The process of straw decomposition is dynamic and is accompanied by the succession of the microbial decomposing community, which is driven by poorly understood interactions between microorganisms. Soil is a complex ecological niche, and the soil microbiome can serve as a source of potentially active cellulolytic microorganisms. Here, we performed an experiment on the de novo colonization of oat straw by the soil microbial community by placing nylon bags with sterilized oat straw in the pots filled with chernozem soil and incubating them for 6 months. The aim was to investigate the changes in decomposer microbiota during this process using conventional sequencing techniques. The bacterial succession during straw decomposition occurred in three phases: the early phase (first month) was characterized by high microbial activity and low diversity, the middle phase (second to third month) was characterized by low activity and low diversity, and the late phase (fourth to sixth months) was characterized by low activity and high diversity. Analysis of amplicon sequencing data revealed three groups of co-changing phylotypes corresponding to these phases. The early active phase was abundant in the cellulolytic members from Pseudomonadota, Bacteroidota, Bacillota, and Actinobacteriota for bacteria and Ascomycota for fungi, and most of the primary phylotypes were gone by the end of the phase. The second intermediate phase was marked by the set of phylotypes from the same phyla persisting in the community. In the mature community of the late phase, apart from the core phylotypes, non-cellulolytic members from Bdellovibrionota, Myxococcota, Chloroflexota, and Thermoproteota appeared. Full metagenome sequencing of the microbial community from the end of the middle phase confirmed that major bacterial and fungal members of this consortium had genes of glycoside hydrolases (GH) connected to cellulose and chitin degradation. The real-time analysis of the selection of these genes showed that their representation varied between phases, and this occurred under the influence of the host, and not the GH family factor. Our findings demonstrate that soil microbial community may act as an efficient source of cellulolytic microorganisms and that colonization of the cellulolytic substrate occurs in several phases, each characterized by its own taxonomic and functional profile.

Recycling plant matter is one of the challenges facing humanity today and depends on efficient lignocellulose degradation. Although many bacterial strains from natural substrates demonstrate cellulolytic activities, the CAZymes (Carbohydrate-Active enZYmes) responsible for these activities are very diverse and usually distributed among different bacteria in one habitat. Thus, using microbial consortia can be a solution to rapid and effective decomposition of plant biomass. Four cellulolytic consortia were isolated from enrichment cultures from composting natural lignocellulosic substrates—oat straw, pine sawdust, and birch leaf litter. Enrichment cultures facilitated growth of similar, but not identical cellulose-decomposing bacteria from different substrates. Major components in all consortia were from Proteobacteria, Actinobacteriota and Bacteroidota, but some were specific for different substrates—Verrucomicrobiota and Myxococcota from straw, Planctomycetota from sawdust and Firmicutes from leaf litter. While most members of the consortia were involved in the lignocellulose degradation, some demonstrated additional metabolic activities. Consortia did not differ in the composition of CAZymes genes, but rather in axillary functions, such as ABC-transporters and two-component systems, usually taxon-specific and associated with CAZymes. Our findings show that enrichment cultures can provide reproducible cellulolytic consortia from various lignocellulosic substrates, the stability of which is ensured by tight microbial relations between its components.

Crop rotation is one of the oldest and most effective methods of restoring soil fertility, which declines when the same plant is grown repeatedly. One of the reasons for a reduction in fertility is the accumulation of pathogenic and unfavorable microbiota. The modern crop rotation schemes (a set of plant species and their order in the crop rotation) are highly effective but are designed without considering soil microbiota dynamics. The main goal of this study was to perform a short-term experiment with multiple plant combinations to access the microbiological effects of crop rotation. It could be useful for the design of long-term crop rotation schemes that take the microbiological effects of the crop rotation into account. For the analysis, five plants (legumes: vetch, clover, and cereals: oats, wheat, and barley) were used. These five plants were separately grown in pots with soil. After the first phase of vegetation, the plants were removed from the soil and a new crop was planted. Soil samples from all 25 possible combinations of primary and secondary crops were investigated using v4-16S rDNA gene sequencing. It was shown that the short-term experiments (up to 40 days of growing) are effective enough to find microbial shifts in bulk soil from different plants. Both primary and secondary cultures are significant factors for the microbial composition of microbial soil communities. Changes are the most significant in the microbial communities of vetch soils, especially in the case of vetch monoculture. Growing clover also leads to changes in microbiota, especially according to beta-diversity. Data obtained can be used to develop new crop rotation schemes that take into account the microbiological effects of various crops.

Significance of soil genesis for the composition and succession of bacterial communities during straw decomposition has been studied. Sterile grinded oat straw in nylon bags was placed in humus horizons of two soils (soddy-podzolic and chernozem; Albic Retisol (Abruptic, Ochric) and Haplic Chernozem (Pachic)) and incubated in the laboratory under constant hydrothermal conditions. On the basis of respiration dynamics (measured by absorption method) the stages of straw decomposition (early, middle and late) were specified. For each stage, the composition of bacterial communities was determined by high-performance sequencing of amplicon libraries of the variable region V4 of the 16S rRNA gene. It has been shown that carbon losses during decomposition of straw from the soddy-podzolic soil were higher than those from chernozem: 3913 ± 668 and 2981 ± 297 CO₂ mg/m² day, respectively. Phylogenetic analysis showed an increase in the diversity of the bacterial community in the process of straw decomposition: from 51 and 79 on the third day, up to 213 and 310 phylotypes from 17 phyla on the last day, for chernozem and soddy-podzolic soil, respectively. On the third day, Proteobacteria, Firmicutes, and Bacteroidetes were mainly present; on the 161st day, Actinobacteria were added. Soil had a significant impact on the taxonomic composition of straw communities. For the microbial community of straw formed on the basis of the microbiocenosis of soddy-podzolic soil the proportion of Proteobacteria was higher, but Bacteroidetes was lower, and the contribution of unidentified prokaryotes was more significant. Bacterial succession during straw decomposition had common features for both soils. The decomposition started with the quick consuming of easily available organic compounds of straw by copiotrophs, representatives of the Pseudomonas genus, the Stenotrophomonas genus from the family of Xanthomonaceae, and the Chitinophaga (Bacteroidia) genus. In addition to actinobacteria, the oligotrophs were represented by Firmicutes and part of Bacteroidetes. Throughout the entire observation period, probably due to the formation of available organic compounds during the decomposition of straw, the contribution of bacteria of the Rhizobiaceae family was significant.

Soil properties and functions are largely determined by the amount of available organic matter, which is most significant for the vital activity of microorganisms. The influence of the content of available soil organic matter on the composition and functioning of microbial community during the transformation of barley straw in the soil was studied. Samples from the upper 20-cm-thick layer of soddy-podzolic soil (Umbric Albic Retisols (Abruptic)) were incubated (T = 25°C, 60% TFC) for 4 months, and a model soil with a reduced content of available organic matter was obtained. Then, we performed a laboratory experiment with the application of barley straw into native and model soils. The dynamics (0, 7, 40, and 70 days) of soil respiration, microbial biomass (SIR), the number of microorganisms, and the taxonomic composition of the microbial community (16S-rRNA sequencing) were analyzed. The quality of soil organic matter was assessed from data on the contents of total organic carbon (C_tot) and its available (C_avail), water-soluble (C_wat), and labile (C_lab) fractions. It was shown that the amount of C_wat and C_avail in the model soil decreased by half in the absence of significant differences in C_tot. The aggregate structure of the soil worsened, and the straw transformation proceeded 25% faster as compared with that in the native soil. The taxonomic composition of the soil bacterial community was influenced by the amount of available organic matter in the soil, the addition of straw, and the incubation period. A decrease in the content of available organic matter caused changes in the composition of the microbial community: the portions of the phyla Acidobacteria and Firmicutes decreased, while those of Actinobacteria, Bacteroidetes, Chloroflexi, Planctomycetes, and archaea increased. It was found that the main part (50% of the total) of the microbial community of the depleted soil is characterized by great diversity and oligotrophy. Indicators for comparing soils by the degree of oligotrophy of the microbial community are proposed on the basis of data on its taxonomic composition.

TAXONOMIC COMPOSITION AND ORGANIZATION OF THE MICROBIAL COMMUNITY OF SODDY-PODZOLIC SOILS AFTER APPLICATION OF STRAW OF CEREAL CROPS AND USING OF THE BARKON BIOPREPARATION O.V. Orlova, E.L. Chirak, N.I. Vorob’ev, O.V. Sviridova, T.O. Lisina, E.E. Andronov