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DOE OSTI2024

Eco-evolutionary strategies for relieving carbon limitation under salt stress differ across microbial clades

With the continuous expansion of saline soils under climate change, understanding the eco-evolutionary tradeoff between the microbial mitigation of carbon limitation and the maintenance of functional traits in saline soils represents a significant knowledge gap in predicting future soil health and ecological function. Through shotgun metagenomic sequencing of coastal soils along a salinity gradient, we show contrasting eco-evolutionary directions of soil bacteria and archaea that manifest in changes to genome size and the functional potential of the soil microbiome. In salt environments with high carbon requirements, bacteria exhibit reduced genome sizes associated with a depletion of metabolic genes, while archaea display larger genomes and enrichment of salt-resistance, metabolic, and carbon-acquisition genes. This suggests that bacteria conserve energy through genome streamlining when facing salt stress, while archaea invest in carbon-acquisition pathways to broaden their resource usage. These findings suggest divergent directions in eco-evolutionary adaptations to soil saline stress amongst microbial clades and serve as a foundation for understanding the response of soil microbiomes to escalating climate change.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1992

Long-term lunar stations: Some ecological considerations

A major factor for long-term success of a lunar station is the ability to keep an agroecosystem functioning at a desirable, stable steady-state with ecological stability and reliability. Design for a long-lived extraterrestrial manned station must take into account interactions among its subsystems to insure that overall functionality is enhanced (or at least not compromised). Physical isolation of feed production, human living areas, recycling, and other systems may be straightforward, however, microbiological isolation will be very difficult. While it is possible to eliminate plant-associated microbiological communities by growing the plants asepticallly, it is not practical to keep plants germ-free on a large scale if humans are working with them. Ecological theory strongly suggests that some kinds of communities or organisms effectively increase the stability of ecosystems and will protect the plants from potential pathogens. A carefully designed and maintained (lunar-derived) soil can provide a variety of habitats for effective microbial buffers while adding structure to the agroecosystem. A soil can also increase ecosystem reliability through buffering otherwise large element and compound fluctuations (of nutrients, wastes, etc.) as well as buffering temperature level and atmosphere composition. We are doing experiments in ecological dynamics and attempting to extend the relevant theories.

Maguire, Bassett, Jr.↗

DOE OSTI2023

Reducing uncertainty of high-latitude ecosystem models through identification of key parameters

Abstract Climate change is having significant impacts on Earth’s ecosystems and carbon budgets, and in the Arctic may drive a shift from an historic carbon sink to a source. Large uncertainties in terrestrial biosphere models (TBMs) used to forecast Arctic changes demonstrate the challenges of determining the timing and extent of this possible switch. This spread in model predictions can limit the ability of TBMs to guide management and policy decisions. One of the most influential sources of model uncertainty is model parameterization. Parameter uncertainty results in part from a mismatch between available data in databases and model needs. We identify that mismatch for three TBMs, DVM-DOS-TEM, SIPNET and ED2, and four databases with information on Arctic and boreal above- and belowground traits that may be applied to model parametrization. However, focusing solely on such data gaps can introduce biases towards simple models and ignores structural model uncertainty, another main source for model uncertainty. Therefore, we develop a causal loop diagram (CLD) of the Arctic and boreal ecosystem that includes unquantified, and thus unmodeled, processes. We map model parameters to processes in the CLD and assess parameter vulnerability via the internal network structure. One important substructure, feed forward loops (FFLs), describe processes that are linked both directly and indirectly. When the model parameters are data-informed, these indirect processes might be implicitly included in the model, but if not, they have the potential to introduce significant model uncertainty. We find that the parameters describing the impact of local temperature on microbial activity are associated with a particularly high number of FFLs but are not constrained well by existing data. By employing ecological models of varying complexity, databases, and network methods, we identify the key parameters responsible for limited model accuracy. They should be prioritized for future data sampling to reduce model uncertainty.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Hidden Processes During Seasonal Isolation of a High-Altitude Watershed

Biogeochemical processes capable of altering global carbon systems occur frequently in Earth’s Critical Zone–the area spanning from vegetation canopy to saturated bedrock–yet many of these phenomena are difficult to detect. Observation of these processes is limited by the seasonal inaccessibility of remote ecosystems, such as those in mountainous, snow- and ice-dominated areas. This isolation leads to a distinct gap in biogeochemical knowledge that ultimately affects the accuracy and confidence with which these ecosystems can be computationally modeled for the purpose of projecting change under different climate scenarios. To examine a high-altitude, headwater ecosystem’s role in methanogenesis, sulfate reduction, and groundwater-surface water exchange, water samples were continuously collected from the river and hyporheic zones (HZ) during winter isolation in the East River (ER), CO watershed. Measurements of continuously collected ER surface water revealed up to 50 μM levels of dissolved methane in July through September, while samples from 12 cm deep in the hyporheic zone at the same location showed a spring to early summer peak in methane with a strong biogenic signature (<65 μM, δ13C-CH4, -60.76‰) before declining. Continuously collected δ 18 O-H 2 O and δ 2 H-H 2 O isotopes from the water column exhibited similar patterns to discrete measurements, while samples 12 cm deep in the hyporheic zone experienced distinct fluctuations in δ 18 O-H 2 O, alluding to significant groundwater interactions. Continuously collected microbial communities in the river in the late fall and early winter revealed diverse populations that reflect the taxonomic composition of ecologically similar river systems, including taxa indicative of methane cycling in this system. These measurements captured several biogeochemical components of the high-altitude watershed in response to seasonality, strengthening our understanding of these systems during the winter months.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1992

Survival of epiphytic bacteria from seed stored on the Long Duration Exposure Facility (LDEF)

Microbial contamination in American spacecraft has previously been documented, however, potential risks to plants and humans in future space based controlled ecological life support systems (CELSS) have yet to be addressed directly. The current study was designed to determine the survival of microorganisms exposed to the relatively harsh conditions found in low Earth orbit (LEO). Total mean dosage for flight and ground control seeds were 210.2 and 0.9 rads, respectively. Bacteria were isolated by plating samples of seedwashings onto dilute tryptic soy agar. Pure isolates of morphologically distinct bacteria were obtained by standard microbiological procedures. Bacteria were grouped according to colony type and preliminary identification was completed using a fatty acid analysis system. Bacillus spp. were the primary microorganisms that survived on seed during the experiment. Results support the hypothesis that terrestrial microorganisms can survive long periods of time in relatively harsh LEO environments.

Schuerger, Andrew C.↗

DOE OSTI2021

Microbial Biomass in Soils Receiving Varying Levels of Organic Inputs - A Data Compilation

This dataset contains soil microbial biomass data compiled from published laboratory studies and field manipulations of organic inputs to soils. Each study included at least three levels of a given type of organic input applied to a given type of soil. Studies were selected from the literature that had experimentally manipulated organic input rates to soils using unburned, non-synthetic material (e.g. plant litters, manures, and composts). Fifty-five (55) studies, conducted from 1997 to October 2019, were chosen and compiled into a dataset with 358 observations from 96 combinations of a given organic material applied to a given soil in agricultural systems, laboratory incubations, forests, or grasslands. • Studies were selected when biomass measurements used the chloroform fumigation-extraction procedure followed by carbon analysis, or, in two instances, studies estimated microbial biomass using phospholipid fatty acid analysis. • Studies that used fewer than three input rates or characterized microbial biomass via substrate induced respiration were excluded. • The temporal and spatial aspects of the laboratory and field studies were not essential to the analyses (Craig et al., 2021) and were not included with the measurement data. These data were used to assess the relationship between organic input amounts and microbial biomass. Complete reference citations are provided if additional information is needed. The compiled data are provided in two .csv files: (1) soil treatments and microbial biomass data and (2) literature citations. The “Study” field is the cross reference between files. Also provided is the R code for reproducing the results in the related publication.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient

Anthropogenic-driven climate change is accelerating permafrost thaw, threatening to release vast carbon stores through increased microbial activity. While microbial roles are increasingly studied, the contributions of viruses remain largely unexplored, in part due to soil-associated technical challenges that have hindered their detection and characterization. Here, we applied an optimized virion enrichment workflow along a permafrost thaw gradient, identifying 9,963 viral populations (vOTUs), including single- and double-stranded DNA viruses, with 99.9% novelty compared to other soils. Hosts were predicted for 38% of vOTUs, spanning nine archaeal, and 36 bacterial phyla, 22% of which were linked to metagenome-assembled genomes, including key carbon-cycling taxa. Genomic analyses revealed 811 putative auxiliary metabolic genes (AMGs) from 658 vOTUs, nearly half involved in carbon processing. These included 59 glycoside hydrolases (GH) across nine GH families, 45 for monosaccharide degradation, and seven involved in short-chain fatty acid and C1 metabolism, linking viruses to both early and late stages of carbon turnover. Additionally, six vOTUs carried racD, which may stabilize microbial necromass and promote long-term carbon storage. Viral and AMG functional diversity increased with thaw stage, indicating that viruses might participate in a broadening range of microbial metabolic processes as permafrost thaws. These findings expand our understanding of virus contributions in microbial carbon processing and suggest their important role in deciphering soil carbon fate under changing climate conditions.

Biological and medical sciences↗

DOE OSTI2020

Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom

Background: Lagoons are common along coastlines worldwide and are important for biogeochemical element cycling, coastal biodiversity, coastal erosion protection and blue carbon sequestration. These ecosystems are frequently disturbed by weather, tides, and human activities. Here, we investigated a shallow lagoon in New England. The brackish ecosystem releases hydrogen sulfide particularly upon physical disturbance, causing blooms of anoxygenic sulfur-oxidizing phototrophs. To study the habitat, microbial community structure, assembly and function we carried out in situ experiments investigating the bloom dynamics over time. Results: Phototrophic microbial mats and permanently or seasonally stratified water columns commonly contain multiple phototrophic lineages that coexist based on their light, oxygen and nutrient preferences. We describe similar coexistence patterns and ecological niches in estuarine planktonic blooms of phototrophs. The water column showed steep gradients of oxygen, pH, sulfate, sulfide, and salinity. The upper part of the bloom was dominated by aerobic phototrophic Cyanobacteria, the middle and lower parts by anoxygenic purple sulfur bacteria (Chromatiales) and green sulfur bacteria (Chlorobiales), respectively. We show stable coexistence of phototrophic lineages from five bacterial phyla and present metagenome-assembled genomes (MAGs) of two uncultured Chlorobaculum and Prosthecochloris species. In addition to genes involved in sulfur oxidation and photopigment biosynthesis the MAGs contained complete operons encoding for terminal oxidases. The metagenomes also contained numerous contigs affiliating with Microviridae viruses, potentially affecting Chlorobi. Our data suggest a short sulfur cycle within the bloom in which elemental sulfur produced by sulfide-oxidizing phototrophs is most likely reduced back to sulfide by Desulfuromonas sp. Conclusions: The release of sulfide creates a habitat selecting for anoxygenic sulfur-oxidizing phototrophs, which in turn create a niche for sulfur reducers. Strong syntrophism between these guilds apparently drives a short sulfur cycle that may explain the rapid development of the bloom. The fast growth and high biomass yield of Chlorobi-affiliated organisms implies that the studied lineages of green sulfur bacteria can thrive in hypoxic habitats. This oxygen tolerance is corroborated by oxidases found in MAGs of uncultured Chlorobi. The findings improve our understanding of the ecology and ecophysiology of anoxygenic phototrophs and their impact on the coupled biogeochemical cycles of sulfur and carbon.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Microbial sensor variation across biogeochemical conditions in the terrestrial deep subsurface

ABSTRACT Microbes can be found in abundance many kilometers underground. While microbial metabolic capabilities have been examined across different geochemical settings, it remains unclear how changes in subsurface niches affect microbial needs to sense and respond to their environment. To address this question, we examined how microbial extracellular sensor systems vary with environmental conditions across metagenomes at different Deep Mine Microbial Observatory (DeMMO) subsurface sites. Because two-component systems (TCSs) directly sense extracellular conditions and convert this information into intracellular biochemical responses, we expected that this sensor family would vary across isolated oligotrophic subterranean environments that differ in abiotic and biotic conditions. TCSs were found at all six subsurface sites, the service water control, and the surface site, with an average of 0.88 sensor histidine kinases (HKs) per 100 genes across all sites. Abundance was greater in subsurface fracture fluids compared with surface-derived fluids, and candidate phyla radiation (CPR) bacteria presented the lowest HK frequencies. Measures of microbial diversity, such as the Shannon diversity index, revealed that HK abundance is inversely correlated with microbial diversity ( r 2 = 0.81). Among the geochemical parameters measured, HK frequency correlated most strongly with variance in dissolved organic carbon ( r 2 = 0.82). Taken together, these results implicate the abiotic and biotic properties of an ecological niche as drivers of sensor needs, and they suggest that microbes in environments with large fluctuations in organic nutrients (e.g., lacustrine, terrestrial, and coastal ecosystems) may require greater TCS diversity than ecosystems with low nutrients (e.g., open ocean). IMPORTANCE The ability to detect extracellular environmental conditions is a fundamental property of all life forms. Because microbial two-component sensor systems convert information about extracellular conditions into biochemical information that controls their behaviors, we evaluated how two-component sensor systems evolved within the deep Earth across multiple sites where abiotic and biotic properties vary. We show that these sensor systems remain abundant in microbial consortia at all subterranean sampling sites and observe correlations between sensor system abundances and abiotic (dissolved organic carbon variation) and biotic (consortia diversity) properties. These results suggest that multiple environmental properties may drive sensor protein evolution and highlight the need for further studies of metagenomic and geochemical data in parallel to understand the drivers of microbial sensor evolution.

response regulator↗

DOE OSTI2023

Nutrients strengthen density dependence of per-capita growth and mortality rates in the soil bacterial community

Density dependence in an ecological community has been observed in many macro-organismal ecosystems and is hypothesized to maintain biodiversity but is poorly understood in microbial ecosystems. Here, in this study, we analyze data from an experiment using quantitative stable isotope probing (qSIP) to estimate per-capita growth and mortality rates of bacterial populations in soils from several ecosystems along an elevation gradient which were subject to nutrient addition of either carbon alone (glucose; C) or carbon with nitrogen (glucose + ammonium-sulfate; C + N). Across all ecosystems, we found that higher population densities, quantified by the abundance of genomes per gram of soil, had lower per-capita growth rates in C + N-amended soils. Similarly, bacterial mortality rates in C + N-amended soils increased at a significantly higher rate with increasing population size than mortality rates in control and C-amended soils. In contrast to the hypothesis that density dependence would promote or maintain diversity, we observed significantly lower bacterial diversity in soils with stronger negative density-dependent growth. Here, density dependence was significantly but weakly responsive to nutrients and was not associated with higher bacterial diversity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Microbial Drivers of Plant Performance during Drought Depend upon Community Composition and the Greater Soil Environment

The increasing occurrence of drought is a global challenge that threatens food security through direct impacts to both plants and their interacting soil microorganisms. Plant growth promoting microbes are increasingly being harnessed to improve plant performance under stress. However, the magnitude of microbiome impacts on both structural and physiological plant traits under water limited and water replete conditions are not well-characterized. Using two microbiomes sourced from a ponderosa pine forest and an agricultural field, we performed a greenhouse experiment that used a crossed design to test the individual and combined effects of the water availability and the soil microbiome composition on plant performance. Specifically, we studied the structural and leaf functional traits of maize that are relevant to drought tolerance. We further examined how microbial relationships with plant phenotypes varied under different combinations of microbial composition and water availability. We found that water availability and microbial composition affected plant structural traits. Surprisingly, they did not alter leaf function. Maize grown in the forest-soil microbiome produced larger plants under well-watered and water-limited conditions, compared to an agricultural soil community. Although leaf functional traits were not significantly different between the watering and microbiome treatments, the bacterial composition and abundance explained significant variability in both plant structure and leaf function within individual treatments, especially water-limited plants. Our results suggest that bacteria-plant interactions that promote plant performance under stress depend upon the greater community composition and the abiotic environment.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Antarctic lake viromes reveal potential virus associated influences on nutrient cycling in ice-covered lakes

The McMurdo Dry Valleys (MDVs) of Antarctica are a mosaic of extreme habitats which are dominated by microbial life. The MDVs include glacial melt holes, streams, lakes, and soils, which are interconnected through the transfer of energy and flux of inorganic and organic material via wind and hydrology. For the first time, we provide new data on the viral community structure and function in the MDVs through metagenomics of the planktonic and benthic mat communities of Lakes Bonney and Fryxell. Viral taxonomic diversity was compared across lakes and ecological function was investigated by characterizing auxiliary metabolic genes (AMGs) and predicting viral hosts. Our data suggest that viral communities differed between the lakes and among sites: these differences were connected to microbial host communities. AMGs were associated with the potential augmentation of multiple biogeochemical processes in host, most notably with phosphorus acquisition, organic nitrogen acquisition, sulfur oxidation, and photosynthesis. Viral genome abundances containing AMGs differed between the lakes and microbial mats, indicating site specialization. Using procrustes analysis, we also identified significant coupling between viral and bacterial communities (p = 0.001). Finally, host predictions indicate viral host preference among the assembled viromes. Collectively, our data show that: (i) viruses are uniquely distributed through the McMurdo Dry Valley lakes, (ii) their AMGs can contribute to overcoming host nutrient limitation and, (iii) viral and bacterial MDV communities are tightly coupled.

Microbiology↗

DOE OSTI2022

Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

When deep-sea hydrothermal fluids mix with cold oxygenated fluids, minerals precipitate out of solution and form hydrothermal deposits. These actively venting deep-sea hydrothermal deposits support a rich diversity of thermophilic microorganisms which are involved in a range of carbon, sulfur, nitrogen, and hydrogen metabolisms. Global patterns of thermophilic microbial diversity in deep-sea hydrothermal ecosystems have illustrated the strong connectivity between geological processes and microbial colonization, but little is known about the genomic diversity and physiological potential of these novel taxa. Here we explore this genomic diversity in 42 metagenomes from four deep-sea hydrothermal vent fields and a deep-sea volcano collected from 2004 to 2018 and document their potential implications in biogeochemical cycles. Our dataset represents 3635 metagenome-assembled genomes encompassing 511 novel and recently identified genera from deep-sea hydrothermal settings. Some of the novel bacterial (107) and archaeal genera (30) that were recently reported from the deep-sea Brothers volcano were also detected at the deep-sea hydrothermal vent fields, while 99 bacterial and 54 archaeal genera were endemic to the deep-sea Brothers volcano deposits. We report some of the first examples of medium- (≥ 50% complete, ≤ 10% contaminated) to high-quality (> 90% complete, < 5% contaminated) MAGs from phyla and families never previously identified, or poorly sampled, from deep-sea hydrothermal environments. We greatly expand the novel diversity of Thermoproteia, Patescibacteria (Candidate Phyla Radiation, CPR), and Chloroflexota found at deep-sea hydrothermal vents and identify a small sampling of two potentially novel phyla, designated JALSQH01 and JALWCF01. Metabolic pathway analysis of metagenomes provides insights into the prevalent carbon, nitrogen, sulfur, and hydrogen metabolic processes across all sites and illustrates sulfur and nitrogen metabolic “handoffs” in community interactions. We confirm that Campylobacteria and Gammaproteobacteria occupy similar ecological guilds but their prevalence in a particular site is driven by shifts in the geochemical environment. Our study of globally distributed hydrothermal vent deposits provides a significant expansion of microbial genomic diversity associated with hydrothermal vent deposits and highlights the metabolic adaptation of taxonomic guilds. Collectively, our results illustrate the importance of comparative biodiversity studies in establishing patterns of shared phylogenetic diversity and physiological ecology, while providing many targets for enrichment and cultivation of novel and endemic taxa.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Effect of CO 2 Concentration on the Microbial Activity of Orenia metallireducens (Strain Z6) in Surface Inert Materials

Carbon dioxide (CO 2 ) sequestration has garnered widespread attention as a key strategy for mitigating CO 2 emissions and combating the greenhouse effect. However, the mechanisms underlying the interactions between CO 2 , widespread siliceous minerals and biological processes remain unclear. The present study explored the potential impacts of different CO 2 concentrations on microbial activity, environmental conditions and their feedback on the fate of CO 2 . A total of 20 experimental conditions was created, with the variables including different natural and synthetic siliceous minerals (e.g., quartz sand and a type of commercial glass beads), the presence or absence of the iron-reducing microorganism Orenia metallireducens (strain Z6) and varying CO 2 concentrations (0%, 20%, 50%, 100%) in the presence of ferrihydrite and pyruvate. Geochemical, microbial and mineralogical analyses revealed that elevated CO 2 concentrations significantly inhibited microbial Fe(III) reduction and pyruvate metabolism. Interestingly, compared to cultures without mineral amendments or those with glass beads alone, the addition of quartz sand enabled strain Z6 to better withstand the environmental stress caused by elevated CO 2 , promoting pyruvate fermentation and iron reduction. In addition to an increased pH, the formation of siderite, hematite and vivianite was also observed in the bioactive systems. Although both glass beads and quartz sand were primarily composed of silica, differences in the mineral structure, elemental composition and acid neutralization capacity rendered quartz sand more chemically active and unexpectedly led to greater CO 2 sequestration.

CO2 stress↗

DOE OSTI2024

Species-specific ribosomal RNA-FISH identifies interspecies cellular-material exchange, active-cell population dynamics and cellular localization of translation machinery in clostridial cultures and co-cultures

ABSTRACT The development of synthetic microbial consortia in recent years has revealed that complex interspecies interactions, notably the exchange of cytoplasmic material, exist even among organisms that originate from different ecological niches. Although morphogenetic characteristics, viable RNA and protein dyes, and fluorescent reporter proteins have played an essential role in exploring such interactions, we hypothesized that ribosomal RNA-fluorescence in situ hybridization (rRNA-FISH) could be adapted and applied to further investigate interactions in synthetic or semisynthetic consortia. Despite its maturity, several challenges exist in using rRNA-FISH as a tool to quantify individual species population dynamics and interspecies interactions using high-throughput instrumentation such as flow cytometry. In this work, we resolve such challenges and apply rRNA-FISH to double and triple co-cultures of Clostridium acetobutylicum, Clostridium ljungdahlii, and Clostridium kluyveri . In pursuing our goal to capture each organism’s population dynamics, we demonstrate dynamic rRNA, and thus ribosome, exchange between the three species leading to the formation of hybrid cells. We also characterize the localization patterns of the translation machinery in the three species, identifying distinct, dynamic localization patterns among them. Our data also support the use of rRNA-FISH to assess the culture’s health and expansion potential, and, here again, our data find surprising differences among the three species examined. Taken together, our study argues for rRNA-FISH as a valuable and accessible tool for quantitative exploration of interspecies interactions, especially in organisms which cannot be genetically engineered or in consortia where selective pressures to maintain recombinant species cannot be used. IMPORTANCE Though dyes and fluorescent reporter proteins have played an essential role in identifying microbial species in co-cultures, we hypothesized that ribosomal RNA-fluorescence in situ hybridization (rRNA-FISH) could be adapted and applied to quantitatively probe complex interactions between organisms in synthetic consortia. Despite its maturity, several challenges existed before rRNA-FISH could be used to study Clostridium co-cultures of interest. First, species-specific probes for Clostridium acetobutylicum and Clostridium ljungdahlii had not been developed. Second, “state-of-the-art” labeling protocols were tedious and often resulted in sample loss. Third, it was unclear if FISH was compatible with existing fluorescent reporter proteins. We resolved these key challenges and applied the technique to co-cultures of C. acetobutylicum , C. ljungdahlii , and Clostridium kluyveri . We demonstrate that rRNA-FISH is capable of identifying rRNA/ribosome exchange between the three organisms and characterized rRNA localization patterns in each. In combination with flow cytometry, rRNA-FISH can capture sub-population dynamics in co-cultures.

Hill, John D.↗

NASA NTRS2004

Microbial Response to Microgravity and Other Low Shear Environments

Microbial existence and survival requires the ability to sense and respond to environmental changes, including changes in physical forces. This is because microbes inhabit an amazingly diverse range of ecological niches and therefore must constantly adapt to a wide variety of changing environmental conditions, including alterations in temperature, pH, nutrient availability, oxygen levels, and osmotic pressure gradients. Microbes sense their environment through a variety of sensors and receptors which serve to integrate the different signals into the appropriate cellular response(s) that is optimal for survival. While numerous environmental stimuli have been examined for their effect on microorganisms, effects due to changes in mechanical and/or physical forces are also becoming increasingly apparent. Recently, several important studies have demonstrated a key role for microgravity and the low fluid shear dynamics associated with microgravity in the regulation of microbial gene expression, physiology and pathogenesis. The mechanosensory response of microorganisms to these environmental signals, which are relevant to those encountered during microbial life cycles on Earth, may provide insight into their adaptations to physiologically relevant conditions and may ultimately lead to eludicidation of the mechanisms important for mechanosensory transduction in living cells. This review summarizes the recent and potential future research trends aimed at understanding the effect of changes in mechanical forces that occur in microgravity and other low shear environments on different microbial parameters. The results of these studies provide an important step towards understanding how microbes integrate information from multiple mechanical stimuli to an appropriate physiological response.

Nickerson, C.↗

DOE OSTI2021

Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes

Although secondary metabolites are typically associated with competitive or pathogenic interactions, the high bioactivity of endophytic fungi in the Xylariales, coupled with their abundance and broad host ranges spanning all lineages of land plants and lichens, suggests that enhanced secondary metabolism might facilitate symbioses with phylogenetically diverse hosts. Here, we examined secondary metabolite gene clusters (SMGCs) across 96 Xylariales genomes in two clades (Xylariaceae s.l. and Hypoxylaceae), including 88 newly sequenced genomes of endophytes and closely related saprotrophs and pathogens. We paired genomic data with extensive metadata on endophyte hosts and substrates, enabling us to examine genomic factors related to the breadth of symbiotic interactions and ecological roles. All genomes contain hyperabundant SMGCs; however, Xylariaceae have increased numbers of gene duplications, horizontal gene transfers (HGTs) and SMGCs. Enhanced metabolic diversity of endophytes is associated with a greater diversity of hosts and increased capacity for lignocellulose decomposition. Our results suggest that, as host and substrate generalists, Xylariaceae endophytes experience greater selection to diversify SMGCs compared with more ecologically specialised Hypoxylaceae species. Altogether, our results provide new evidence that SMGCs may facilitate symbiosis with phylogenetically diverse hosts, highlighting the importance of microbial symbioses to drive fungal metabolic diversity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Changing Microbiomes: A Symposium Hosted by the Microbiome Center at the Pennsylvania State University

The first “Changing Microbiomes” conference was successfully held at the Pennsylvania State University from May 31st – June 3rd, 2022. The overall goal of the symposium was to provide space for researchers to connect, exchange knowledge, and partner to advance our understanding of the mechanisms and applications of ecological and evolutionary changes in microbiomes across systems. The symposium spanned terrestrial and aquatic contexts and host-associated and free-living microbial communities. As such, the symposium will enable cross-disciplinary knowledge and idea exchange to promote future interdisciplinary collaborations. In addition, the program allowed formal and informal interactions between and among students, postdocs, PIs, and industry scientists.

54 ENVIRONMENTAL SCIENCES↗