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At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The survivor strain: isolation and characterization of Phormidium yuhuli AB48, a filamentous phototactic cyanobacterium with biotechnological potential

Despite their recognized potential, current applications of cyanobacteria as microbial cell factories remain in early stages of development. This is partly due to the fact that engineered strains are often difficult to grow at scale. This technical challenge contrasts with the dense and highly productive cyanobacteria populations thriving in many natural environments. It has been proposed that the selection of strains pre-adapted for growth in industrial photobioreactors could enable more productive cultivation outcomes. Here, we described the initial morphological, physiological, and genomic characterization of Phormidium yuhuli AB48 isolated from an industrial photobioreactor environment. P. yuhuli AB48 is a filamentous phototactic cyanobacterium with a growth rate comparable to Synechocystis sp . PCC 6803. The isolate forms dense biofilms under high salinity and alkaline conditions and manifests a similar nutrient profile to Arthrospira platensis ( Spirulina ). We sequenced, assembled, and analyzed the P. yuhuli AB48 genome, the first closed circular isolate reference genome for a member of the Phormidium genus. We then used cultivation experiments in combination with proteomics and metabolomics to investigate growth characteristics and phenotypes related to industrial scale cultivation, including nitrogen and carbon utilization, salinity, and pH acclimation, as well as antibiotic resistance. These analyses provide insight into the biological mechanisms behind the desirable growth properties manifested by P. yuhuli AB48 and position it as a promising microbial cell factory for industrial-scale bioproduction[221, 1631].

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Community structure and function during periods of high performance and system upset in a full-scale mixed microalgal wastewater resource recovery facility

Microalgae have the potential to exceed current nutrient recovery limits from wastewater, enabling water resource recovery facilities (WRRFs) to achieve increasingly stringent effluent permits. The use of photobioreactors (PBRs) and the separation of hydraulic retention and solids residence time (HRT/SRT) further enables increased biomass in a reduced physical footprint while allowing operational parameters (e.g., SRT) to select for desired functional communities. However, as algal technology transitions to full-scale, there is a need to understand the effect of operational and environmental parameters on complex microbial dynamics among mixotrophic microalgae, bacterial groups, and pests (i.e., grazers and pathogens) and to implement robust process controls for stable long-term performance. Here, we examine a full-scale, intensive WRRF utilizing mixed microalgae for tertiary treatment in the US (EcoRecover, Clearas Water Recovery Inc.) during a nine-month monitoring campaign. We investigated the temporal variations in microbial community structure (18S and 16S rRNA genes), which revealed that stable system performance of the EcoRecover system was marked by a low-diversity microalgal community (D INVSIMPSON = 2.01) dominated by Scenedesmus sp. (MRA = 55 %-80 %) that achieved strict nutrient removal (effluent TP < 0.04 mg·L -1 ) and steady biomass concentration (TSS monthly avg . = 400–700 mg·L −1 ). Operational variables including pH, alkalinity, and influent ammonium (NH 4 + ), correlated positively (p < 0.05, method = Spearman) with algal community during stable performance. Further, the use of these parameters as operational controls along with N/P loading and SRT allowed for system recovery following upset events. Importantly, the presence or absence of bacterial nitrification did not directly impact algal system performance and overall nutrient recovery, but partial nitrification (potentially resulting from NO 2 − accumulation) inhibited algal growth and should be considered during long-term operation. The microalgal communities were also adversely affected by zooplankton grazers (ciliates, rotifers) and fungal parasites (Aphelidium), particularly during periods of upset when algal cultures were experiencing culture turnover or stress conditions (e.g., nitrogen limitation, elevated temperature). Altogether, the active management of system operation in order to maintain healthy algal cultures and high biomass productivity can result in significant periods (>4 months) of stable system performance that achieve robust nutrient recovery, even in winter months in northern latitudes (WI, USA).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2022

Mineral Protection and Resource Limitations Combine to Explain Profile-Scale Soil Carbon Persistence

The fate of soil carbon (C) is largely controlled by microbial oxidation of organic matter (OM), which is constrained by a variety of mechanisms. OM association with soil minerals provides pronounced protection against microbial decomposition. However, factors such as climate, occlusion, and resource limitations also contribute to OM preservation. Here, we explore the factors explaining C distribution and age within an upland rainforest soil in Hawai'i, a site with abundant preferential flow paths (PFPs) and high short-range order (SRO) mineral content. We characterized lateral and vertical changes in Δ 14 C, SRO mineral content, C-functional group chemistry, and microbial community composition to elucidate the contributions of multiple protection mechanisms to OM preservation. Consistent with our expectation, SRO mineral content and Δ 14 C were strongly correlated (R 2 = 0.95), indicating strong mineral protection of OM throughout the profile. Surprisingly, distance from PFP was also a significant predictor of Δ 14 C and improved model fit, particularly in the shallow horizons (R 2 = 0.97). Elevated C/N ratios, decreased microbial abundance, and greater SRO mineral content suggest nitrogen limitations and enhanced mineral protection constrain OM turnover with distance from PFPs in deep, subsurface mineral horizons. Steady microbial abundance, increasing putative anaerobe abundance, and changes in C-functional group chemistry indicate oxygen limitations constrain OM turnover in the matrix of shallow mineral horizons. Given that oxygen and nutrient limitations contribute to OM preservation in this high SRO system—an exemplar of mineral protection—resource limitations may play an even more important role in OM preservation in other well-structured soils.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Effect of tectonic processes on biosphere–geosphere feedbacks across a convergent margin

The subsurface is among Earth’s largest biomes, but the extent to which microbial communities vary across tectonic plate boundaries or interact with subduction-scale geological processes remains unknown. Here we compare bacterial community composition with deep-subsurface geochemistry from 21 hot springs across the Costa Rican convergent margin. We find that cation and anion compositions of the springs reflect the dip angle and position of the underlying tectonic structure and also correlate with the bacterial community. Co-occurring microbial cliques related to cultured chemolithoautotrophs that use the reverse tricarboxylic acid cycle (rTCA) as well as abundances of metagenomic rTCA genes correlate with concentrations of slab-volatilized carbon. This, combined with carbon isotope evidence, suggests that fixation of slab-derived CO2 into biomass may support a chemolithoautotrophy-based subsurface ecosystem. We calculate that this forearc subsurface biosphere could sequester 1.4 × 10 9 to 1.4 × 10 10 mol of carbon per year, which would decrease estimates of the total carbon delivered to the mantle by 2 to 22%. Furthermore, based on the observed correlations, we suggest that distribution and composition of the subsurface bacterial community are probably affected by deep tectonic processes across the Costa Rican convergent margin and that, by sequestering carbon volatilized during subduction, these chemolithoautotrophic communities could in turn impact the geosphere.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2017

Field Exploration and Life Detection Sampling Through Planetary Analogue Sampling (FELDSPAR).

Exploration missions to Mars rely on rovers to perform analyses over small sampling areas; however, landing sites for these missions are selected based on large-scale, low-resolution remote data. The use of Earth analogue environments to estimate the multi-scale spatial distributions of key signatures of habitability can help ensure mission science goals are met. A main goal of FELDSPAR is to conduct field operations analogous to Mars sample return in its science, operations, and technology from landing site selection, to in-field sampling location selection, remote or stand-off analysis, in situ analysis, and home laboratory analysis. Lava fields and volcanic regions are relevant analogues to Martian landscapes due to desiccation, low nutrient availability, and temperature extremes. Operationally, many Icelandic lava fields are remote enough to require that field expeditions address several sampling constraints that are experienced in robotic exploration, including in situ and sample return missions. The Fimmvruhls lava field was formed by a basaltic effusive eruption associated with the 2010 Eyjafjallajkull eruption. Mlifellssandur is a recently deglaciated plain to the north of the Myrdalsjkull glacier. Holuhraun was formed by a 2014 fissure eruptions just north of the large Vatnajkull glacier. Dyngjusandur is an alluvial plain apparently kept barren by repeated mechanical weathering. Informed by our 2013 expedition, we collected samples in nested triangular grids every decade from the 10 cm scale to the 1 km scale (as permitted by the size of the site). Satellite imagery is available for older sites, and for Mlifellssandur, Holuhraun, and Dyngjusandur we obtained overhead imagery at 1 m to 200 m elevation. PanCam-style photographs were taken in the field by sampling personnel. In-field reflectance spectroscopy was also obtained with an ASD spectrometer in Dyngjusandur. All sites chosen were 'homogeneous' in apparent color, morphology, moisture, grain size, and reflectance spectra at all scales greater than 10 cm. Field lab assays were conducted to monitor microbial habitation, including ATP quantification, qPCR for fungal, bacterial, and archaeal DNA, and direct cell imaging using fluorescence microscopy. Home laboratory analyses include Raman spectroscopy and community sequencing. ATP appeared to be significantly more sensitive to small changes in sampling location than qPCR or fluorescence microscopy. Bacterial and archaeal DNA content were more consistent at the smaller scales, but similarly variable across more distant sites. Conversely, cell counts and fungal DNA content have significant local variation but appear relatively homogeneous over scales of 1 km. ATP, bacterial DNA, and archaeal DNA content were relatively well correlated at many spatial scales. While we have observed spatial variation at various scales and are beginning to observe how that variation fluctuates over time as biodiversity recovers after an eruption, we do not yet fully understand what parameters lead to the observed spatial variation. Home laboratory analyses will help us further understand the elemental and structural composition of the basaltic matrices, but further field analyses are vital for the understanding how temperature, moisture, incident radiation, and so forth influence the habitability of a microclimate.

Field↗
DOE OSTI2026

Harnessing photoenzymatic reactions for unnatural biosynthesis in microorganisms

Photobiocatalysis provides a powerful strategy for integrating light and biological catalysts to drive abiological transformations. However, its scalability is hindered by high enzyme loading, reliance on costly cofactors and instability under radical-generating conditions. Here we report the integration of light-driven enzymatic reactions into the cellular metabolism of Escherichia coli, bridging flavin-based photobiocatalysis with biosynthesis. Using synthetic biology strategies, we engineered microbial cells to continuously produce olefin substrates and ene-reductase while regenerating cofactors directly from glucose. By externally supplying radical precursors or introducing synthetic pathways for their in situ production, we enabled fermentation-based microbial photobiosynthesis, achieving high titres and demonstrating feasibility for scale-up in a bioreactor. This approach extends photobiocatalysis from in vitro applications to in vivo semi- and complete biosynthesis, revealing its full potential for integrating light-driven reactions into cellular metabolism.

Biocatalysis↗
DOE OSTI2026

Multidimensional scaling informed by F -statistic: Visualizing grouped microbiome data with inference

Multidimensional scaling (MDS) is a widely used dimensionality reduction technique in microbial ecology data analysis that captures the multivariate structure of the data while preserving pairwise distances between samples. While improvements in MDS have enhanced the ability to reveal group-specific data patterns, these MDS-based methods require prior assumptions for inference, limiting their application in general microbiome analysis. Here, in this study, we introduce a new MDS-based ordination method, “F-informed MDS,” which configures the data distribution based on the F-statistic, the ratio of dispersion between groups sharing common and different characteristics. Using semisynthetic datasets, we demonstrate that the proposed method is robust to hyperparameter selection while maintaining statistical significance throughout the ordination process. Various quality metrics for evaluating dimensionality reduction confirm that F-informed MDS is comparable to state-of-the-art methods in preserving both local and global data structures. Its application to a diatom-associated bacterial community suggests the role of this new method in interpreting the community’s response to the host. Our approach offers a well-founded refinement of MDS that aligns with statistical test results, which can be beneficial for broader multidimensional data analyses in microbiology and ecology. This new visualization tool can be incorporated into standard microbiome data analyses.

Biological and medical sciences↗
DOE OSTI2025

Potential Risks Associated with Short-Term Hydrogen Storage in Methane Reservoirs

Hydrogen (H2) has been identified as a flexible energy carrier with zero emissions. It is possible to utilize H2 by storing Hyblend, or H2 blended with CH4, in existing natural gas infrastructure. However, the compatibility of adapting the current CH4 storage strategies to include H2 injection has not been fully demonstrated. It is essential that we understand the impact of H2 gas on the naturally occurring microbial community of subsurface storage reservoirs before deploying large-scale H2-CH4 storage. We designed a series of experiments that allowed us to identify potential challenges of HyBlend Storage in existing methane reservoirs (Figure 1). First, we characterized two field fluid samples from a methane reservoir located in Western United States. Next, we used these samples to complete a series of short-term reactor experiments at reservoir conditions for a natural gas (100% CH4) and HyBlend (80% CH4/20% H2) storage environment.

geomicrobiology↗
DOE OSTI2021

Contrasting Community Assembly Forces Drive Microbial Structural and Potential Functional Responses to Precipitation in an Incipient Soil System

Microbial communities in incipient soil systems serve as the only biotic force shaping landscape evolution. However, the underlying ecological forces shaping microbial community structure and function are inadequately understood. We used amplicon sequencing to determine microbial taxonomic assembly and metagenome sequencing to evaluate microbial functional assembly in incipient basaltic soil subjected to precipitation. Community composition was stratified with soil depth in the pre-precipitation samples, with surficial communities maintaining their distinct structure and diversity after precipitation, while the deeper soil samples appeared to become more uniform. The structural community assembly remained deterministic in pre- and post-precipitation periods, with homogenous selection being dominant. Metagenome analysis revealed that carbon and nitrogen functional potential was assembled stochastically. Sub-populations putatively involved in the nitrogen cycle and carbon fixation experienced counteracting assembly pressures at the deepest depths, suggesting the communities may functionally assemble to respond to short-term environmental fluctuations and impact the landscape-scale response to perturbations. We propose that contrasting assembly forces impact microbial structure and potential function in an incipient landscape; in situ landscape characteristics (here homogenous parent material) drive community structure assembly, while short-term environmental fluctuations (here precipitation) shape environmental variations that are random in the soil depth profile and drive stochastic sub-population functional dynamics.

16S amplicon sequencing↗
DOE OSTI2022

Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station

The International Space Station (ISS) is a unique and complex built environment with the ISS surface microbiome originating from crew and cargo or from life support recirculation in an almost entirely closed system. The Microbial Tracking 1 (MT-1) project was the first ISS environmental surface study to report on the metagenome profiles without using whole-genome amplification. The study surveyed the microbial communities from eight surfaces over a 14-month period. The Microbial Tracking 2 (MT-2) project aimed to continue the work of MT-1, sampling an additional four flights from the same locations, over another 14 months. Eight surfaces across the ISS were sampled with sterile wipes and processed upon return to Earth. DNA extracted from the processed samples (and controls) were treated with propidium monoazide (PMA) to detect intact/viable cells or left untreated and to detect the total DNA population (free DNA/compromised cells/intact cells/viable cells). DNA extracted from PMA-treated and untreated samples were analyzed using shotgun metagenomics. Samples were cultured for bacteria and fungi to supplement the above results. Staphylococcus sp. and Malassezia sp. were the most represented bacterial and fungal species, respectively, on the ISS. Overall, the ISS surface microbiome was dominated by organisms associated with the human skin. Multi-dimensional scaling and differential abundance analysis showed significant temporal changes in the microbial population but no spatial differences. The ISS antimicrobial resistance gene profiles were however more stable over time, with no differences over the 5-year span of the MT-1 and MT-2 studies. Twenty-nine antimicrobial resistance genes were detected across all samples, with macrolide/lincosamide/streptogramin resistance being the most widespread. Metagenomic assembled genomes were reconstructed from the dataset, resulting in 82 MAGs. Functional assessment of the collective MAGs showed a propensity for amino acid utilization over carbohydrate metabolism. Co-occurrence analyses showed strong associations between bacterial and fungal genera. Culture analysis showed the microbial load to be on average 3.0 × 10 5 cfu/m 2 . Utilizing various metagenomics analyses and culture methods, we provided a comprehensive analysis of the ISS surface microbiome, showing microbial burden, bacterial and fungal species prevalence, changes in the microbiome, and resistome over time and space, as well as the functional capabilities and microbial interactions of this unique built microbiome. Data from this study may help to inform policies for future space missions to ensure an ISS surface microbiome that promotes astronaut health and spacecraft integrity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Evaluation of Degradation Mechanisms for Solid Secondary Waste Grout Waste Forms

The overall objective of this work is to provide defensibility for the long-term performance of grouted Hanford SSW streams when disposed in a near surface disposal facility, IDF, on the Hanford Site. Providing defensibly for the long-term performance of the grouted waste forms is consistent with the research and development activities identified in the Performance Assessment Maintenance Plan, (Westcott et al. 2019), that are necessary to address the assumptions made in the PA. Specifically, this work addresses two areas identified for further research and development activities in the plan: (1) “Evaluate ongoing research on transport characteristics of cementitious materials using accelerated tests to approximate the effects of aging/alteration/weathering”; and (2) “Evaluate ongoing research on microbial effects on transport processes in cementitious materials.” The assembled subject matter expert team evaluated a list of degradation mechanisms and supporting processes and provided rankings of areas where further research and development (R&D) are needed. From this assessment, high priority R&D areas include: (1) the effects of carbonation, Ca leaching, and SSW dimensional change in grout waste forms; (2) updated model representations of grouted waste forms; and (3) scaled testing demonstrations. Moderate priority items including a paper study on possible microbial influence, reoxidation rates, radionuclide/contaminant dissolution from SSW in the grout and freeze thaw behavior. Other processes evaluated were either deemed unlikely to occur, to have little impact on the SSW waste forms, or to occur at time frames beyond those considered (>10,000 years). The assessments and proposed R&D approaches are expected to support an update to the WRPS SSW roadmap.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
NASA NTRS2020

Environmental factors driving spatial heterogeneity in desert halophile microbial communities

Spatial heterogeneity in microbial communities is observed in all-natural ecosystems and can stem from both adaptations to local environmental conditions as well as stochastic processes. Extremophile microbial communities inhabiting evaporitic halite nodules (salt rocks) in the Atacama Desert, Chile, are a good model ecosystem for investigating factors leading to microbiome heterogeneity, due to their diverse taxonomic composition and the spatial segregation of individual nodules. We investigated the abiotic factors governing microbiome composition across different spatial scales, allowing for insight into the factors that govern halite colonization from regional desert-wide scales to micro-scales within individual nodules. We found that water availability and community drift account for microbiome assembly differently at different distance scales, with higher rates of cell dispersion at the smaller scales resulting in a more homogenous composition. This trend likely applies to other endoliths, and to non desert communities, where dispersion between communities is limited. At the intra-nodule scales, a light availability gradient was most important in determining the distribution of microbial taxa despite intermixing by water displacement via capillary action.

microbiome extremophile, desert, heterogeneity, Me↗
DOE OSTI2023

Root and Microbial Soil CO 2 and CH 4 Fluxes Respond Differently to Seasonal and Episodic Environmental Changes in a Temperate Forest

Upland forest soils are typically major atmospheric carbon dioxide (CO 2 ) sources and methane (CH 4 ) sinks, but the contributions of root and microbial processes, as well as their separate temporal responses to environmental change, remain poorly understood. This 2-year study was conducted in a temperate, deciduous forest located on the Chesapeake Bay in Maryland, USA. We used temporal CO 2 and CH 4 flux measurements, exclusion-source partitioning, and an ecosystem-scale flooding experiment to understand how carbon (C) fluxes, and their root and microbial sources, respond to seasonal and episodic environmental change. Here, we show that the root-and-rhizosphere component of soil CO 2 and CH 4 flux is significant and that its dependence on soil temperature and volumetric water content (VWC) influences soil C dynamics at seasonal timescales. Experimental flooding shows that CO 2 and CH 4 flux responses to episodic moisture change were driven by suppression of soil heterotrophs, while root respiration did not respond to transient hydrologic disturbance. Methane uptake responded strongly to episodic inundation, reinforcing the important role of soil moisture in the short-term control of the forest soil CH 4 sink. However, despite the clear seasonality of CH 4 uptake, as well as its strong response to short-term experimental inundation, temperature and VWC were weak predictors of CH 4 uptake at a seasonal timescale. We suggest that CH 4 consumption in the long-term may be determined by vegetation, nutrients, microbial communities, or other factors correlated with seasonal changes. Our results indicate that root and microbial sources of both CO 2 and CH 4 flux respond differently in timing and magnitude to seasonal and episodic environmental change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology

Abstract Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine

The human microbiome influences the efficacy and safety of a wide variety of commonly prescribed drugs. Designing precision medicine approaches that incorporate microbial metabolism would require strain- and molecule-resolved, scalable computational modeling. Here, we extend our previous resource of genome-scale metabolic reconstructions of human gut microorganisms with a greatly expanded version. AGORA2 (assembly of gut organisms through reconstruction and analysis, version 2) accounts for 7,302 strains, includes strain-resolved drug degradation and biotransformation capabilities for 98 drugs, and was extensively curated based on comparative genomics and literature searches. The microbial reconstructions performed very well against three independently assembled experimental datasets with an accuracy of 0.72 to 0.84, surpassing other reconstruction resources and predicted known microbial drug transformations with an accuracy of 0.81. We demonstrate that AGORA2 enables personalized, strain-resolved modeling by predicting the drug conversion potential of the gut microbiomes from 616 patients with colorectal cancer and controls, which greatly varied between individuals and correlated with age, sex, body mass index and disease stages. AGORA2 serves as a knowledge base for the human microbiome and paves the way to personalized, predictive analysis of host–microbiome metabolic interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

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.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2022

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 semi-translucent 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 waging war using the Type VI Secretion System (T6SS) and hypoliths favoring 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.

Biological soil crusts↗