Metagenomic assessment of the ecological functions of the soil: analysis of the soil microbiota associated with the gigantism of the plants of the Chernevaya Taiga of Siberia

RSF («Conducting basic research and exploratory research by individual research groups»), 2019-2021, # 19-16-00049

Grant PI:
Alla Lapidus (SPbU)

Co-PI(s):
Evgeniy Abakumov (SPbU)
Anastasia Kulemzina (ICG SB RAS)
Mikhail Rayko (SPbU)

Participants:
Evgeniy Andronov (FSBSI RRIAM, SPbU)
Nikolay Laschinsky (Central-Siberian Botanical Garden)
Georgy Istigichev (TSU; TomskNIPIneft)
Anton Korobeynikov (SPbU)
Alexey Gurevich (SPbU)
Alexey Smirnov (SPbU)
Anna Glotova (SPbU)

Global changes in the environment and climate, food and energy shortages, loss of biodiversity and the sustainability of ecosystems are among the most important problems of the current century. As a result, modern humanity should be engaged in the preservation and protection of soil, since soil resources are the basis of the food and ecological security of the nation. Prolonged use of soil in agricultural production has a wide range of negative consequences for soil properties, among them: degradation of organic matter, increased greenhouse gas emissions, changes in soil acidity, soil depletion, etc. Use of agricultural technologies (plowing and loosening, use of mineral and organic fertilizers, etc.) causes a significant change in the biogeochemical cycles performed by a complex of soil microorganisms. In this sense, the soils of the chernevaya taiga represent a unique model that is distinguished not only by extremely high fertility, realized from internal biotic and abiotic resources, and not by agrotechnical methods, but also by the preserved “pre-agricultural” microbiome, not affected by the long-term agricultural practices.

The soil microbiota plays a decisive role in maintaining the homeostasis of the soil ecosystem, performing key functions in ensuring the growth and development of plants and actively participating in the carbon cycle. As a part of the existing scientific paradigm, soil organic matter is predominantly microbial in origin and consists of individual chemicals combined by non-covalent bonds to humic assemblies (Kleber, Johnson, 2010; Piccolo, 2002; Schmidt et al., 2011; Simpson et al., 2007; Von Lützow et al., 2006; Von Lützow et al., 2007; Von Lützow et al., 2008). The study of the kinetics and dynamics of the processes of microbial transformation of organic substances under the different soil conditions is the basis for solving the problem of rational use of soil fertility and limiting CO2 emissions to the atmosphere during agricultural use of soil (Janzen, 2006). Understanding the transformation of organic matter in soil and managing the soil carbon balance is a priority for modern farming systems and agricultural technologies, since it is organic matter that is responsible for numerous soil properties, including agroecosystem functioning and crop productivity of agricultural plants (Gattinger et al, 2012; Powlson et al, 2011).

The use of metagenomic approaches for monitoring soil ecosystems will significantly change our understanding of the diversity and functional role of the microbiome in maintaining the soil health. The change in the stocks of organic carbon (Corg) is one of the most important indicators of ecosystem activity (SemenioJanzen et al., 2011). Even small changes in organic carbon stocks can lead to disproportionately large positive or negative effects on key soil properties. In this case, the peculiarities of the soil microbiome, the main driver of the processes of transformation and mineralization of organic matter, can serve as a universal and very sensitive indicator of the state of the soil, including the optimization and “biologization” of farming systems (Pershina et al., 2018, Ivanova et al., 2017, Pershina et al., 2015, Chirac et al., 2013). The development of new approaches to assess the impact of agrobiotechnologies on soil health and quality, combined with the metagenomic characteristics and indication of the transformation of organic matter in the soil, is one of the most promising direction for diagnostics the state of organic carbon flux in terrestrial ecosystems, and, consequently, the state of the soil as a whole.

In the past decade, several global projects have been initiated to study the soil microbiomes, the most famous of them is the Earth Microbiome project (http://www.earthmicrobiome.org/). One of the features of this project is the absence of soil samples from Russia. It is necessary to recognize that, despite the importance of microbiome research in all areas of fundamental and applied biology, Russia, admittedly, is not yet in any acceptable positions in the field of metagenomic research. Within the framework of this project, it is proposed to drastically improve the current situation by creating a modern metagenomics laboratory at St. Petersburg State University and developing newest research programs for studying microbiota that will fill gaps in understanding important processes carried out by microorganisms. Significant assistance in the implementation of this project will be provided by the use of an unprecedented diversity of Russian soils, often formed under unique natural conditions and possessing great agricultural and ecological importance.

The main goal of the project is not to copy or compete with existing metagenomic projects implemented in North America or Europe, but to develop and implement original approaches to the study of soil metagenomes, which will allow obtaining qualitatively new and practically significant biological knowledge. From this point of view, the obtaining of sequencing data using modern high-performance technologies is only the starting point and the basis for further analysis. The results of this analysis should be practically significant and supported by appropriate agrochemical, geological and biochemical analyzes, as well as be accompanied by further experimental studies.

As it was already noted, the backlog of domestic science in the field of metagenomics is very large, so the achievement of compliance with the world level, high scientific and social significance of the project can be achieved through the use of unique objects. Without a doubt, such an object is the soil of chernevaya taiga. The analysis of the peculiarities of the soil, the height of grasses in which, without using any fertilizers or agrotechnical measures, can reach 2 m, will certainly cause public interest. And if the fundamentals of such properties (presumably rooted in the taxonomic and functional structure of the microbiome) are thoroughly studied and understood, then in the future, you can expect to receive specific microbial preparations that can at least partially incorporate the unique properties of chernevaya taiga soils into traditional farming practice. This may be especially relevant for such agro technics as “zero treatment”, which is in many respects typologically similar to the conditions of vegetation in the chernevaya taiga. The potential of chernevaya -taiga microbiome may have an invaluable impact on the creation of new types of drugs that provide fast and effective decomposition of crop residues. In turn, the value of the analysis of previously unexplored unique soils for the search for new biologically active compounds is difficult to overestimate. The basis of many modern antibiotics are biologically active compounds of natural origin. Since the main producers of such molecules are plants and microorganisms, the analysis of soil samples with a wide variety of bacteria living in them has great potential for the detection of new biologically active substances. The results of this study will be relevant not only in terms of creating new drugs, but also for a fundamental scientific understanding of the process of synthesizing such compounds in bacteria.

Thus, the realization of the hidden potential of unique objects is one of the most promising directions in Russian metagenomic studies.

Media about the project

Scientists will find out the reasons for the gigantism of plants in the “Siberian jungle” (in Russian)

Software created within the project scope

MetaplasmidSPAdes: a method for plasmid detection and assembly in genomic and metagenomic data sets. Antipov, Raiko, Lapidus, Pevzner. Genome Research, 2019.
NPS: an MS/MS-based approach for accurate peptidic natural product (PNP) discovery. Tagirdzhanov, Shlemov, Gurevich. Bioinformatics, 2019
MetaMiner: a peptidogenomics approach for the discovery of ribosomally synthesized and post-translationally modified peptides (RiPPs) from microbial communities. Cao, Gurevich, et al. Cell Systems, 2019
CDSnake: a snakemake pipeline for retrieval of annotated OTUs from paired-end reads in metagenomic studies. Kondratenko, Korobeynikov, Lapidus. BMC Bioinformatics, 2020
CycloNovo: a tool for de novo sequencing of cyclopeptides in various environments. Behsaz, Mohimani, Gurevich, et al. Cell Systems, 2020
MetaFlye: a long-read metagenome assembler.  Kolmogorov, Bickhart, Behsaz, Gurevich, Rayko, et al. Nature Methods, 2020
BGC analysis pipeline: a set of scripts for analysis of biosynthetic gene clusters (BGCs) in large metagenome assemblies.