In all testes samples, the most abundant phylum was Acidobacteriota. Acidobacteriota is ubiquitous in diverse terrestrial environments including peatlands, sediments, grasslands, forests, agricultural lands, tundra, as well as desert soils.
The available information about the functional role of Acidobacteria in soil ecosystems includes data on their involvement in the destruction of various biopolymers, as well as participation in the global carbon, iron and hydrogen cycles [12].
Their ecological functions and interactions with other soil microbial communities remain unclear [13]. Data from 16S rRNA gene inventories revealed the essence of their bioactivity and their ecological functions in plant-soil ecosystems [13].
Acidobacteria are also involved in soil matrix formation and plant growth promotion. Because of their abundant presence in rhizosphere microbial communities, these bacteria might be a significant component of the crop’s natural environment [13]. Phylum Acidobacteriota is underexplored, but by many authors it is recognized as source possessing great potential for further exploration and exploitation [13]. Despite high abundance of Acidobacteria in many environments, the number of thoroughly studied genomes is very few. Acidobacteria genomes possess set of genes that allow them to adapt to various ecological niches, involved in regulating carbon, nitrogen, and sulfur cycles, and required for degrading different complex polysaccharides [14, 15].
Second the most abundant phylum in tested samples was Proteobacteria. Proteobacteria is a large group of Gram-negative bacilli and cocci. This phylum is divided into five classes: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria. Obtained results indicated the presence of OTUs of Alphaproteobacteria and Gammaproteobacteria.
Many of the bacteria species with unique features belong to both classes.
Among Alphaproteobacteria, OTUs of Rhizobiales were identified at order level.
Strains, belonging to this group of bacteria possess a great potential.
For instance, bacteria of Methylobacterium (Order: Rhizobiales, Family: Beijerinckiaceae) may produce plant growth promoting substances [16, 17]. Plant growth-promoting rhizobacteria (PGPR) are free-living bacteria having beneficial effects on plant health and growth, suppressing disease-causing microbes and accelerating nutrient availability and assimilation [18].
Wegner et al. (2021) described extracellular and intracellular accumulation of lanthanides and their storage in the periplasm of Beijerinckiaceae bacterium RH AL1 (Rhizobiales), a newly isolated and recently characterized methylotroph [19].
Very interesting group of Alphaproteobacteria, identified in tested samples are bacteria belonging to Acetobacterales order. Bacteria of Acetobacteraceae family (Order: Acetobacterales) are also known as acetic acid bacteria. They conduct an incomplete oxidation of sugars and alcohols to produce organic acids as final product of their metabolism. They are widely used in biotechnology, among others in production of vinegar, fermented beverages, microbial production of cellulose biotransformation of glucose to gluconic acid and its ketoderivatives, production of non‐caloric sugar d‐tagalose and shikimate that is an intermediate in the production of many antibiotics [20, 21].
Genus Rhodoplanes of Xanthobacteraceae family (Rhizobiales order) was isolated from a rhizosphere sample. Wegner et al. (2021) described extracellular and intracellular accumulation of lanthanides and their storage in the periplasm of Beijerinckiaceae bacterium RH AL1 (Rhizobiales), a newly isolated and recently characterized methylotroph [19].
The group of bacteria of Magnetospirillaceae family (Order: Rhodospirillales, Family: Magnetospirillaceae) the OTUs of which were identified in our research may possess unique features. Usually, they are isolated from fresh water sediments. With the use of growth mediums and magnetic isolation techniques established, a considerable number of the magnetotactic bacteria isolated to date have been found to be members of this family. Magnetotactic bacteria synthesize bacterial magnetic particles (BacMPs) of well-controlled size and morphology [22, 23].
Among Gammaproteobacteria, Burkholderia-Caballeronia-Paraburkholderia genus present in our samples, has potential for commercial use. According to Hetz and Horn (2021) research, Burkholderia-Caballeronia-Paraburkholderia affiliated taxa play a prominent role in dissimilatory nitrate reduction including denitrification [24].
Nitrous oxide (N2O) is a potent greenhouse gas with a global warming potential about 300 times higher than CO2, and a long atmospheric half-life of estimated 120 years [24–26]. The main source of N2O is microbial denitrification, i.e., the sequential reduction of nitrate (NO3-) or nitrite (NO2-) via the intermediates nitric oxide (NO) and N2O to dinitrogen gas (N2) under the exclusion of oxygen [24]. Denitrifiers use low molecular weight organic carbon (LMWOC) as carbon source and electron donors in many peatland systems and sediments [25].
The Gallionellaceae Family possess the ribulose-1,5-bisphosphate carboxylase / oxygenase (Rubisco), the key enzyme of the Calvin-Benson-Bassham cycle, to reduce carbon dioxide in organic carbon molecules [26]. They have recently been shown to possess genes allowing dissimilatory oxidation of sulfur compounds. The microaerobic lifestyle of the Gallionellaceae is enabled by the presence of high-affinity terminal oxidases which allow them to respire O2 in microoxic conditions [26]. They were first described as chemolithotrophs capable of gaining energy from the oxidation of iron coupled to the reduction of oxygen [26].
The family Methylophilaceae includes organisms that are specialized in methylotrophy. Methylotrophy is a metabolic strategy used by bacteria to derive energy and carbon for growth from reduced onecarbon (C1) compounds (molecules with no C–C bonds) [27, 28]. Their most typical substrates being methanol and methylated amines [28]. Their abilities were used in 1980s in industry e.g. in production of bulk protein or of value added compounds, based on their high carbon conversion efficiency [28]. Methylophilaceae have emerged as important species in carbon cycling in both terrestrial and marine environments [28].
The Nitrosomonadaceae comprise a monophyletic phylogenetic group within the Gammaproteobacteria, all their cultivated representatives are lithoautotrophic ammonia oxidizers [29]. Therefore, they play major roles in control of the nitrogen cycle in terrestrial, freshwater, and marine environments and in wastewater treatment. They are also of significant economic and environmental importance, leading to loss of ammonium-based fertilizers, nitrous oxide production, and nitrate pollution.
Both nitrosomonads and nitrosospiras have been isolated from soil and were considered to be the major contributors to soil ammonia oxidation [29].
Phylum Verrucomicrobiota is a core group of the PVC superphylum (Planctomycetes–Verrucomicrobiota–Chlamydiae, as well as Lentisphaerae, Kirimatiellaeota, and some uncultured candidate phyla) [30]. Verrucomicrobia form important members of global soil microbial communities [31]. Verrucomicrobiota are ubiquitous in soils, more frequently detected using molecular techniques, but rarely isolated on media [32]. Nevertheless, novel strains are isolated. Bünger et al. (2020) reported about divergent strains of Verrucomicrobia from rice roots or rhizomes. Two of them were demonstrated for the first time to be root endophytic in gnotobiotic cultures, what was a novel feature of Verrucomicrobia [33].
They are important and unusual from many perspectives, especially in terms of their brilliant potential to degrade the sulfated polysaccharides [31, 34]. Accumulated evidence indicates that Verrucomicrobia play critical roles in environmental carbon cycling and (poly)saccharide degradation, as they can have high coding densities for glycoside hydrolase genes [33, 35, 36]. According to results published by Bünger et al., 2020 they add a large set of carbohydrate hydrolysing enzymes to the endomicrobiome [33].
Carbohydrate-active enzymes (CAZymes) are phylogenetically conserved, varying significantly among microbial phyla. When focusing on the most populated phyla, those with the highest CAZy count were, among others, Verrucomicrobiota (106 ± 2) and Acidobacteriota (99 ± 3) [37].
López-Mondéjar et al. (2022) analysed high-quality metagenome-assembled genomes (MAGs) from the recently compiled Genomes from Earth’s Microbiomes (GEM) catalogue. MAGs of Verrucomicrobiota contained genes of 44 ± 1 CAZy families per genome and Acidobacteriota 41 ± 1 [37].
Wertz et al. (2012) considered that Verrucomicrobia may exert a great impact with regard to nitrogen availability in certain ecosystems, including oligotrophic environments [38]. Navarrete et al. 2015 showed that the verrucomicrobial community structure and abundance were affected by soil chemical factors linked to soil fertility, such as total N, P, K and sum of bases, i.e., the sum of calcium, magnesium and K contents [39].
Other Phyla identified in tested samples were Desulfobacterota. Although Desulfobacterota (formerly Deltaproteobacteria) [40] belongs to bacteria often found in soil [41] and other environments, they remain understudied. Desulfobacterota are known for their ability to respire sulfate utilizing protein complexes sulfate adenylyltransferase (Sat), adenylyl sulfate reductase (Apr), and dissimilatory sulfite reductase (Dsr), and have been identified from the environment based on the presence of the dsrA gene [42, 43]. Moreover, Desulfobacterota perform other metabolic activities like sulfite and thiosulfate disproportionation, mercury methylation, aliphatic and aromatic hydrocarbon degradation, nitrogen fixation, organohalide respiration and dissimilatory iron reduction.
Methagenomic analysis revealed that all tested samples contain Actinobacteriota. This phylum is the greatest source of microorganisms producing substances with antimicrobial activity.
Actinobacteria are common in soils, 1g of soil sample may contains 106 – 109 actinobacterial cells. Thanks to the production of hydrolytic exoenzymes such us: cellulaze, chitinase, xylanases [44], they play important role in circulation of matter [45]. Some of the species are able to fix nitrogen and come into symbiosis with higher plants [45]. They produce many bioactive secondary metabolites, showing, among others antibacterial, antifungal, immunosuppressive, and herbicidal activity [46] . Bioactive secondary metabolites may not only constitute a potential drug, but also serve as starting molecules for the chemical synthesis of new compounds with higher activity [47]. Actinomycetes when associated to root systems may behave as PGPR, showing good potential as inducers of induction of systemic disease resistance (ISR) [18].
Moreover, many secondary metabolites with antimicrobial activity produced by the Burkholderia species have been identified [48]. Compounds produced by them exhibit antibacterial and antifungal properties [48].
Growing problem of antimicrobial resistance forces to explore new niches to find potential antimicrobials. According to the results presented in this article, “Puścizna Wielka” peat bog may be the source of microorganisms that produce such substances.