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.

Localization of agriculture with the aim of local food support has become a very urgent topic for Yamal region. The most fertile soils of this region are sandy textured anthropogenically affected soils. Microbiomes from disturbed soils of the Nadym region were studied using analysis of 16S rRNA metagenomic libraries. It was shown that plant cover is a driving force of microbiome composition. Forest soils covered with aeolian transfers from the quarry retaids a typical forest microbiome with the following dominant bacterial phyla: Proteobateria, Acidobacteria, Verrucomicrobia, Planctomycetes and Bacteroidetes. However, it contains significantly less Planctomycetes, which indicates greater aridity of the soil. The microbiomes of the overgrown quarries were strikingly differ from the soil microbiome and resemble those of arctic soils being dominated by Proteobacteria, Chloroflexi, Acidobacteria and Cyanobacteria. Absence of dense vegetation cover and availability of nutrients facilitated the formation of autotrophic microbial mats. The microbiome of the lower horizons of the quarry is characterised by Proteobacteria, Actinobacteria and Firmicutes. Presumably, most of the time these bacteria reside in a dormant state with short periods of activity due to nutrient uptake from the upper horizons.

High-throughput 16S rRNA sequencing was performed to compare the microbiomes inhabiting two contrasting soil types—sod-podzolic soil and chernozem—and the corresponding culturome communities of potentially cellulolytic bacteria cultured on standard Hutchinson media. For each soil type, soil-specific microorganisms have been identified: for sod-podzolic soil—Acidothermus, Devosia, Phenylobacterium and Tumebacillus, and for chernozem soil—Sphingomonas, Bacillus and Blastococcus. The dynamics of differences between soil types for bulk soil samples and culturomes varied depending on the taxonomic level of the corresponding phylotypes. At high taxonomic levels, the number of common taxa between soil types increased more slowly for bulk soil than for culturome. Differences between soil-specific phylotypes were detected in bulk soil at a low taxonomic level (genus, species). A total of 13 phylotypes were represented both in soil and in culturome. No relationship was shown between the abundance of these phylotypes in soil and culturome.

The soil microbiome is composed of various communities that play an important role in the existence of ecosystem services and the sustainable functioning of ecosystems under high anthropogenic loads. The transition of soils to a fallow state and their subsequent transformation lead to a notable alteration in the taxonomic composition of the soil microbiome, impacting the biochemical processes within the soil and its fertility levels. The object of this study comprised different-aged fallow soils of the southern taiga in the vicinity of Ban’kovo village, Leningrad region. The method comprising the high-throughput sequencing of 16S rRNA gene fragments using an Illumina MiSEQ sequencer was used to analyze the microbial community. The general processing of sequences was carried out with the dada2 (v1.14.1) package. It was found that the morphological organization of fallow soils has significant differences from the native podzol. In fallow soils, there are signs of leaching expressed in the accumulation of leached mineral particles, which indicates the degradation of the fallow–arable horizon. At the same time, there is a decrease in the content of P₂O₅ and K₂O and an increase in the content of N-NH₄ and N-NO₃ in fallow soil. The analysis of alpha diversity index values showed that the highest level of alpha diversity in the microbial community is characteristic of 40-year-old soil, the alpha diversity index decreased with the increasing time of the fallow state, and the lowest alpha diversity index was observed in the native podzol. According to the values of the beta diversity index, a high correlation between the soil microbiome and the physicochemical characteristics of the soil was revealed, which indicates the formation of functional specialization in the studied microbial communities. As a result of the study of the taxonomic composition of microbial communities in fallow soils, it was found that the most represented microbial communities in fallow soils belong to Nitrosomonadaceae (Pseudomonadota), Mycobacterium (Actinobacteria), Nitrospira (Nitrospirota), and Luteolibacter (Verrucomicrobiota). The duration of post-agrogenic transformation is the leading factor influencing the changes in microbial communities; so, with an increase in the time that soils were in a fallow state, an increase in the oligotrophic microbial community was observed.

The filamentous cyanobacterium Anabaena sp. PCC 7120 produces, during the differentiation of heterocysts, a short peptide PatS and a protein HetN, both containing an RGSGR pentapeptide essential for activity. Both act on the master regulator HetR to guide heterocyst pattern formation by controlling the binding of HetR to DNA and its turnover. A third small protein, PatX, with an RG(S/T)GR motif is present in all HetR-containing cyanobacteria. In a nitrogen-depleted medium, inactivation of patX does not produce a discernible change in phenotype, but its overexpression blocks heterocyst formation. Mutational analysis revealed that PatX is not required for normal intercellular signaling, but it nonetheless is required when PatS is absent to prevent rapid ectopic differentiation. Deprivation of all three negative regulators—PatS, PatX, and HetN—resulted in synchronous differentiation. However, in a nitrogen-containing medium, such deprivation leads to extensive fragmentation, cell lysis, and aberrant differentiation, while either PatX or PatS as the sole HetR regulator can establish and maintain a semiregular heterocyst pattern. These results suggest that tight control over HetR by PatS and PatX is needed to sustain vegetative growth and regulated development. The mutational analysis has been interpreted in light of the opposing roles of negative regulators of HetR and the positive regulator HetL.