Distinct Microbial Communities in Adjacent Rock and Soil Substrates on a High Arctic Polar Desert

Distinct microbial communities under different rock-associated microhabitats in the Qaidam Desert

Hypolithic communities, which occupy highly specialised microhabitats beneath translucent rocks in desert and arid environments, have assembly mechanisms and ecosystem functions are not fully understood. Thus, in this study, we aimed to examine the microbial community structure, assembly, and function of light-accessible (under quartz, calcite, and hypolithic lichen-dominated biocrusts) and light-inaccessible microhabitats (under basalt and adjacent soil) in the Qaidam Desert, China. The results showed that hypolithic communities have different characteristics compared with microbial communities of light-inaccessible microhabitats. Notably, hypolithic bacterial communities were dominated by Cyanobacteria, whereas light-inaccessible microhabitats showed a predominance of Bacteroidetes and Proteobacteria. Although the class Dothideomycetes (phylum: Ascomycota) dominated the fungal communities between the two microhabitat types, Sordariomycetes were more prevalent in light-accessible microhabitats. Network and robustness analyses showed that hypolithic communities were less complex and more resilient than microbial communities in light-inaccessible microhabitats. Our results indicated that deterministic processes, specifically homogeneous selection, govern the establishment of bacterial and fungal communities in light-accessible and light-inaccessible microhabitats. The hypolithic community showed an increased frequency of phylotypes that exhibited increased tolerance to functional stress response pathways. In contrast to light-inaccessible microhabitats, light-accessible microhabitats showed a slight decrease and a notable increase in the prevalence of carbon fixation pathways in prokaryotes and carbon fixation in photosynthetic organisms, respectively. For fungi, light-accessible microhabitats enriched saprotrophic and ectomycorrhizal groups. These results highlight the importance of complex and diverse microhabitats in desert regions, which serve as vital shelters for microbes. Combining future research on interactions between hypolithic communities and environments may enhance our current understanding of their pivotal roles in sustaining desert ecosystems. This knowledge then be applied to design and implement informed conservation efforts to preserve these unique rock-associated microhabitats in desert ecosystems.

The hidden network of biocrust successional stages in the High Arctic: Revealing abiotic and biotic factors shaping microbial and metazoan communities

Despite the important role that biocrust communities play in maintaining ecosystem structure and functioning in deglaciated barren soil, few studies have been conducted on the dynamics of biotic communities and the impact of physicochemical characteristics in shaping the different successional stages. In this study an integrated approach encompassing physicochemical parameters and molecular taxonomy was used for identifying the indicator taxa and the presence of intra- and inter-kingdom interactions in five different crust/biocrust successional stages: i) physical crust, ii) cyanobacteria-dominated biocrust, iii) cyanobacteria/moss-dominated biocrust, iv) moss-dominated biocrust and v) bryophyte carpet. The phylum Gemmatimonadota was the bacterial indicator taxon in the early stage, promoting both inter- and intra-kingdom interactions, while Cyanobacteria and Nematoda phyla played a pivotal role in formation and dynamics of cyanobacteria-dominated biocrusts. A multitrophic community, characterized by a shift from oligotrophic to copiotrophic bacteria and the presence of saproxylic arthropod and herbivore insects was found in the cyanobacteria/moss-dominated biocrust, while a more complex biota, characterized by an increased fungal abundance (classes Sordariomycetes, Leotiomycetes, and Dothideomycetes, phylum Ascomycota), associated with highly trophic consumer invertebrates (phyla Arthropoda, Rotifera, Tardigrada), was observed in moss-dominated biocrusts. The class Bdelloidea and the family Hypsibiidae (phyla Rotifera and Tardigrada, respectively) were metazoan indicator taxon in bryophyte carpet, suggesting their potential role in shaping structure and function of this late successional stage. Nitrogen and phosphorus were the main physicochemical limiting factors driving the shift among different crust/biocrust successional stages. Identification and characterization of indicator taxa, biological intra- and inter-kingdom interactions and abiotic factors driving the shift among different crust/biocrust successional stages provide a detailed picture on crust/biocrust dynamics, revealing a strong interconnection among micro- and macrobiota systems. These findings enhance our understanding of biocrust ecosystems in High Arctic, providing valuable insights for their conservation and management in response to environmental shifts due to climate change.

Aridity drives the variability of desert soil microbiomes across north-western China

Dryland covers >35 % of the terrestrial surface and the global extent of dryland increases due to the forecasted increase in aridity driven by climate change. Due to the climate change-driven aridity ecosystems, deserts provide one of the most hostile environments for microbial life and survival. Therefore, a detailed study was carried out to explore the deserts with different aridity levels (exposed to severe climate change) influence on microbial (bacteria, fungi, and protist) diversity patterns, assembly processes, and co-occurrence. The results revealed that the aridity (semi-arid, arid, and hyper-arid) patterns caused distinct changes in environmental heterogeneity in desert ecosystems. Similarly, microbial diversities were also reduced with increasing the aridity pattern, and it was found that environmental heterogeneity is highly involved in affecting microbial diversities under different ecological niches. Interestingly, it was found that certain microbes, including bacterial (Firmicutes), fungal (Sordariomycetes), and protistan (Ciliophora) abundance increased with increasing aridity levels, indicating that these microbes might possess the capability to tolerate the environmental stress conditions. Moreover, microbial community turnover analysis revealed that bacterial diversities followed homogenous selection, whereas fungi and protists were mostly driven by the dispersal limitation pattern. Co-occurrence network analysis showed that hyper-arid and arid conditions tightened the bacterial and fungal communities and had more positive associations compared to protistan. In conclusion, multiple lines of evidence were provided to shed light on the habitat specialization impact on microbial (bacteria, fungi, and protists) communities and composition under different desert ecosystems.

Soil Alveolata diversity in the undisturbed steppe and wheat agrocenoses under different tillage

Microeukaryotes are vital for maintaining soil quality and ecosystem functioning, however, their communities are less studied than bacterial and fungal ones, especially by high throughput sequencing techniques. Alveolates are important members of soil microbial communities, being consumers and/or prey for other microorganisms. We studied alveolate diversity in soil under the undisturbed steppe (US) and cropped for wheat using two tillage practices (conventional, CT, and no-till, NT) by amplifying the ITS2 marker with ITS3_KYO2/ITS4 primers and sequencing amplicons using Illumina MiSeq. A total of 198 Alveolata OTUs were identified, with 158 OTUs attributed to the Ciliophora phylum, containing five classes: Litostomatea, Spirotrichea and Oligohymenophorea, Nassophorea and Phyllopharyngea. Litostomatea and Phyllopharyngea were more abundant in US as compared with CT and NT. The observed OTU richness was higher in US than in CT and NT. The β-biodiversity of soil ciliates also very distinctly differentiated the US field from CT and NT. In the US, Nassophorea and Spirotrichea correlated positively with sand and negatively with clay, silt and SOM contents. This is the first report about soil ciliates diversity in Siberia as assessed by metabarcoding technique. The revealed clear effect of land use on the relative abundance of some taxa and a lack of tillage effect suggest the importance of the quantity and quality of plant material input for shaping the prey for ciliates. The ITS-metabarcoding technique was used for the first time in the research of ciliates diversity; further studies, embracing diverse aspects of soil ciliates by combining -omics methodology with the traditional one, are needed to get a better insight on the ecological roles of the main ciliate taxa in the complex soil system.

Spatial distribution patterns across multiple microbial taxonomic groups

Even in the vertical dimension, soil bacterial communities are spatially distributed in a distance-decay relationship (DDR). However, whether this pattern is universal among all soil microbial taxonomic groups, and how body size influences this distribution, remains elusive. Our study consisted of obtaining 140 soil samples from two adjacent ecosystems in the Yellow River Delta (YRD), both nontidal and tidal, and measuring the DDR between topsoil and subsoil for bacteria, archaea, fungi and protists (rhizaria). Our results showed that the entire community generally fitted the DDR patterns (P < 0.001), this was also true at the kingdom level (P < 0.001, with the exception of the fungal community), and for most individual phyla (47/75) in both ecosystems and with soil depth. Meanwhile, these results presented a general trend that the community turnover rate of nontidal soils was higher than tidal soils (P < 0.05), and that the rate of topsoil was also higher than that of subsoil (P < 0.05). Additionally, microbial spatial turnover rates displayed a negative relationship with body sizes in nontidal topsoil (R² = 0.29, P = 0.009), suggesting that the smaller the body size of microorganisms, the stronger the spatial limitation was in this environment. However, in tidal soils, the body size effect was negligible, probably owing to the water's fluidity. Moreover, community assembly was judged to be deterministic, and heterogeneous selection played a dominant role in the different environments. Specifically, the spatial distance was much more influential, while the soil salinity in these ecosystems was the major environmental factor in selecting the distributions of microbial communities. Overall, this study revealed that microbial community compositions at different taxonomic levels followed relatively consistent distribution patterns and mechanisms in this coastal area.

Rock Traits Drive Complex Microbial Communities at the Edge of Life

Antarctic deserts are among the driest and coldest ecosystems of the planet; there, some microbes survive under these extreme conditions inside porous rocks, forming the so-called endolithic communities. Yet the contribution of distinct rock traits to support complex microbial assemblies remains poorly determined. Here, we combined an extensive Antarctic rock survey with rock microbiome sequencing and ecological networks and found that contrasting combinations of microclimatic and rock traits such as thermal inertia, porosity, iron concentration, and quartz cement can help explain the multiple complex microbial assemblies found in Antarctic rocks. Our work highlights the pivotal role of rocky substrate heterogeneity in sustaining contrasting groups of microorganisms, which is essential to understand life at the edge on Earth and for the search for life on other rocky planets such as Mars.

Niche-mediated bacterial community composition in continental glacier alluvial valleys under cold and arid environments

Introduction

Bacteria are an essential component of glacier-fed ecosystems and play a dominant role in driving elemental cycling in the hydrosphere and pedosphere. However, studies of bacterial community composition mechanisms and their potential ecological functions from the alluvial valley of mountain glaciers are extremely scarce under cold and arid environments.

Methods

Here, we analyzed the effects of major physicochemical parameters related to soil on the bacterial community compositions in an alluvial valley of the Laohugou Glacier No. 12 from the perspective of core, other, and unique taxa and explored their functional composition characteristics.

Results and discussion

The different characteristics of core, other, and unique taxa highlighted the conservation and difference in bacterial community composition. The bacterial community structure of the glacial alluvial valley was mainly affected by the above sea level, soil organic carbon, and water holding capacity. In addition, the most common and active carbon metabolic pathways and their spatial distribution patterns along the glacial alluvial valley were revealed by FAPTOTAX. Collectively, this study provides new insights into the comprehensive assessment of glacier-fed ecosystems in glacial meltwater ceasing or glacier disappearance.

Culturomics- and metagenomics-based insights into the microbial community and function of rhizosphere soils in Sinai desert farming systems

BACKGROUND

The microbiome of the Sinai Desert farming system plays an important role in the adaptive strategy of growing crops in a harsh, poly-extreme, desert environment. However, the diversity and function of microbial communities under this unfavorable moisture and nutritional conditions have not yet been investigated. Based on culturomic and metagenomic methods, we analyzed the microbial diversity and function of a total of fourteen rhizosphere soil samples (collected from twelve plants in four farms of the Sinai desert), which may provide a valuable and meaningful guidance for the design of microbial inoculants.

RESULTS

The results revealed a wide range of microbial taxa, including a high proportion of novel undescribed lineages. The composition of the rhizosphere microbial communities differed according to the sampling sites, despite similarities or differences in floristics. Whereas, the functional features of rhizosphere microbiomes were significantly similar in different sampling sites, although the microbial communities and the plant hosts themselves were different. Importantly, microorganisms involved in ecosystem functions are different between the sampling sites, for example nitrogen fixation was prevalent in all sample sites while microorganisms responsible for this process were different.

CONCLUSION

Here, we provide the first characterization of microbial communities and functions of rhizosphere soil from the Sinai desert farming systems and highlight its unexpectedly high diversity. This study provides evidence that the key microorganisms involved in ecosystem functions are different between sampling sites with different environment conditions, emphasizing the importance of the functional microbiomes of rhizosphere microbial communities. Furthermore, we suggest that microbial inoculants to be used in future agricultural production should select microorganisms that can be involved in plant-microorganism interactions and are already adapted to a similar environmental setting.

Mercury and other trace elements distribution and profiling of microbial community in the surface sediments of East Siberian Sea

In this study, total mercury (THg), methylmercury (MeHg), various trace elements, and microbial communities were measured in surface sediments of the East Siberian Sea (ESS). The results showed that the average values of THg and MeHg were 58.8 ± 15.21 μg/kg and 0.50 ± 0.22 μg/kg, respectively. The notable levels of trace elements present in both surface sediment and porewater were Al, Fe, and Mn. The enrichment factor and geoaccumulation index analyses found that both natural phenomena and anthropogenic activities contributed to elevated concentrations of metals in the ESS. The redox proxy metals, pH, and SO₄^2- were the major factors influencing the THg and MeHg distributions. Microbial profiles were substantially affected by metals and other abiotic factors. Proteobacteria and Thaumarchaeota were the most abundant phyla. Overall, the findings presented here facilitate the understanding of the current status of metal contamination, its influencing factors, and metal-microbiota-interactions in ESS.

Dynamic trophic shifts in bacterial and eukaryotic communities during the first 30 years of microbial succession following retreat of an Antarctic glacier

We examined microbial succession along a glacier forefront in the Antarctic Peninsula representing ∼30 years of deglaciation to contrast bacterial and eukaryotic successional dynamics and abiotic drivers of community assembly using sequencing and soil properties. Microbial communities changed most rapidly early along the chronosequence, and co-occurrence network analysis showed the most complex topology at the earliest stage. Initial microbial communities were dominated by microorganisms derived from the glacial environment, whereas later stages hosted a mixed community of taxa associated with soils. Eukaryotes became increasingly dominated by Cercozoa, particularly Vampyrellidae, indicating a previously unappreciated role for cercozoan predators during early stages of primary succession. Chlorophytes and Charophytes (rather than cyanobacteria) were the dominant primary producers and there was a spatio-temporal sequence in which major groups became abundant succeeding from simple ice Chlorophytes to Ochrophytes and Bryophytes. Time since deglaciation and pH were the main abiotic drivers structuring both bacterial and eukaryotic communities. Determinism was the dominant assembly mechanism for Bacteria, while the balance between stochastic/deterministic processes in eukaryotes varied along the distance from the glacier front. This study provides new insights into the unexpected dynamic changes and interactions across multiple trophic groups during primary succession in a rapidly changing polar ecosystem.

Insight into bacterial community profiles of oil shale and sandstone in ordos basin by culture-dependent and culture-independent methods

To promote the exploitation of unconventional oil resources by indigenous microorganisms, the bacterial community profiles of oil shale and sandstone in Ordos Basin were investigated using Illumina Miseq sequencing combined with the culture-based method, which was performed and reported in this literature for the first time. A total of 601 operational taxonomic units (OTUs) were obtained from collected samples, the predominant phylum present in all samples was Proteobacteria (76.96%-93.07%). Discriminatory bacterial community profiles existed in those samples by culture-dependent and culture-independent methods, with variations not only in diversity indices but also in the abundance of bacteria at different genus levels. The dominant genera in cultured sandstone sample (SCB), uncultured sandstone sample (SUB), cultured shale sample (YCB), uncultured shale sample (YUB) were Enhydrobacter (71.62%), Acidovorax (42.44%), Pseudomonas (40.13%), Variovorax (70.02%), respectively. Both sample sources and culturing methods were the principal factors affecting the variation, while the communities' structures were favored primarily by culture-dependent or culture-independent approaches. The high abundance of hydrocarbon degradation-related genes was exhibited in YCB, which reveals a great potential for utilization of the culture-dependent method in shale oil exploitation. This study provided guidance for the exploitation of shale oil and sandstone oil by artificial utilization of indigenous bacteria.

Rocks support a distinctive and consistent mycobiome across contrasting dry regions of Earth

Rock-dwelling fungi play critical ecological roles in drylands, including soil formation and nutrient cycling; however, we know very little about the identity, function and environmental preferences of these important organisms, and the mere existence of a consistent rock mycobiome across diverse arid regions of the planet remains undetermined. To address this knowledge gap, we conducted a meta-analysis of rock fungi and spatially associated soil communities, surveyed across 28 unique sites spanning four major biogeographic regions (North America, Arctic, Maritime and Continental Antarctica) including contrasting climates, from cold and hot deserts to semi-arid drylands. We show that rocks support a consistent and unique mycobiome that was different to that found in surrounding soils. Lichenized fungi from class Lecanoromycetes were consistently indicative of rocks across contrasting regions, together with ascomycetous representatives of black fungi in Arthoniomycetes, Dothideomycetes, and Eurotiomycetes. In addition, comparing to soil, rocks had a lower proportion of saprobes and plant symbiotic fungi. The main drivers structuring rock fungi distribution were spatial distance and, to a larger extent, climatic factors regulating moisture and temperature (i.e. mean annual temperature and mean annual precipitation), suggesting that these paramount and unique communities might be particularly sensitive to increases in temperature and desertification.

Amplicon Sequencing of Rock-Inhabiting Microbial Communities from Joshua Tree National Park, USA

Endolithic microorganisms have been reported to date in hot and cold drylands worldwide, where they represent the prevailing life forms ensuring ecosystem functionality, playing a paramount role in global biogeochemical processes. We report here an amplicon sequencing characterization of rocks collected from Joshua Tree National Park (JTNP), USA.

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.