Microbiomes of different ages in Rendzic Leptosols in the Crimean Peninsula

Anastasiia K Kimeklis; Grigory V Gladkov; Aleksei O Zverev; Arina A Kichko; Evgeny E Andronov; Elena I Ergina; Igor V Kostenko; Evgeny V Abakumov

doi:10.7717/peerj.10871

Microbiomes of different ages in Rendzic Leptosols in the Crimean Peninsula

PeerJ. 2021 Feb 18:9:e10871. doi: 10.7717/peerj.10871. eCollection 2021.

Authors

Anastasiia K Kimeklis^#^{1

2}, Grigory V Gladkov^#^{1

2}, Aleksei O Zverev^{1

2}, Arina A Kichko^{1

2}, Evgeny E Andronov^{2

3

4}, Elena I Ergina⁵, Igor V Kostenko⁶, Evgeny V Abakumov^{1

2}

Affiliations

¹ Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia.
² Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia.
³ Genetics and Biotechnology, St. Petersburg State University, Saint-Petersburg, Russia.
⁴ V.V. Dokuchaev Soil Science Institute, Moscow, Russia.
⁵ V.I. Vernadsky Crimean Federal University, Simferopol, Russia.
⁶ Nikitsky Botanical Garden -National Scientific Center, Yalta, Russia.

^# Contributed equally.

Abstract

Rendzic Leptosols are intrazonal soils formed on limestone bedrock. The specialty of these soils is that parent rock material is more influential in shaping soil characteristics than zonal factors such as climate, especially during soil formation. Unlike fast evolving Podzols due to their leaching regime, Leptosols do not undergo rapid development due to the nature of the limestone. Little is known how microbiome reflects this process, so we assessed microbiome composition of Rendzic Leptosols of different ages, arising from disruption and subsequent reclamation. The mountains and foothills that cover much of the Crimean Peninsula are ideal for this type of study, as the soils were formed on limestone and have been subjected to anthropogenic impacts through much of human history. Microbiomes of four soil sites forming a chronosequence, including different soil horizons, were studied using sequencing of 16S rRNA gene libraries and quantitative PCR. Dominant phyla for all soil sites were Actinobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, Thaumarchaeota, Planctomycetes, Verrucomicrobia and Firmicutes. Alpha diversity was similar across sites and tended to be higher in topsoil. Beta diversity showed that microbiomes diverged according to the soil site and the soil horizon. The oldest and the youngest soils had the most similar microbiomes, which could have been caused by their geographic proximity. Oligotrophic bacteria from Chitinophagaceae, Blastocatellaceae and Rubrobacteriaceae dominated the microbiome of these soils. The microbiome of 700-year old soil was the most diverse. This soil was from the only study location with topsoil formed by plant litter, which provided additional nutrients and could have been the driving force of this differentiation. Consistent with this assumption, this soil was abundant in copiotrophic bacteria from Proteobacteria and Actinobacteria phyla. The microbiome of 50-year old Leptosol was more similar to the microbiome of benchmark soil than the microbiome of 700-year old soil, especially by weighted metrics. CCA analysis, in combination with PERMANOVA, linked differences in microbiomes to the joint change of all soil chemical parameters between soil horizons. Local factors, such as parent material and plant litter, more strongly influenced the microbiome composition in Rendzic Leptosols than soil age.

Keywords: 16S rRNA library sequencing; Chronosequence; Pedogenesis; Rendzic Leptosol; Soil liming; Soil microbiome.

Grants and funding

This work was supported by the grant of the Russian Scientific Foundation, project 17-16-01030. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.