Mikhail V. Semenov

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• PhD
• Head of Lab at V.V. Dokuchaev Soil Science Institute

Modern progress in soil biology is associated with the use of new molecular biology methods based on the isolation of total DNA from soil and its further analysis. The two main approaches to the study of soil microbial DNA are metabarcoding, the identification of the community composition via analysis of the sequences of barcode marker genes, and m...

Temperature sensitivity (Q10) of soil organic matter (SOM) decomposition is a crucial parameter to predict the fate of soil carbon (C) under global warming. Nonetheless, the response pattern of Q10 to continuous warming and the underlying mechanisms are still under debate, especially considering the complex interactions between Q10, SOM quality, an...

Manure inputs into soil strongly affect soil microbial communities leading to shifts in microbial diversity and activity. It is still not clear whether these effects are caused mainly by the survival of microbes introduced with manure or by activation of the soil-borne microbiome. Here, we investigated how the soil microbiome was changed after the...

Fungi represent a diverse group of organisms that play an essential role in maintaining soil health and ecosystem functioning. Plant root exudates form nutrient-rich niches that harbor specific fungal communities, or so-called rhizosphere mycobiomes. The long-term application of fertilizers supplies the soil with nutrients that may override the pla...

Microbial adaptive evolution and regulation strategies response to carbon (C) heterogeneity in paddy fields at large spatial scales remain poorly understood. Here, we employed gene-and genomic-centric metagenomic approaches to explore soil microbial biogeographic patterns and functional traits regulating C metabolisms across 120 soils derived from...

Agricultural practices significantly impact soil properties and ecological functions, highlighting the importance of comprehensive soil health assessments. Traditionally, these assessments have focused on physical and chemical indicators, often neglecting microbiological properties. This review explores the potential of microbiological indicators i...

The study was carried out in blueberry pine forests of the middle taiga subzone of Karelia. The results of complex studies of the microbiocenosis of Al-Fe-humus soils (Albic Podzols) formed on fluvioglacial deposits are presented. The methods of luminescent microscopy and substrateinduced respiration were used to assess the carbon of microbial biom...

The summarized data on the content of organic carbon (Corg) in the subtypes of gray forest soils occurring on the territory of Russia was presented. It was shown that the humus horizons of virgin light-gray, typical-gray, and dark-gray forest soils contain, on average, 2.16 ± 0.67, 2.42 ± 0.61, and 3.58 ± 0.95% Сorg, respectively, while the plowing...

Boreal peatlands store most of their carbon in layers deeper than 0.5 m under anaerobic conditions, where carbon dioxide and methane are produced as terminal products of organic matter degradation. Since the global warming potential of methane is much greater than that of carbon dioxide, the balance between the production rates of these gases is im...

The article summarizes the results of recent research by the staff of Soil Biology Department Faculty of Soil Science of Lomonosov Moscow State University in the field of assessing the genetic potential of microbial communities of soils and their application in the development of fundamental soil and environmental technologies. Promising areas of f...

An aim of analytical review is to systematize information about quantitative characteristics of changeability in the content and storage of organic carbon (Corg) in soils. The review considers evaluations of validity and reproducibility of Corg determination, spatial variability and heterogeneity of Corg at different hierarchic levels of soil cover...

The application of manure has the potential to enhance soil health by increasing organic matter content and stimulating dormant soil-borne microorganisms. However, this treatment also carries the risk of side effects, including the invasion and spread of manure-borne pathogens. To assess the survival of manure-borne microbes in soil and their intro...

The studies were performed with samples from different horizons of soddy podzolic soils (Albic Retisols) and typical chernozem (Haplic Chernozems) collected under natural lands and arable fields. The carbon contents in structural (particulate organic matter of 2-0.05 mm in size (C-POM) and mineral-associated organic matter of <0.05 mm in size (C-MA...

Bacteria are the most abundant organisms in soil. Despite small size and relative simplicity of prokaryotic cells, bacteria are the key players in soil processes, participating in biogeochemical cycles and maintaining soil health. The ability of bacteria to thrive in soil is due to their unequaled metabolic versatility and phenotypic plasticity, wh...

Since the discovery of the Archaea as the third domain of life along with prokaryotes and eukaryotes, much has changed in terms of understanding their ecology and distribution. New molecular methodologies have revealed the wide distribution of Archaea in soils and their crucial roles in global carbon and nitrogen cycles, including influencing green...

Chicken manure and composts derived from it are valuable organic fertilizers that have a positive impact on soil fertility and significantly enhance crop yields. However, the application of fresh manure can lead to excessive concentrations of nitrogen and other nutrients in the soil, as well as contamination of the soil with microorganisms that are...

Исследования проводили с образцами разных горизонтов дерново-подзолистой почвы (Albic Retisol) и типичного чернозема (Haplic Chernozem), отобранными под естественными угодьями и пашней. Определяли содержание углерода в структурных (твердые органические частицы размером 2–0.05 мм, CРОМ и минерально-ассоциированное органическое вещество размером <0.0...

The regular application of mineral and organic fertilizers is one of the essential components of the agricultural intensification. The applied fertilizers lead to artificial enrichment of the soil environment with readily available substrates and biophilic elements, which can have a significant impact on the soil and rhizosphere microbiome. The aim...

The loss of soil organic matter (SOM) due to agricultural land use has a negative impact on soil properties and is one of the major contributors to the increase in atmospheric CO2 concentrations. An appropriate way for simultaneous restoration of POM stocks and deposition of sequestered carbon is the straw application to the soil. The aim of the st...

The separation of soil organic matter (SOM) into pools and fractions allows to understand the nature and functions of SOM as well as to characterize its quality, composition and properties. The study presents an analysis of approaches, methods and results of determining various pools and fractions of SOM using the gray and agrogray soils (Haplic Lu...

Pesticides are widely used in agriculture as a pest control strategy. Despite the benefits of pesticides on crop yields, the persistence of chemical residues in soil has an unintended impact on non-targeted microorganisms. In the present study, we evaluated the potential adverse effects of a mixture of fungicides (difenoconazole, epoxiconazole, and...

The genus Fusarium includes many pathogenic species causing a wide range of plant diseases that lead to high economic losses. In this review, we describe how the Fusarium taxonomy has changed with the development of microbiological methods. We specify the ecological traits of this genus and the methods of its identification in soils, particularly t...

Под агрогенной эвтрофикацией почвы понимается ее искусственное обогащение органическим углеродом и питательными элементами в результате внесения минеральных и органических удобрений с целью повышения плодородия почвы и продуктивности растений. Эвтрофикация серой лесной почвы (Luvic Retic Greyzemic Phaeozems (Loamic)) создавалась ежегодным внесением...

Agrogenic eutrophication implies the artificial enrichment of soil with organic carbon and nutrients as a result of applying mineral and organic fertilizers to increase soil fertility and plant productivity. Eutrophication of gray forest soil, Luvic Retic Greyzemic Phaeozems (Loamic), has been created by annual application of increasing doses of mi...

The relationships between the rhizosphere factor R f values for a number of indices of soil biological activity, allocation in soil horizons, and bacterial community structure in the rhizosphere and the bulk soil of Retisol under spruce trees (Picea abies L.) have been studied in the Central Forest Nature Reserve (Tver oblast, Russia). The R f expr...

The relationships between the rhizosphere effects, allocation in soil horizons and bacterial community structure in the rhizosphere and the bulk soil of Retisol under spruce trees (Tver region, Russia) were studied. The rhizosphere factors (Rf) expressed as ratios of soil characteristics in the rhizosphere to that in the bulk soil were determined f...

Pesticides are widely used in agriculture as a pest control strategy. Despite the benefits of pesticides on crop yields, the persistence of chemical residues in soil have an unintended impact on non-targeted microorganisms. In this study, we evaluated the impact of the combined fungicide (difenoconazole, epoxiconazole, and kresoxim-methyl) on funga...

Температура и влажность являются главными внешними факторами, контролирующими разложение и минерализацию органического вещества в почве. В двух многомесячных опытах исследовали влияние температуры (8 и 22°C) и влажности (15, 30 и 45 мас. %) серой лесной почвы (Luvic Retic Greyzemic Phaeozems (Loamic)) на разложение остатков деревьев (листья, мелкие...

Temperature and moisture are the main external factors controlling organic matter decomposition and mineralization in soil. The effect of temperature (8 and 22°C) and moisture (15, 30, and 45 mass %) of gray forest soil (Luvic Retic Greyzemic Phaeozems (Loamic)) on decomposition of tree residues (leaves, small twigs, thin roots) and agricultural pl...

The temperature sensitivity (Q10) of soil respiration (Rs) is crucial for assessing the carbon (C) budget of terrestrial ecosystems under global warming. The changes in Q10 along a climatic gradient as well as its seasonal dynamics remain unclear, and the underlying microbial mechanisms are not well known. Here, the seasonal Q10 of Rs at the northe...

The review summarizes the most relevant microbiological characteristics that can serve as indicators of soil ecological functions: bioresource, phytosanitary, as well as the functions of carbon transformation and plant nutrition. The indices of diversity and taxonomic structure of microbial communities as well as abundance of certain groups of micr...

Plants, fungi, bacteria and protozoa are highly interconnected in constructed wetlands. These heterogeneous groups of organisms constitute a single system with complex internal trophic interactions. Thus, the joint activity of micro- and macroorganisms in constructed wetlands provides highly efficient wastewater treatment: both nutrients and comple...

The collapse of collective farming in Russia after 1990 led to the abandonment of 23% of the agricultural area. Microbial biomass is a transit pool between fresh and soil organic matter; therefore, structural changes in soil microbial community determine the carbon cycle processes caused by self-restoration of arable lands after abandonment. Here,...

The possibilities of regulating soil microbial communities via various agricultural practices and the application of microbial preparations are considered. The total biomass, diversity and activity of microorganisms , as well as the intensity of certain processes, such as nitrogen transformation, can be regulated by agricultural practices. The comp...

The prospects for application of metagenomic technologies in environmental studies are discussed. The advantages in investigating the taxonomic composition of aquatic and terrestrial ecosystems, as well as examples of trophic and phoric relationships found in ecosystems using the metagenomic approach, are described. The capabilities of metagenomics...

Simple Summary The Qinghai–Tibet Plateau is known as the “third pole of the world”. Due to the extreme geographical location, Qinghai–Tibet Plateau has unique ecosystems characterized by oxygen deficiency, low temperature, high salinity and alkalinity. We carried out the current study to explore the excellent extremophilic Bacillus strains via pote...

The role of methane as a greenhouse gas in the concept of global climate changes is well known. Methanogens and methanotrophs are two microbial groups which contribute to the biogeochemical methane cycle in soil, so that the total emission of CH4 is the balance between its production and oxidation by microbial communities. Traditional identificatio...

Constructed wetlands (CWs) are complicated ecosystems that include vegetation, sediments, and the associated microbiome mediating numerous processes in wastewater treatment. CWs have various functional zones where contrasting biochemical processes occur. Since these zones are characterized by different particle-size composition, physicochemical con...

The rhizosphere microbiome plays an important role in disease-suppressive soils and is closely related to plant health. While a key role of plant-related factors in shaping the rhizosphere microbiome is well known for natural ecosystems and similarly fertilized agricultural systems, the interaction between fertilization and plant species effects on...

The relevance of polar research is constantly increasing due to the higher response of Arctic and Antarctic ecosystems to global climate warming compared to other areas of the planet. The increase in average annual temperatures leads to the melting of glaciers, inundation of a part of the territory and, consequently, to the expansion of areas of su...

Проанализирована таксономическая структура микробных сообществ разновозрастных позднеплейстоценовых палеопочв на среднерусской возвышенности, сформированных при контрастных климатических условиях. Рассматривались гумусовые горизонты палеопочв интерстадиалов ранневалдайского (105–95 тыс. лет) и средневалдайского (33–24 тыс. лет) возраста, микулинско...

Abstract—The effect of commercial humic product Lignohumate® on the biological activity of Latosol underlong-term agricultural use with application of pesticides at the Bali Island (Indonesia) was evaluated in modelexperiments. It was shown that the application of lignohumate in a concentration gradient 0.025–2.5 mg/gresulted in increase in soil mi...

The physicochemical parameters, plant community, and the structure of prokaryotic complexes of differently-aged young soils formed in the Kursk magnetic anomaly region (KMA, Russia) are analyzed. The objects were technozems of 1-year (with and without vegetative cover), as well as 25- and 50-year-old embryonic soils. Prokaryotic communities of tech...

The pmoA gene number is considered as a soil microbiological parameter indicating abundance and potential activity of methanotrophic bacteria. The efficiency of this parameter for prediction and modeling of the real soil methane consumption rates remains an open issue. In the current study rate of methane oxidation by soil at its ambient concentrat...

Using the method of inoculation on elective nutrient media, the abundance and activity of taxonomic (bacteria, actinomycetes, micromycetes) and functional (nitrogen fixers, ammonifiers, denitrifiers of amylolytic, cellulolytic) groups of microorganisms in agrochernozems of the Stavropol region under the influence of various tillage systems – direct...

Modern progress in soil biology is related to the use of new molecular-biological methods based on the isolation of total DNA from soil and its further analysis. The two main approaches to the study of soil microbial DNA are metabarcoding (identification of community composition by analyzing the sequences of marker barcode genes) and metagenomics (...

The pmoA gene number is considered as a soil microbiological parameter indicating abundance and potential activity of methanotrophic bacteria. The efficiency of this parameter for prediction and modeling of the real soil methane consumption rates remains an open issue. In the current study rate of methane oxidation by soil at its ambient concentrat...

Rai IN, Suada IK, Proborini M, Wiraatmaja IW, Semenov M, Krasnov G. 2019. Indigenous endomycorrhizal fungi at salak (Salacca zalacca) plantations in Bali, Indonesia and their colonization of the roots. Biodiversitas 20: 2410-2416. Cultivation of snake fruit, commonly known as salak usually done organically on dry land with limited fertilizer in Bal...

The data have been presented on the microbial biomass content and on the abundances and taxonomic structure of bacterial and archaeal communities in the upper horizons of gray forest (Eutric Retisol (Loamic, Cutanic, Humic)) and alluvial-meadow (Fluvic Gleyic Phaeozem (Loamic, Pachic)) soils of the autonomous, transitional, and accumulative positio...

A chronosequence approach, i.e., a comparison of spatially distinct plots with different stages of succession, is commonly used for studying microbial community dynamics during paedogenesis. The successional traits of prokaryotic communities following sand fixation processes have previously been characterized for arid and semi-arid regions, but the...

The taxonomic composition, abundance, and diversity of bacterial and fungal communities in the rhizosphere loci and bulk mass of the gray forest soil (Eutric Retisol (Loamic, Aric, Cutanic, Humic)) under potatoes, maize, and white mustard grown with the application of mineral and organic fertilizers were compared. Among bacteria, Bacillus megateriu...

The research of fungal biomass and species diversity of the cultivated microscopic fungi and yeast of the Northbrook Island (Franz Josef Land) was carried out. Biomass of fungi depending on type of substratum varied from 129 to 634 mkg/g of a substratum. The share of viable biomass in the majority of objects made about 60–70%, decreasing to 30–40%...

A chronosequence approach, i.e., a comparison of spatially distinct plots with different stages of succession, is commonly used for studying microbial community dynamics during paedogenesis. The successional traits of prokaryotic communities following sand fixation processes have previously been characterized for arid and semi-arid regions, but the...

The applicability of DNA-based analysis of soil microbial biomass was proven under conditions when the common approaches – chloroform fumigation-extraction (CFE) and substrate-induced respiration (SIR) – are restricted. These restrictions include certain soil properties typical for arid areas (alkaline or carbonaceous soils) or limitation by sample...

Land use affects physical, chemical and biological properties and processes in soil. Long-term field experiments were employed to reveal changes of soil characteristics induced by land use. Using high-throughput 16S rRNA gene amplicon sequencing and quantitative PCR, comparative analyses were conducted on prokaryotic community structure in differen...

Although soil microorganisms spend most of their lifetime at dormant or resting states, they are quickly activated by substrate input and easily switch to growth. Under steady-state, the double-stranded DNA (dsDNA) content is considered as a measure of total microbial biomass while the RNA content mainly indicates the active microbial fraction. In...

Daily dynamics of greenhouse gas (GHG) emissions and cultivable bacterial populations have rarely been examined. The objectives were: (1) to investigate if dynamics of GHG emissions can be described by harmonics and are related to those of cultivable bacteria after soil disturbances in three grassland management systems; (2) to determine to which e...

The assessment of the microbial biomass structure in the soil samples from A and C horizons, stored at the temperature of +5 and -70ºС was conducted by a luminescence method. For the samples from the humus layer a significant decrease of biomass during the cryostorage was revealed. However, in the sample from the mineral layer at the same storage c...

The distribution of metabolically active cells of archaea and bacteria in the profiles of typical chernozems (Voronezh oblast) and brown semidesert soils (Astrakhan oblast) of natural and agricultural ecosystems was studied using the method of fluorescent in situ hybridization (FISH). The studied soils differed sharply in the microbial biomass and...

The rhizosphere reflects a sphere of high substrate input by means of rhizodeposits. Active microorganisms and extracellular enzymes are known to be responsible for substrate utilization in soil, especially in rooted soil. We tested for microbial‐ and enzyme activities in arable soil, in order to investigate the effects of continuous input of easil...

The structure of the microbial community (the fungi-to-bacteria ratio) has been assessed by selective inhibition of the substrate-induced respiration (SIR) using streptomycin sulfate and cycloheximide antibiotics in the gray forest soil of eluvial, transite, transite-accumulative, and accumulative (meadow alluvial) parts of slope landscape on the r...

The flux rates of carbon dioxide, methane, and nitrous oxide in the soils on autonomous, transitional, transitional-accumulative, and accumulative positions of a catena on the Oka River’s right bank (Moscow oblast) were assessed using the chamber method. The lowest rate of C-CO2 emission (18.8–29.8 mg/m2 per hour) was found for the gray forest soil...

The exchange processes of greenhouse gases in the soil–atmosphere system are discussed, including their production and microbial reutilization in the soil, emission from the soil surface, and consumption from the atmosphere. It was shown that the effect of soil–ecological conditions on the emission of greenhouse gases is manifested through the chan...