Microbial diversity and mineral composition of weathered serpentine rock of the Khalilovsky massif

Our plain-English summary of Microbial diversity and mineral composition of weathered serpentine rock of the Khalilovsky massif, by I.V. Khilyas, A.V. Sorokina, A.A. Elistratova, et al (PloS One, 2019).

The study

• Authors: I.V. Khilyas, A.V. Sorokina, A.A. Elistratova, M.I. Markelova, M.N. Siniagina, M.R. Sharipova, T.A. Shcherbakova, M.E. D'Errico, M.F. Cohen
• Journal: PloS One
• Published: 2019;14(12):e0225929
• Cited by: 17 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

Endolithic microbial communities survive nutrient and energy deficient conditions while contributing to the weathering of their mineral substrate. This study examined the mineral composition and microbial communities of fully serpentinized weathered rock from 0.1 to 6.5 m depth at a site within the Khalilovsky massif, Orenburg Region, Southern Ural Mountains, Russia. The mineral composition includes a major content of serpentinite family (mostly consisting of lizardite and chrysotile), magnesium hydrocarbonates (hydromagnesite with lesser amounts of hydrotalcite and pyroaurite) concentrated in the upper layers, and clay minerals. We found that the deep-seated weathered serpentinites are chrysotile-type minerals, while the middle and surface serpentinites mostly consist of lizardite and chrysotile types. Microbial community analysis, based on 16S rRNA gene sequencing, showed a similar diversity of phyla throughout the depth profile. The dominant bacterial phyla were the Actinobacteria (of which unclassified genera in the orders Acidimicrobiales and Actinomycetales were most numerous), Chloroflexi (dominated by an uncultured P2-11E order) and the Proteobacteria (predominantly class Betaproteobacteria). Densities of several groups of bacteria were negatively correlated with depth. Occurrence of the orders Actinomycetales, Gaiellales, Solirubrobacterales, Rhizobiales and Burkholderiales were positively correlated with depth. Our findings show that endolithic microbial communities of the Khalilovsky massif have similar diversity to those of serpentine soils and rocks, but are substantially different from those of the aqueous environments of actively serpentinizing systems.

In plain English

This study examined rock, not people. The authors drilled a single core 6.85 m deep from weathered serpentine rock in the central Khalilovsky massif, Orenburg Region, Russia, in August 2017. They analyzed the minerals at depths from 0.1 m to 6.85 m and identified the bacteria in the rock by DNA (16S rRNA gene) sequencing. Averaged over duplicate samples, serpentinite minerals made up 72.3 ±2.5% at 0.1 m and 93.5 ±1.1% at 6.85 m, while magnesium hydrocarbonate minerals decreased with depth. Near the surface the serpentine was mostly plate-shaped lizardite with a few fibers. At 6.85 m the authors saw hollow, needle-shaped fibers characteristic of chrysotile. At the phylum level the bacterial communities were similar at all depths, with Actinobacteria, Proteobacteria and Chloroflexi most abundant, although dominant orders and genera differed and some groups changed with depth. Genes linked to methane production and hydrogen metabolism were not detected. The authors concluded that these communities differed substantially from those in water at actively serpentinizing sites and resembled those of fully serpentinized rock surfaces and soils. They could not tell whether the microbes helped deposit hydromagnesite.

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 study of one rock core, combining mineral analysis (X-ray diffraction, scanning and transmission electron microscopy, elemental analysis) with 16S rRNA gene sequencing of the bacteria in the rock
• Who was studied: Duplicate samples taken at depths from 0.1 m to 6.85 m from a single core of weathered serpentine rock with no soil cover, drilled in the central part of the Khalilovsky massif, Orenburg Region, Southern Ural Mountains, Russia, in August 2017. No people were studied.
• Exposure: Not a study of human exposure. The material studied was fully serpentinized weathered rock made up of serpentinite minerals (lizardite and chrysotile), hydromagnesite, hydrotalcite-type and pyroaurite group minerals, clay minerals and traces of calcite.
• Main results:
  • Serpentinite minerals increased with depth, from 72.3 ±2.5% at 0.1 m to 93.5 ±1.1% at 6.85 m (means with ranges of duplicate samples). Magnesium hydrocarbonate minerals decreased with depth: hydromagnesite was 15.1 ±1% at 0.1 m and absent at 6.85 m.
  • At 0.1 m depth the serpentinite showed a plate-like shape characteristic of lizardite, with a minor inclusion of cylindrical fibers. At 6.85 m depth it showed oriented, needle-shaped hollow fibers (nanotubes) characteristic of chrysotile.
  • Particle sizes in the samples ranged from less than 1 μm to greater than 200 μm.
  • Nickel and chromium were detected in the upper layers and only nickel in the middle layers. Neither was found in the deepest serpentinites.
  • Community composition was similar at all depths at the phylum/class level. Of 31 phyla found, Actinobacteria, Proteobacteria and Chloroflexi were the most abundant in all samples. Differences were found in dominant orders and genera.
  • An unclassified genus of the order Acidimicrobiales made up 11.0% to 38.0% of all OTU sequences, and the order Actinomycetales made up 9.9% to 21.5% of OTUs.
  • Microbial communities from the different depths were closely related.
  • Certain orders were positively correlated with depth: Acidimicrobiales, Gaiellales, Solirubrobacterales, Gemmatimonadetes, Rhizobiales, Burkholderiales, P2-11E, and unidentified members related to GAL15. Several other orders were negatively correlated with depth.
  • The mcrA gene (an indicator of methane production) and the hydA gene (a marker of bacterial hydrogen metabolism) were not detected. The hydrogen-oxidizing genus Hydrogenophaga did not exceed 0.26% of sequences in any core sample.
• The authors' conclusion: The authors concluded that the rock-core microbial communities were substantially different from those of aqueous serpentine environments and relatively close to those of fully serpentinized rock surfaces and soils, notably in the predominance of Actinobacteria. They also stated that the microbial community does not appear to substantially alter its serpentine mineral substrate.
• Limitations the authors state:
  • The authors stated that their results cannot show whether the microbes in the rock fissures contributed to hydromagnesite deposition.
  • The authors stated that the reason particular bacterial groups dominate in this habitat remains to be determined.

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, Serpentinite, Lizardite, Chrysotile.

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• Microbial diversity in The Cedars, an ultrabasic, ultrareducing, and low salinity serpentinizing ecosystem — S. Suzuki, S. Ishii, et al. (2013)
• Weathering of chrysotile asbestos by the serpentine rock-inhabiting fungus Verticillium leptobactrum — S. Daghino, F. Turci, et al. (2009)
• Serpentine soils do not limit mycorrhizal fungal diversity — S. Branco, R.H. Ree (2010)
• Serpentine soils promote ectomycorrhizal fungal diversity — S. Branco (2010)

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