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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Dynamic Rhizodeposition in the Woody Perennial Populus trichocarpa

Plants undergo physiological and metabolic changes that release specific molecules into the surrounding soil, a process collectively known as rhizodeposition. These compounds play crucial roles in plant‐microbe‐soil interactions, such as supporting plant development and resilience in changing environments. Under nutrient‐limited conditions, these plant‐derived compounds modify the rhizosphere environment, mobilizing otherwise inaccessible nutrients and recruiting stress‐adaptive microbial communities that support stress resilience. Currently, the chemical diversity of rhizodeposition has yet to be fully realized but is expected to be a complex mixture that includes soluble organic compounds excreted from root cells, along with products of root cell turnover, sloughed‐off root cap and border cells, and mucilage. Here, we developed a methodological and conceptual framework for an in‐depth measurement of rhizodeposition through critical advancements in untargeted metabolomics. Further, this approach provided foundational insights into the dynamic changes in rhizodeposition for the woody perennial Populus trichocarpa and rhizodeposit profiles varying by genotype, time, location, and environment. More broadly, this study provides a framework that will help formulate the next steps to effectively study rhizodeposition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

PPI DataHub Project Data Package: S. elongatus PCC 7942 Limited Proteolysis and Thermal Proteome Profiling Structural Proteomics (JM-PB-DP3)

The purpose of this experiment was to investigate structural alterations in proteins involved in central carbon metabolism and photosynthetic electron transfer pathways in Synechococcus elongatus PCC 7942. Sample data was obtained from S. elongatus cell lysates using three complementary mass spectrometry (MS) techniques using limited proteolysis (LiP-MS), thermal proteome profiling (TPP-MS), and redox enrichment (Redox-MS) in evaluating alterations solvent accessibility and structural stability caused by light perturbation at the molecular level. Experimentally processed sample data for LiP and TPP proteomic datasets were derived from the same cell culture stock, prepared simultaneously in parallel, and acquired by mass spectrometry. Processed datasets are openly accessible from the download button and contain secondary processed proteomic results files, computed outputs, and supporting metadata materials. Experimental samples processed for LiP-MS label-free quantification (LFQ) or TPP-MS tandem mass tag (TMT) 10-plex were acquired using a Q-Exactive HF-X mass spectrometer and processed/compiled using either MSGF+ (v2024.03.26) or ​​​​PlexedPiper for proteome evaluation. Additional software supporting downstream proteomic analysis include FragPipe (v.4.0), MSFragger (v.22.1), and an adapted Microbial Isolate LiP Analysis Workflow (located at Zenodo). Processed proteomic data downloads include a sample naming key, normalized quantification results files, and processed protein annotated abundance files.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Deciphering exopolysaccharide functional specificity via visualization of chemical motifs that mediate microbial-microenvironment interactions in soil micromodels

Exopolysaccharides (EPS) are carbohydrate-based matrices of microbial biofilms that microbes use to adapt to their surroundings. Microbial EPS also promotes soil aggregate stability and contributes toward soil health by reducing erosion caused by continued land use. The chemical structure of EPS, even within single species biofilms, can vary greatly: from repeating units and branching patterns to the non-carbohydrate decorations. Despite the wealth of knowledge on EPS chemistry, many unresolved questions regarding the biological implications of EPS chemical variations remain. Here, we develop a mass spectrometry imaging toolbox that reveal how EPS chemistry enables microbial adaptation to different microenvironments such as specific moisture, soil-biofilm interfaces, and food source proximity. First, we developed emulated soil micromodels (ESMs), microfluidic channels that simulate the physical properties of soil, for biofilm formation in different microenvironments. Then, in order to map chemical features of EPS in these micromodels, we develop strategies for in-situ releasing of oligosaccharides using specific enzymes. Lastly, we optimized matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging (MSI) to spatially analyze the released compounds in ESMs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Improving dairy manure hydrolysis and acidification through microbial community restructuring by adaptation to hyperthermophilic conditions

Dairy manure (DM) contributes significantly to greenhouse gas emissions and ecosystem degradation, yet its resistance to biodegradation hinders widespread bioprocessing applications. Lignocellulosic materials in DM pose a particular challenge because of their recalcitrance. Bioprocessing under hyperthermophilic (≥70 °C) conditions potentially offers an advantage over traditional fermentation temperatures due to enhanced activity of enzymes and the kinetics of enzymatic reactions. This can lead to a higher conversion rate and a greater extent of biomass hydrolysis and acidification. To test the validity of this hypothesis, the current study evaluated the efficacy of anaerobic hydrolysis and acidogenic fermentation of DM under mesophilic, thermophilic, and hyperthermophilic conditions. All inocula were adapted to corresponding temperatures but were derived from the same mesophilic source. Hyperthermophilic conditions resulted in superior DM hydrolysis efficiency (53%) compared to mesophilic (34%) and thermophilic (42%) conditions. The hyperthermophilic environment was particularly favorable to the decomposition of crude proteins and hemicellulose, which were reduced by 64% and 54%, respectively. Furthermore, hyperthermophilic fermentation also yielded the highest volatile fatty acid (VFA) production rate of 460 mg/L/day during the first four days, representing improvements of 50% and 90% over mesophilic and thermophilic conditions. In part, this was attributed to the enhanced production of branched-chain VFAs, including an increase of 6–10% in isobutyric acid and 12–13% in isovaleric acid. At hyperthermophilic conditions, however, there was no accumulation of VFAs during the days 5–8 of fermentation, which could be due to acetate conversion by the syntrophic acetate-oxidizing bacteria. A considerable gain in hydrolysis efficiency and VFA production rate were accompanied by a reduction in microbial diversity, which suggests that hyperthermophilic temperature is a favorable environment for the selection of organisms with enhanced DM hydrolysis and fermentation capabilities. A significantly increased relative abundance of xylanolytic Caldicoprobacter (23% of population) and proteolytic Thermovirga (9% of population) could be the major contributors to improved decomposition of hemicellulose and protein. As revealed by the techno-economic analysis, acidogenic fermentation of DM at 70 °C and a retention period of 4 days provides the greatest positive net present value, highest internal rate of return of 9.2%, and shortest investment payback period of 9 years. Furthermore, this study demonstrates that hyperthermophilic conditions enable superior deconstruction and bioconversion of lignocellulose-containing biomass into VFAs under reduced retention times, offering a promising approach for improving DM management and generating bioproducts.

09 BIOMASS FUELS↗
DOE OSTI2025

Editorial: Ecology, evolution, and biodiversity of microbiomes and viromes from extreme environments

Ecology, evolution, and biodiversity of microbiomes and viromes in extreme environments are key areas of research that explore how microbial communities adapt, survive, and thrive under harsh conditions. The studies published in our Research Topic advance our understanding of microbial and viral diversity, evolutionary processes, and the ecological roles of these communities, with implications for biotechnology, climate resilience, and even astrobiology.

adaptation↗
DOE OSTI2024

Thermal Adaptation of Enzyme‐Mediated Processes Reduces Simulated Soil CO2 Fluxes Upon Soil Warming

Abstract Understanding factors influencing carbon effluxes from soils to the atmosphere is important in a world experiencing climatic change. Two important uncertainties related to soil organic carbon (SOC) stock responses to a changing climate are (a) whether soil microbial communities acclimate or adapt to changes in soil temperature and (b) how to represent this process in SOC models. To further explore these issues, we included thermal adaptation of enzyme‐mediated processes in a mechanistic SOC model (ReSOM) using the macromolecular rate theory. Thermal adaptation is defined here to encompass all potential responses of soil microbes and microbial communities following a change in temperature. To assess the effects of thermal adaptation of enzyme‐mediated processes on simulated SOC losses, ReSOM was applied to data collected from a 13‐year soil warming experiment. Results show that a model omitting thermal adaptation of enzyme‐mediated processes substantially overestimates observed CO 2 effluxes during the initial years of soil warming. The bias against observed CO 2 effluxes was lower for models including thermal adaptation of enzyme‐mediated processes. In addition, for a simulated linear 3°C soil warming over 100 years, models including thermal adaptation of enzyme‐mediated processes simulated SOC losses of a factor of three smaller than models omitting this process. As thermal adaptation of microbial community characteristics is generally not included in models simulating feedback between the soil, biosphere and atmosphere, we encourage future studies to assess the potential impact that microbial adaptation has on soil carbon – climate feedback representations in models. Plain Language Summary A major uncertainty in projecting how much soil organic carbon (SOC) will be converted to CO 2 as a consequence of climate change is related to how soil microbes may adapt to increasing soil temperatures. While this “microbial thermal adaptation” has been shown to occur in short‐term lab incubation experiments, its effect on SOC cycling on a decadal timescale is not clear. To address this knowledge gap, a mechanistic SOC model was used to simulate data collected from a 13‐year soil warming experiment, to assess how microbial thermal adaptation affects predicted SOC losses upon soil warming. The model results show that incorporating microbial thermal adaptation into the model led to reduced CO 2 effluxes from the soil to the atmosphere compared to the common approach of omitting this mechanism. Our results imply that projected SOC losses for the decades to come may be reduced when this mechanism is incorporated in land models. We therefore advocate for more research on the mechanisms controlling microbial thermal adaptation, and how to implement this mechanism in SOC models. Key Points A crucial aspect of soil organic carbon (SOC) models is the representation of soil microbes Predicted soil CO 2 fluxes upon soil warming are reduced when accounting for microbial thermal adaptation On a centennial time scale, this thermal adaptation results in up to a factor of three lower predicted SOC loss

Van de Broek, Marijn↗
DOE OSTI2023

Microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics

This study describes the composition and potential metabolic adaptation of microbial communities in northeastern Siberia, a repository of the oldest permafrost in the Northern Hemisphere. Samples of contrasting depth (1.75 to 25.1 m below surface), age (from ~ 10 kyr to 1.1 Myr) and salinity (from low 0.1–0.2 ppt and brackish 0.3–1.3 ppt to saline 6.1 ppt) were collected from freshwater permafrost (FP) of borehole AL1_15 on the Alazeya River, and coastal brackish permafrost (BP) overlying marine permafrost (MP) of borehole CH1_17 on the East Siberian Sea coast. To avoid the limited view provided with culturing work, we used 16S rRNA gene sequencing to show that the biodiversity decreased dramatically with permafrost age. Nonmetric multidimensional scaling (NMDS) analysis placed the samples into three groups: FP and BP together (10–100 kyr old), MP (105–120 kyr old), and FP (> 900 kyr old). Younger FP/BP deposits were distinguished by the presence of Acidobacteriota, Bacteroidota, Chloroflexota_A, and Gemmatimonadota, older FP deposits had a higher proportion of Gammaproteobacteria, and older MP deposits had much more uncultured groups within Asgardarchaeota, Crenarchaeota, Chloroflexota, Patescibacteria, and unassigned archaea. The 60 recovered metagenome-assembled genomes and un-binned metagenomic assemblies suggested that despite the large taxonomic differences between samples, they all had a wide range of taxa capable of fermentation coupled to nitrate utilization, with the exception of sulfur reduction present only in old MP deposits.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Soil microbial EPS resiliency is influenced by carbon source accessibility

The adaptability of soil microbial communities to prolonged periods of drought is influenced by their ability to produce extracellular polymeric substances (EPS) with sufficient water retention properties. Microbial EPSs as water reservoirs during drought have been extensively investigated, but it remains unknown how carbon substrate accessibility to soil microbial communities will affect the chemical properties of the EPS they generate, and whether this in turn will alter their water retention ability. In this work, we observed that the accessibility of carbon substrates influenced microbial community structure and, consequently, the chemical properties of EPS produced by the microbial communities. Further, our results demonstrated that an insoluble carbon substrate (i.e., chitin), stimulated microbial communities to produce EPS with better water retention properties in comparison to a soluble carbon substrate (i.e., N-acetylglucosamine; NAG). In all, this study demonstrates the importance of carbon substrate accessibility by soil microorganisms in regulating the community structure and consequently, the EPS carbon chemistry, which in turn can greatly influence the adaptability of soil microbial communities to drought.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Adaptive modification of antiviral defense systems in microbial community under Cr-induced stress

Background The prokaryotic antiviral defense systems are crucial for mediating prokaryote-virus interactions that influence microbiome functioning and evolutionary dynamics. Despite the prevalence and significance of prokaryotic antiviral defense systems, their responses to abiotic stress and ecological consequences remain poorly understood in soil ecosystems. We established microcosm systems with varying concentrations of hexavalent chromium (Cr(VI)) to investigate the adaptive modifications of prokaryotic antiviral defense systems under abiotic stress. Results Utilizing hybrid metagenomic assembly with long-read and short-read sequencing, we discovered that anti- viral defense systems were more diverse and prevalent in heavily polluted soils, which was corroborated by meta-analyses of public datasets from various heavy metal-contaminated sites. As the Cr(VI) concentration increased, prokaryotes with defense systems favoring prokaryote-virus mutualism gradually supplanted those with defense systems incurring high adaptive costs. Additionally, as Cr(VI) concentrations increased, enriched antiviral defense systems exhibited synchronization with microbial heavy metal resistance genes. Furthermore, the proportion of antiviral defense systems carried by mobile genetic elements (MGEs), including plasmids and viruses, increased by approximately 43% and 39%, respectively, with rising Cr concentrations. This trend is conducive to strengthening the dissemination and sharing of defense resources within microbial communities. Conclusions Overall, our study reveals the adaptive modification of prokaryotic antiviral defense systems in soil ecosystems under abiotic stress, as well as their positive contributions to establishing prokaryote-virus mutualism and the evolution of microbial heavy metal resistance. These findings advance our understanding of microbial adaptation in stressful environments and may inspire novel approaches for microbiome manipulation and bioremediation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Quantitative genetic-by-soil microbiome interactions in a perennial grass affect functional traits

Plants interact with diverse microbiomes that can impact plant growth and performance. Recent studies highlight the potential beneficial aspects of plant microbiomes, including the possibility that microbes facilitate the process of local adaptation in their host plants. Microbially mediated local adaptation in plants occurs when local host genotypes have higher fitness than foreign genotypes because of their affiliation with locally beneficial microbes. Here, plant adaptation results from genetic interactions of the host with locally beneficial microbes (e.g. host genotype-by-microbiome interactions). We used a recombinant inbred line (RIL) mapping population derived from upland and lowland ecotypes of the diploid C4 perennial bunch grass Panicum hallii to explore quantitative genetic responses to soil microbiomes focusing on functional root and shoot traits involved in ecotypic divergence. We show that the growth and development of ecotypes and their trait divergence depends on soil microbiomes. Moreover, we find that the genetic architecture is modified by soil microbiomes, revealing important plant genotype-by-microbiome interactions for quantitative traits. We detected a number of quantitative trait loci (QTL) that interact with the soil microbiome. Our results highlight the importance of microbial interactions in ecotypic divergence and trait genetic architecture in C4 perennial grasses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Characterization of prokaryotic communities in Puerto Rican caves using 16S rDNA amplicon sequencing

The cave ecosystems host microbial communities adapted to extreme environments. This study utilized 16S rDNA to investigate the prokaryotic diversity across seven caves in Puerto Rico’s northern limestone karst belt. Microbial profiling revealed distinct subterranean communities, enhancing our understanding of cave microbiology and potential applications in environmental conservation and microbial research.

16S↗
DOE OSTI2024

From wolves to humans: oral microbiome resistance to transfer across mammalian hosts

The mammalian mouth is colonized by complex microbial communities, adapted to specific niches, and in homeostasis with the host. Individual microbes interact metabolically and rely primarily on nutrients provided by the host, with which they have potentially co-evolved along the mammalian lineages. The oral environment is similar across mammals, but the diversity, specificity, and evolution of community structure in related or interacting mammals are little understood. Here, we compared the oral microbiomes of dogs with those of wild wolves and humans. In dogs, we found an increased microbial diversity relative to wolves, possibly related to the transition to omnivorous nutrition following domestication. This includes a larger diversity of Patescibacteria than previously reported in any other oral microbiota. The oral microbes are most distinct at bacterial species or strain levels, with few if any shared between humans and canids, while the close evolutionary relationship between wolves and dogs is reflected by numerous shared taxa. More taxa are shared at higher taxonomic levels including with humans, supporting their more ancestral common mammalian colonization followed by diversification. Phylogenies of selected oral bacterial lineages do not support stable human-dog microbial transfers but suggest diversification along mammalian lineages (apes and canids). Therefore, despite millennia of cohabitation and close interaction, the host and its native community controls and limits the assimilation of new microbes, even if closely related. Higher resolution metagenomic and microbial physiological studies, covering a larger mammalian diversity, should help understand how oral communities assemble, adapt, and interact with their hosts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The gut microbiome mediates adaptation to scarce food in Coleoptera

Beetles are ubiquitous cave invertebrates worldwide that adapted to scarce subterranean resources when they colonized caves. Here, we investigated the potential role of gut microbiota in the adaptation of beetles to caves from different climatic regions of the Carpathians. The beetles’ microbiota was host-specific, reflecting phylogenetic and nutritional adaptation. The microbial community structure further resolved conspecific beetles by caves suggesting microbiota-host coevolution and influences by local environmental factors. The detritivore species hosted a variety of bacteria known to decompose and ferment organic matter, suggesting turnover and host cooperative digestion of the sedimentary microbiota and allochthonous-derived nutrients. The cave Carabidae, with strong mandibula, adapted to predation and scavenging of animal and plant remains, had distinct microbiota dominated by symbiotic lineages Spiroplasma or Wolbachia. All beetles had relatively high levels of fermentative Carnobacterium and Vagococcus involved in lipid accumulation and a reduction of metabolic activity, and both features characterize adaptation to caves.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Dairy manure acidogenic fermentation at hyperthermophilic temperature enabled superior activity of thermostable hydrolytic enzymes linked to the genus Caldicoprobacter

In this study, fermentation experiments were conducted under mesophilic, thermophilic, and hyperthermophilic conditions to investigate adaptation of microbial communities and its effect on extracellular enzyme activities toward degradation of cellulose, hemicellulose and proteins in dairy manure. Here, hyperthermophilic conditions transformed the microbiome structure and stimulated activity of extracellular proteolytic, cellulolytic, and hemicellulolytic enzymes. Specifically, the activities of protease, cellulose 1,4-β-cellobiosidase, and β-glucosidase secreted by hyperthermophilic microbes were higher by 22%, 47% and 49% compared to those produced by mesophilic and thermophilic communities. Enhanced hydrolytic activity of hyperthermophilic microbes enabled improved feedstock solubilization and production of 39% and 22% more soluble COD than mesophilic and thermophilic microbes, respectively. Connections between hydrolytic function and microbial community structure at various temperatures were assessed using the PICRUSt2 computational tool. Genus Caldicoprobacter was identified as the primary candidate responsible for increased production of thermostable endo-1,4-β-glucanase, β-glucosidase and endo-1,4-β-xylanase, and enhanced hydrolytic performance of hyperthermophilic microbial community.

09 BIOMASS FUELS↗
DOE OSTI2023

Uncovering the dominant role of root metabolism in shaping rhizosphere metabolome under drought in tropical rainforest plants

Plant-soil-microbe interactions are crucial for driving rhizosphere processes that contribute to metabolite turnover and nutrient cycling. With the increasing frequency and severity of water scarcity due to climate warming, understanding how plant-mediated processes, such as root exudation, influence soil organic matter turnover in the rhizosphere is essential. In this study, we used 16S rRNA gene amplicon sequencing, rhizosphere metabolomics, and position-specific 13 C-pyruvate labeling to examine the effects of three different plant species (Piper auritum, Hibiscus rosa sinensis, and Clitoria fairchildiana) and their associated microbial communities on soil organic carbon turnover in the rhizosphere. Here, our findings indicate that in these tropical plants, the rhizosphere metabolome is primarily shaped by the response of roots to drought rather than direct shifts in the rhizosphere bacterial community composition. Specifically, the reduced exudation of plant roots had a notable effect on the metabolome of the rhizosphere of P. auritum, with less reliance on neighboring microbes. Contrary to P. auritum, H. rosa sinensis and C. fairchildiana experienced changes in their exudate composition during drought, causing alterations to the bacterial communities in the rhizosphere. This, in turn, had a collective impact on the rhizosphere's metabolome. Furthermore, the exclusion of phylogenetically distant microbes from the rhizosphere led to shifts in its metabolome. Additionally, C. fairchildiana appeared to be associated with only a subset of symbiotic bacteria under drought conditions. These results indicate that plant species-specific microbial interactions systematically change with the root metabolome. As roots respond to drought, their associated microbial communities adapt, potentially reinforcing the drought tolerance strategies of plant roots. These findings have significant implications for maintaining plant health and preference during drought stress and improving plant performance under climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Salinity tolerance mechanisms of an Arctic Pelagophyte using comparative transcriptomic and gene expression analysis

Abstract Little is known at the transcriptional level about microbial eukaryotic adaptations to short-term salinity change. Arctic microalgae are exposed to low salinity due to sea-ice melt and higher salinity with brine channel formation during freeze-up. Here, we investigate the transcriptional response of an ice-associated microalgae over salinities from 45 to 8. Our results show a bracketed response of differential gene expression when the cultures were exposed to progressively decreasing salinity. Key genes associated with salinity changes were involved in specific metabolic pathways, transcription factors and regulators, protein kinases, carbohydrate active enzymes, and inorganic ion transporters. The pelagophyte seemed to use a strategy involving overexpression of Na + -H + antiporters and Na + -Pi symporters as salinity decreases, but the K + channel complex at higher salinities. Specific adaptation to cold saline arctic conditions was seen with differential expression of several antifreeze proteins, an ice-binding protein and an acyl-esterase involved in cold adaptation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Clostridioides difficile utilizes siderophores as an iron source and FhuDBGC contributes to ferrichrome uptake

ABSTRACT Clostridioides difficileremains a public health threat commonly observed following antibiotic use. Due to the importance of iron in many cell processes, most bacteria, includingC. difficile, have multiple mechanisms of acquiring iron. Previous studies have examined ferrous iron uptake inC. difficile; here we focus on the role of siderophores. In a growth assay, we show thatC. difficilecan use a variety of siderophores as the sole iron source. InC. difficile,two ABC transporters induced under low iron conditions are predicted siderophore importers: FhuDBGC and YclNOPQ. We hypothesized that these transporters are responsible for the uptake of the siderophores we tested. To investigate the specificity of these transporters, we purified the substrate binding proteins and examined siderophore binding using thermal shift. We demonstrate increased stability between one siderophore binding protein, FhuD, and the siderophore ferrichrome, suggesting a binding interaction. This specificity correlates with the inability of anΔfhuDBGCmutant to grow efficiently under iron limiting conditions in the presence of ferrichrome. WhileC. difficileused additional siderophores in our growth experiments, we did not observe increased thermal stability between the receptor proteins and any of the other siderophores tested, suggesting these siderophores do not bind these receptors and other siderophore import mechanisms remain to be elucidated. Redundancy in iron acquisition is a microbial survival adaptation to cope with the constant battle for iron within a host. Greater knowledge about howC. difficileacquires iron will provide insight about howC. difficilecolonizes and persists in the colon. IMPORTANCE This study is the first example ofC. difficilegrowing with siderophores as the sole iron source and describes the characterization of the ferric hydroxamate uptake ABC transporter (FhuDBGC). This transporter shows specificity to the siderophore ferrichrome. While not required for pathogenesis, this transporter highlights the redundancy in iron acquisition mechanisms thatC. difficileuses to compete for iron during an infection.

Microbiology↗
DOE OSTI2020

Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium

Background: Acidophilic members of the genus Streptomyces can be a good source for novel secondary metabolites and degradative enzymes of biopolymers. In this study, a genome-based approach on Streptomyces yeochonensis CN732, a representative neutrotolerant acidophilic streptomycete, was employed to examine the biosynthetic as well as enzymatic potential, and also presence of any genetic tools for adaptation in acidic environment. Results: A high quality draft genome (7.8Mb) of S. yeochonensis CN732 was obtained with a G+C content of 73.53% and 6549 protein coding genes. The in silico analysis predicted presence of multiple biosynthetic gene clusters (BGCs), which showed similarity with those for antimicrobial, anticancer or antiparasitic compounds. However, the low levels of similarity with known BGCs for most cases suggested novelty of the metabolites from those predicted gene clusters. The production of various novel metabolites was also confirmed from the combined high performance liquid chromatography-mass spectrometry analysis. Through comparative genome analysis with related Streptomyces species, genes specific to strain CN732 and also those specific to neutrotolerant acidophilic species could be identified, which showed that genes for metabolism in diverse environment were enriched among acidophilic species. In addition, the presence of strain specific genes for carbohydrate active enzymes (CAZyme) along with many other singletons indicated uniqueness of the genetic makeup of strain CN732. The presence of cysteine transpeptidases (sortases) among the BGCs was also observed from this study, which implies their putative roles in the biosynthesis of secondary metabolites. Conclusions: This study highlights the bioactive potential of strain CN732, an acidophilic streptomycete with regard to secondary metabolite production and biodegradation potential using genomics based approach. The comparative genome analysis revealed genes specific to CN732 and also those among acidophilic species, which could give some insights into the adaptation of microbial life in acidic environment.

59 BASIC BIOLOGICAL SCIENCES↗