Can biocrust moss hide from climate change? Fine-scale habitat sheltering improves summer stress resistance in Syntrichia caninervis

PREMISE

Mosses provide many ecosystem functions and are the most vulnerable of biocrust organisms to climate change due to their sensitive water relations stressed by summer aridity. Given their small size, moss stress resistance may be more dependent on fine-scale habitat than macroclimate, but the sheltering role of habitat (i.e., habitat buffering) has never been compared to macroclimate and may have important implications for predicting critical biocrust moss refugia in changing climates.

METHODS

We located three populations of a keystone biocrust moss, Syntrichia caninervis, spanning 1200 m of altitude, which comprised three macroclimate (elevation) zones of characterized plant communities in the Mojave Desert. We stratified 92 microsites along three aridity gradients: elevation zone, topography (aspect), and microhabitat (shrub proximity). We estimated summer photosynthetic stress (Fv/Fm) and aridity exposure (macroclimate, irradiance, and shade).

RESULTS

Microsite aridity exposure varied greatly, revealing exposed and buffered microhabitats at all three elevation zones. Moss stress did not differ by elevation zone despite the extensive macroclimate gradient, failing to support the high-elevation refugia hypothesis. Instead, stress was lowest on northerly-facing slopes and in microhabitats with greater shrub shading, while the importance of (and interactions between) topography, irradiance, and shade varied by elevation zone.

CONCLUSIONS

Fine-scale habitat structure appears physiologically more protective than high-elevation macroclimate and may protect some biocrust mosses from the brunt of climate change in widespread microrefugia throughout their current ranges. Our findings support a scale-focused vulnerability paradigm: microrefugia may be more important than macrorefugia for bolstering biocrust moss resistance to summer climate stress.

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.

BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event

Determining which microorganisms are active within soil communities remains a major technical endeavor in microbial ecology research. One promising method to accomplish this is coupling bioorthogonal non-canonical amino acid tagging (BONCAT) with fluorescence activated cell sorting (FACS) which sorts cells based on whether or not they are producing new proteins. Combined with shotgun metagenomic sequencing (Seq), we apply this method to profile the diversity and potential functional capabilities of both active and inactive microorganisms in a biocrust community after being resuscitated by a simulated rain event. We find that BONCAT-FACS-Seq is capable of discerning the pools of active and inactive microorganisms, especially within hours of applying the BONCAT probe. The active and inactive components of the biocrust community differed in species richness and composition at both 4 and 21 h after the wetting event. The active fraction of the biocrust community is marked by taxa commonly observed in other biocrust communities, many of which play important roles in species interactions and nutrient transformations. Among these, 11 families within the Firmicutes are enriched in the active fraction, supporting previous reports indicating that the Firmicutes are key early responders to biocrust wetting. We highlight the apparent inactivity of many Actinobacteria and Proteobacteria through 21 h after wetting, and note that members of the Chitinophagaceae, enriched in the active fraction, may play important ecological roles following wetting. Based on the enrichment of COGs in the active fraction, predation by phage and other bacterial members, as well as scavenging and recycling of labile nutrients, appear to be important ecological processes soon after wetting. To our knowledge, this is the first time BONCAT-FACS-Seq has been applied to biocrust samples, and therefore we discuss the potential advantages and shortcomings of coupling metagenomics to BONCAT to intact soil communities such as biocrust. In all, by pairing BONCAT-FACS and metagenomics, we are capable of highlighting the taxa and potential functions that typifies the microbes actively responding to a rain event.

Adaptation to Environmental Extremes Structures Functional Traits in Biological Soil Crust and Hypolithic Microbial Communities

Biological soil crusts (biocrusts) are widespread in drylands and deserts. At the microhabitat scale, they also host hypolithic communities that live under semitranslucent stones. Both environmental niches experience exposure to extreme conditions such as high UV radiation, desiccation, temperature fluctuations, and resource limitation. However, hypolithic communities are somewhat protected from extremes relative to biocrust communities. Conditions are otherwise similar, so comparing them can answer outstanding questions regarding adaptations to environmental extremes. Using metagenomic sequencing, we assessed the functional potential of dryland soil communities and identified the functional underpinnings of ecological niche differentiation in biocrusts versus hypoliths. We also determined the effect of the anchoring photoautotroph (moss or cyanobacteria). Genes and pathways differing in abundance between biocrusts and hypoliths indicate that biocrust communities adapt to the higher levels of UV radiation, desiccation, and temperature extremes through an increased ability to repair damaged DNA, sense and respond to environmental stimuli, and interact with other community members and the environment. Intracellular competition appears to be crucial to both communities, with biocrust communities using the Type VI Secretion System (T6SS) and hypoliths favoring a diversity of antibiotics. The dominant primary producer had a reduced effect on community functional potential compared with niche, but an abundance of genes related to monosaccharide, amino acid, and osmoprotectant uptake in moss-dominated communities indicates reliance on resources provided to heterotrophs by mosses. Our findings indicate that functional traits in dryland communities are driven by adaptations to extremes and we identify strategies that likely enable survival in dryland ecosystems. IMPORTANCE Biocrusts serve as a keystone element of desert and dryland ecosystems, stabilizing soils, retaining moisture, and serving as a carbon and nitrogen source in oligotrophic environments. Biocrusts cover approximately 12% of the Earth's terrestrial surface but are threatened by climate change and anthropogenic disturbance. Given their keystone role in ecosystem functioning, loss will have wide-spread consequences. Biocrust microbial constituents must withstand polyextreme environmental conditions including high UV exposure, desiccation, oligotrophic conditions, and temperature fluctuations over short time scales. By comparing biocrust communities with co-occurring hypolithic communities (which inhabit the ventral sides of semitranslucent stones and are buffered from environmental extremes), we identified traits that are likely key adaptations to extreme conditions. These include DNA damage repair, environmental sensing and response, and intracellular competition. Comparison of the two niches, which differ primarily in exposure levels to extreme conditions, makes this system ideal for understanding how functional traits are structured by the environment.

Lithic cyanobacterial communities in the polyextreme Sahara Desert: implications for the search for the limits of life

The hyperarid Sahara Desert presents extreme and persistent dry conditions with a limited number of hours during which the moisture availability, temperature and light allow phototrophic growth. Some cyanobacteria can live in these hostile conditions by seeking refuge under (hypolithic) or inside (endolithic) rocks, by colonizing porous spaces (cryptoendoliths) or fissures in stones (chasmoendoliths). Chroococcidiopsis spp. have been reported as the dominant or even the only phototrophs in these hot desert lithic communities. However, the results of this study reveal the high diversity of and variability in cyanobacteria among the sampled habitats in the Sahara Desert. The chasmoendolithic samples presented high coccoid cyanobacteria abundances, although the dominant cyanobacteria were distinct among different locations. A high predominance of a newly described cyanobacterium, Pseudoacaryochloris sahariense, was found in hard, compact, and more opaque stones with cryptoendolithic colonization. On the other hand, the hypolithic samples were dominated by filamentous, non-heterocystous cyanobacteria. Thermophysiological bioassays confirmed desiccation and extreme temperature tolerance as drivers in the cyanobacterial community composition of these lithic niches. The results of the present study provide key factors for understanding life strategies under polyextreme environmental conditions. The isolated strains, especially the newly described cyanobacterium P. sahariense, might represent suitable microorganisms in astrobiology studies aimed at investigating the limits of life.

Insights into dryland biocrust microbiome: geography, soil depth and crust type affect biocrust microbial communities and networks in Mojave Desert, USA

Biocrusts are the living skin of drylands, comprising diverse microbial communities that are essential to desert ecosystems. Despite there being extensive knowledge on biocrust ecosystem functions and lichen and moss biodiversity, little is known about factors structuring diversity among their microbial communities. We used amplicon-based metabarcode sequencing to survey microbial communities from biocrust surface and subsurface soils at four sites located within the Mojave Desert. Five biocrust types were examined: Light-algal/Cyanobacteria, Cyanolichen, Green-algal lichen, Smooth-moss and Rough-moss crust types. Microbial diversity in biocrusts was structured by several characteristics: (i) central versus southern Mojave sites displayed different community signatures, (ii) indicator taxa of plant-associated fungi (plant pathogens and wood saprotrophs) were identified at each site, (iii) surface and subsurface microbial communities were distinct and (iv) crust types had distinct indicator taxa. Network analysis ranked bacteria-bacteria interactions as the most connected of all within-domain and cross-domain interaction networks in biocrust surface samples. Actinobacteria, Proteobacteria, Cyanobacteria and Ascomycota functioned as hubs among all phyla. The bacteria Pseudonocardia sp. (Pseudonocardiales, Actinobacteria) and fungus Alternaria sp. (Pleosporales, Ascomycota) were the most connected had the highest node degree. Our findings provide crucial insights for dryland microbial community ecology, conservation and sustainable management.