Life in Extreme Habitats: Diversity of Endolithic Microorganisms from Cold Desert Ecosystems of Eastern Pamir

The first large scale rDNA amplicon database of soil microbiomes from Pamir Plateau, China

The Eastern Pamir, distinguished with high altitude, extremely arid and cold climate, limited nutrients and sparse vegetation, is a unique ecological reservoir. Microbial communities play a central role in maintaining Eastern Pamir's ecosystem functioning. Despite the ecological significance, due to the difficulty of sample collection and microbial isolation, the microbial diversity and its functionality at the Pamir Plateau have been rarely documented. To fill this gap, 80 soil samples from 17 sites across different elevations were collected, performed the rDNA amplicon sequencing to present the first large-scale overview of bacterial, archaeal, and fungal communities in the Eastern Pamir. Microbiome analysis revealed that the bacteria Actinobacteria, Alphaproteobacteria and Bacteroidia, alongside such as archaea Nitrososphaeria and Halobacteria, and fungi including Dothideomycetes, Sordariomycetes and Eurotiomycetes were dominant lineages at class level in soil microbial communities. The community structure and biodiversity of soil microorganisms provided by this dataset would be pivotal for future studies aimed at understanding the biogeographical distribution, ecological functions and environmental responses of microbial communities of the Pamir Plateau.

Composition and distribution of bacterial communities and potential radiation-resistant bacteria at different elevations in the eastern Pamirs

Altitude and ultraviolet (UV) radiation may affect the community composition and distribution of microorganisms in soil ecosystems. In this study, 49 soil samples from 10 locations were collected from different elevations on the eastern Pamir Plateau and analyzed for soil microbial community structure and function using high-throughput sequencing. The results showed that soil samples from different elevations of the eastern Pamir Plateau contained 6834 OTUs in 26 phyla and 399 genera. The dominant phyla common to different elevations were Actinobacteria, Proteobacteria, Bacteroidota, Acidobacteriota, and Gemmatimonadota. The dominant genera were Rubrobacter, Sphingomonas, Nocardioides, and Solirubrobacter. Species richness increased slightly with elevation, and there were significant differences in community composition between the elevations. Elevation and UV exposure are important factors that drive changes in bacterial communities. The results of the KEGG pathway showed that drug resistance, antineoplastic, aging, replication, and repair were enhanced and then slightly decreased with increasing elevation. Bacterial communities at different elevations were rich in radiation-resistant microorganisms, and the main genera were Rubrobacter, Sphingomonas, Nocardioides, Pontibacter, and Streptomyces. The findings have shown the composition and distribution of bacterial communities at different elevations on the Eastern Pamir Plateau. Potentially radiation tolerant microbial species were also examined. The results are of considerable importance for the succession of bacterial microorganisms in the plateau region, the study of radiation tolerant bacterial germplasm resources, and the application of biofunctionality.

Salinity matters the most: How environmental factors shape the diversity and structure of cyanobacterial mat communities in high altitude arid ecosystems

Introduction

Microbial mats are complex communities of benthic microorganisms that occur at the soil-water interphase in lakes' shores, streams, and ponds. In the cold, mountainous desert of Eastern Pamir (Tajikistan), where scarce water bodies are influenced by extreme environmental conditions, photosynthetic cyanobacteria form diverse mats. The mats are characterized by different morphology and thickness. Their habitats exhibit a wide range of conditions; from oligosaline to hypersaline, oligotrophic to hypertrophic, and from cold ponds to hot springs. The aim of the present study was to reveal the taxonomic composition and structure of these mats and to examine which environmental factors influence them.

Methods

Fifty-one mats were collected from small water bodies around Bulunkul, Karakul, and Rangkul Lakes in 2015 and 2017. The physical and chemical properties of the water were measured in situ, while the concentration of nutrients was analyzed ex-situ. To reveal the taxonomic composition of the mats, the hypervariable V3-V4 region of the 16S rRNA gene was examined using NGS technology.

Results

The results of bioinformatic analyses were compared with microscopic observations. They showed that Cyanobacteria was the dominant phylum, constituting on average 35% of bacterial ASVs, followed by Proteobacteria (28%), Bacteroidota (11%), and Firmicutes (9%). Synechococcales, Oscillatoriales, and Nostocales orders prevailed in Oxyphotobacteria, with a low contribution of Chroococcales, Gloeobacterales, and Chroococcidiopsidales. Occasionally the non-photosynthetic Vampirivibrionia (Melainabacteria) and Sericytochromatia from sister clades to Oxyphotobacteria were noted in the samples. Moreover, there was a high percentage of unidentified cyanobacterial sequences, as well as the recently described Hillbrichtia pamiria gen. et sp. nov., present in one of the samples. Salinity, followed by Na and K concentrations, correlated positively with the composition and structure of Oxyphotobacteria on different taxonomic levels and the abundance of all bacterial ASVs.

Discussion

The study suggests that the investigated communities possibly host more novel and endemic species. Among the environmental factors, salinity influenced the Oxyphotobacteria communities the most. Overall, the microenvironmental factors, i.e. the conditions in each of the reservoirs seemed to have a larger impact on the diversity of microbial mats in Pamir than the "subregional" factors, related to altitude, mean annual air temperature and distance between these subregions.

Connectivity of Edaphic and Endolithic Microbial Niches in Cold Mountain Desert of Eastern Pamir (Tajikistan)

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.

Microenvironmental Conditions Drive the Differential Cyanobacterial Community Composition of Biocrusts from the Sahara Desert

The Sahara Desert is characterized by extreme environmental conditions, which are a unique challenge for life. Cyanobacteria are key players in the colonization of bare soils and form assemblages with other microorganisms in the top millimetres, establishing biological soil crusts (biocrusts) that cover most soil surfaces in deserts, which have important roles in the functioning of drylands. However, knowledge of biocrusts from these extreme environments is limited. Therefore, to study cyanobacterial community composition in biocrusts from the Sahara Desert, we utilized a combination of methodologies in which taxonomic assignation, for next-generation sequencing of soil samples, was based on phylogenetic analysis (16S rRNA gene) in parallel with morphological identification of cyanobacteria in natural samples and isolates from certain locations. Two close locations that differed in microenvironmental conditions were analysed. One was a dry salt lake (a “chott”), and the other was an extension of sandy, slightly saline soil. Differences in cyanobacterial composition between the sites were found, with a clear dominance of Microcoleus spp. in the less saline site, while the chott presented a high abundance of heterocystous cyanobacteria as well as the filamentous non-heterocystous Pseudophormidium sp. and the unicellular cf. Acaryochloris. The cyanobacteria found in our study area, such as Microcoleus steenstrupii, Microcoleus vaginatus, Scytonema hyalinum, Tolypothrix distorta, and Calothrix sp., are also widely distributed in other geographic locations around the world, where the conditions are less severe. Our results, therefore, indicated that some cyanobacteria can cope with polyextreme conditions, as confirmed by bioassays, and can be considered extremotolerant, being able to live in a wide range of conditions.

Endolithic microbial composition in Helliwell Hills, a newly investigated Mars-like area in Antarctica

The diversity and composition of Antarctic cryptoendolithic microbial communities in the Mars-analogue site of Helliwell Hills (Northern Victoria Land, Continental Antarctica) are investigated, for the first time, applying both culture-dependent and high-throughput sequencing approaches. The study includes all the domains of the tree of life: Eukaryotes, Bacteria and Archaea to give a complete overview of biodiversity and community structure. Furthermore, to explore the geographic distribution of endoliths throughout the Victoria Land (Continental Antarctica), we compared the fungal and bacterial community composition and structure of endolithically colonized rocks, collected in >30 sites in 10 years of Italian Antarctic Expeditions. Compared with the fungi and other eukaryotes, the prokaryotic communities were richer in species, more diverse and highly heterogeneous. Despite the diverse community compositions, shared populations were found and were dominant in all sites. Local diversification was observed and included prokaryotes as members of Alphaproteobacteria and Crenarchaeota (Archaea), the last detected for the first time in these cryptoendolithic communities. Few eukaryotes, namely lichen-forming fungal species as Lecidella grenii, were detected in Helliwell Hills only. These findings suggest that geographic distance and isolation in these remote areas may promote the establishment of peculiar locally diversified microorganisms.

Diversity and Colonization Strategies of Endolithic Cyanobacteria in the Cold Mountain Desert of Pamir

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.

Trophic Selective Pressures Organize the Composition of Endolithic Microbial Communities From Global Deserts

Studies of microbial biogeography are often convoluted by extremely high diversity and differences in microenvironmental factors such as pH and nutrient availability. Desert endolithic (inside rock) communities are relatively simple ecosystems that can serve as a tractable model for investigating long-range biogeographic effects on microbial communities. We conducted a comprehensive survey of endolithic sandstones using high-throughput marker gene sequencing to characterize global patterns of diversity in endolithic microbial communities. We also tested a range of abiotic variables in order to investigate the factors that drive community assembly at various trophic levels. Macroclimate was found to be the primary driver of endolithic community composition, with the most striking difference witnessed between hot and polar deserts. This difference was largely attributable to the specialization of prokaryotic and eukaryotic primary producers to different climate conditions. On a regional scale, microclimate and properties of the rock substrate were found to influence community assembly, although to a lesser degree than global hot versus polar conditions. We found new evidence that the factors driving endolithic community assembly differ between trophic levels. While phototrophic taxa, mostly oxygenic photosynthesizers, were rigorously selected for among different sites, heterotrophic taxa were more cosmopolitan, suggesting that stochasticity plays a larger role in heterotroph assembly. This study is the first to uncover the global drivers of desert endolithic diversity using high-throughput sequencing. We demonstrate that phototrophs and heterotrophs in the endolithic community assemble under different stochastic and deterministic influences, emphasizing the need for studies of microorganisms in context of their functional niche in the community.

Actinobacteria and Cyanobacteria Diversity in Terrestrial Antarctic Microenvironments Evaluated by Culture-Dependent and Independent Methods

Bacterial diversity from McMurdo Dry Valleys in Antarctica, the coldest desert on earth, has become more easily assessed with the development of High Throughput Sequencing (HTS) techniques. However, some of the diversity remains inaccessible by the power of sequencing. In this study, we combine cultivation and HTS techniques to survey actinobacteria and cyanobacteria diversity along different soil and endolithic micro-environments of Victoria Valley in McMurdo Dry Valleys. Our results demonstrate that the Dry Valleys actinobacteria and cyanobacteria distribution is driven by environmental forces, in particular the effect of water availability and endolithic environments clearly conditioned the distribution of those communities. Data derived from HTS show that the percentage of cyanobacteria decreases from about 20% in the sample closest to the water source to negligible values on the last three samples of the transect with less water availability. Inversely, actinobacteria relative abundance increases from about 20% in wet soils to over 50% in the driest samples. Over 30% of the total HTS data set was composed of actinobacterial strains, mainly distributed by 5 families: Sporichthyaceae, Euzebyaceae, Patulibacteraceae, Nocardioidaceae, and Rubrobacteraceae. However, the 11 actinobacterial strains isolated in this study, belonged to Micrococcaceae and Dermacoccaceae families that were underrepresented in the HTS data set. A total of 10 cyanobacterial strains from the order Synechococcales were also isolated, distributed by 4 different genera (Nodosilinea, Leptolyngbya, Pectolyngbya, and Acaryochloris-like). In agreement with the cultivation results, Leptolyngbya was identified as dominant genus in the HTS data set. Acaryochloris-like cyanobacteria were found exclusively in the endolithic sample and represented 44% of the total 16S rRNA sequences, although despite our efforts we were not able to properly isolate any strain from this Acaryochloris-related group. The importance of combining cultivation and sequencing techniques is highlighted, as we have shown that culture-dependent methods employed in this study were able to retrieve actinobacteria and cyanobacteria taxa that were not detected in HTS data set, suggesting that the combination of both strategies can be usefull to recover both abundant and rare members of the communities.