (VARA). They also differed in extractable nutrients and metals.
• Main results:
  • Chemically, the VARA samples were set apart from the other sites (56% bootstrap support). BALA samples contained significantly more nickel and copper than the other samples.
  • DNA sequencing of all four sites combined gave 4,952 ITS1 reads, grouped into 791 OTUs (taxonomic units), of which 405 were represented by a single read.
  • Both culturing and DNA sequencing found some fungal taxa shared by all four substrates and several taxa found on only one substrate.
  • Clustering of the fungal communities by site was weak, with low bootstrap support (less than 60%), and did not match the sites' classification by nutrient and metal content.
  • In DNA fingerprinting, similarity among samples from the same site did not differ significantly between the four sites (P = 0.985).
  • Overall similarity between sites did not differ significantly from overall similarity within sites (P = 0.984).
  • Ten of the twelve fungal taxa grown in culture were also detected by DNA sequencing at the same site.
  • Verticillium leptobactrum was not grown from the Balangero samples. Only two DNA units (22 reads), all from the Jouvenceaux site, grouped with this species. The authors had found it very abundant at Balangero in a 2003 sampling.
• The authors' conclusion: The authors concluded that fungal diversity and distribution were independent of substrate composition. They also suggested that rapid changes in serpentine fungal communities may follow disturbance, and that restoration work at the Balangero mine may have affected rare species such as V. leptobactrum.
• Limitations the authors state:
  • Only a small number of fungal types grown in culture were examined.
  • Where samples were collected from the ground with soil, root pieces may have been present in them.
  • Sequencing depth was limited on purpose. The aim was to compare the dominant fungi, not to describe all species.
  • Identification of fungi from DNA sequence matching was less precise than identification by their appearance, partly because public sequence databases are incomplete.
  • When single-read units were included, the sampling curves did not level off, meaning not all diversity was captured.

Mines named here

Asbestos mines this study is about. Each mine's page says who ran it, when it worked, and what it produced.

• Balangero mine, Balangero, about 20 km north of Turin, Piedmont

All asbestos mines

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, Asbestos, Cation.

Related studies

• Serpentine soils do not limit mycorrhizal fungal diversity — S. Branco, R.H. Ree (2010)
• Microbial diversity and mineral composition of weathered serpentine rock of the Khalilovsky massif — I.V. Khilyas, A.V. Sorokina, et al. (2019)
• Serpentine soils promote ectomycorrhizal fungal diversity — S. Branco (2010)
• Soil fungal hyphae bind and attack asbestos fibers — E. Martino, L. Prandi, et al. (2003)
• Weathering of chrysotile asbestos by the serpentine rock-inhabiting fungus Verticillium leptobactrum — S. Daghino, F. Turci, et al. (2009)
• Occurrence of heavy metal-resistance in microflora from serpentine soil of Andaman — A. Pal, S. Dutta, et al. (2005)

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