Microorganisms can survive in extreme environments and oligotrophic habitats thanks to their specific adaptive capacity. Due to its severe and contrasting climate conditions, the cold mountain desert in Eastern Pamir provides a unique environment for analyzing microbial adaptation mechanisms occurring within colonization of endolithic habitats. This study aims to investigate the composition and structure of endolithic microbial communities and analyze the interactions between microorganisms and colonized lithic substrates. Endolithic biofilms were examined using scanning electron microscopy in backscattered electron mode (SEM-BSE) and next-generation sequencing (NGS) applying amplicon sequence variants (ASVs) approach. The investigation of the V3–V4 region of 16S rRNA gene revealed that endolithic communities are dominated by Actinobacteria (26%), Proteobacteria (23%), and Cyanobacteria (11.4%). Cyanobacteria were represented by Oxyphotobacteria with a predominance of subclasses of Oscillatoriophycidae, Synechococcophycideae, and Nostocophycidae as well as the rarely occurring Sericytochromatia. The positive correlation between the contribution of the orders Synechococcales and Rhizobiales to community structure suggests that some functionally closed taxa of Cyanobacteria and Proteobacteria can complement each other, for example, in nitrogen fixation in endolithic communities. The endolithic communities occurring in Eastern Pamir were identified as complex systems whose composition and structure seem to be influenced by the architecture of microhabitats and related microenvironmental conditions.

Toxic metabolites are produced by many cyanobacterial species. There are limited data on toxigenic benthic, mat-forming cyanobacteria, and information on toxic cyanobacteria from Central Asia is even more scarce. In the present study, we examined cyanobacterial diversity and community structure, the presence of genes involved in toxin production and the occurrence of cyanotoxins in cyanobacterial mats from small water bodies in a cold high-mountain desert of Eastern Pamir. Diversity was explored using amplicon-based sequencing targeting the V3-V4 region of the 16S rRNA gene, toxin potential using PCR-based methods (mcy, nda, ana, sxt), and toxins by enzyme-linked immunosorbent assays (ELISAs) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Molecular identification of cyanobacteria showed a high similarity of abundant taxa to Nostoc PCC-73102, Nostoc PCC-7524, Nodularia PCC-935 and Leptolyngbya CYN68. The PCRs revealed the presence of mcyE and/or ndaF genes in 11 samples and mcyD in six. The partial sequences of the mcyE gene showed high sequence similarity to Nostoc, Planktothrix and uncultured cyanobacteria. LC-MS/MS analysis identified six microcystin congeners in two samples and unknown peptides in one. These results suggest that, in this extreme environment, cyanobacteria do not commonly produce microcystins, anatoxins and cylindrospermopsins, despite the high diversity and widespread occurrence of potentially toxic taxa.

Microorganisms are vital in leaf litter decomposition and contribute significantly to global nutrient cycling. However, there is a need for improved understanding of the taxonomic and functional diversity of litter-associated bacteria. The Knyszyn Forest comprises a unique ecosystem providing diverse microhabitats for microorganisms in central Europe, similar to the southwestern taiga in many respects. This study presents the results of high-throughput sequencing performed for Betula pendula, B. pubescens, and Carpinus betulus litter-associated microbial communities from northern Poland. Microbial assemblage composition and structure at different stages of litter decomposition revealed the domination of phyllosphere-associated taxa of Sphingomonas and Pseudomonas in bacterial communities in the early stages. Meanwhile, at the later stages of decomposition, the representation of soil-associated bacterial communities, such as Pedobacter, was higher. This study identifies key bacteria (Pedobacter, Mucilaginibacter, and Luteibacter) as pivotal in nutrient cycling through cellulose and hemicellulose decomposition, dominating later decomposition phases. Taxonomic analysis based on functional markers associated with nitrogen metabolism highlights the pivotal role of specific Pseudomonadota (Proteobacteria) taxa in driving nitrogen cycling dynamics during litter decomposition. Most of these taxa were unclassified at the genus level, particularly in the later stages of litter decomposition, and are crucial in mediating nitrogen transformation processes, underscoring their significance in ecosystem nutrient cycling.

Microbial communities found in arid environments are commonly represented by biological soil crusts (BSCs) and endolithic assemblages. There is still limited knowledge concerning endoliths and BSCs occurring in the cold mountain desert of Pamir. The aim of the study was to investigate the composition and structure of endolithic bacterial communities in comparison to surrounding BSCs in three subregions of the Eastern Pamir (Tajikistan). The endolithic and BSC communities were studied using culture-independent and culture-dependent techniques. The structure of the endolithic bacterial communities can be characterized as Actinobacteria–Proteobacteria–Bacteroidetes–Chloroflexi–Cyanobacteria, while the BSCs’ can be described as Proteobacteria–Actinobacteria–Bacteroidetes–Cyanobacteria assemblages with low representation of other bacteria. The endolithic cyanobacterial communities were characterized by the high percentage of Chroococcidiopsaceae, Nodosilineaceae, Nostocaceae and Thermosynechococcaceae, while in the BSCs were dominated by Nodosilineaceae, Phormidiaceae and Nostocaceae. The analysis of 16S rRNA genes of the cyanobacterial cultures revealed the presence of possibly novel species of Chroococcidiopsis, Gloeocapsopsis and Wilmottia. Despite the niches’ specificity, which is related to the influence of microenvironment factors on the composition and structure of endolithic communities, our results illustrate the interrelation between the endoliths and the surrounding BSCs in some regions. The structure of cyanobacterial communities from BSC was the only one to demonstrate some subregional differences.

The aim of this study was to identify cyanobacteria diversity in rock communities from the cold desert ecosystem in Eastern Pamir Mountains (Tajikistan) and assess if the rock type and rock`s porosity can be indicators of microbial diversity in this extreme environment. Seven samples were collected in July 2015 from hillsides (ca 4000–4500 m a.s.l.) of the Eastern Pamir Mountains. Petrographic and scanning microscopy (SEM) allowed for the characterization of the rocks inhabited by endolithic communities as granite, gneiss and limestone with variable porosity. Based on next-generation sequencing (NGS) of amplicon of V3–V4 hypervariable region of 16S rRNA gene, we established that Actinobacteria, Proteobacteria and Cyanobacteria dominated the endolithic communities of microorganisms in the rocks studied, which distinguishes these communities from those described for other cold arid regions. Chroococcidiopsis and Leptolyngbya were dominant genera in the cyanobacterial communities according to culture-dependent analysis, as well as microscopic analyses of endoliths scraps from the rocks. Culture-independent metagenomic analyses revealed that Microcoleus, Acaryochloris, Chroococcidiopsis and Thermosynechococcus reads were the most abundant from all reads and dominated interchangeably in the samples. Endolithic communities of microorganisms in the rocks from the cold desert shrubland of Eastern Pamir Mts. appear to be diverse and different from communities described for other cold deserts.

In mountain desert ecosystems, wetlands around saline and freshwater lakes allow various organisms to thrive and sometimes serve as the only source of drinking water for wild and domestic animals. We present results concerning diversity and structure of cyanobacterial inoculum from Eastern Pamir Mountains' benthic sediments, collected from small water bodies with contrasting salinity, temperature and other chemical parameters. We used morphological identification and molecular NGS techniques based on the amplification of the V3-V4 hypervariable region of 16S rRNA gene. Only a few cyanobacterial taxa have been identified in the preserved samples, while 27 taxa were successfully isolated and identified from the benthic sediments. Metagenomic analysis revealed that the cyanobacterial contribution to benthic bacterial communities was low. Representatives of the order Nostocales dominated in the samples, followed by Synechococcales, while contributions of Oscillatoriales and Chroococcales was much lower. The correlation matrix for the amplicon-based composition of samples clustered together samples of similar salinity and temperature. However, in hierarchical clustering of taxonomic structure of samples, communities with similar structures were not grouped by salinity or temperature. These results suggest that salinity and to some extent temperature, influence the composition of the inoculum, although the structure of the cyanobacterial communities is further shaped by other factors. Our study also demonstrated that the benthic inoculum for cyanobacterial communities contained potentially toxic taxa characteristic of both benthic and planktonic communities.