Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “microbial hosts”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
NASA NTRS2025

Influence of Microgravity on Bacterial Pathogen Virulence and Immune Cell Function—Relevance for Infectious Disease Risk During Spaceflight

Spaceflight has measurable impacts on astronaut immune profiles as well as the virulence patterns of bacterial pathogens. Data with respect to human immunity indicate diminished T and NK cell function, altered cytokine profiles, persistent inflammation, and latent herpesvirus reactivation. Furthermore, evaluation of International Space Station (ISS) crewmembers gives evidence of compromised immunity, including atypical allergy, infectious disease, and dermatitis. Data with respect to certain human bacterial pathogens suggest modified virulence that may be enhanced. It is therefore critical to examine this interaction of immune dysregulation and increased microbial virulence and whether it might synergistically increase the risk of infectious disease to crew members. The goal of this study is to use modeled microgravity to study the impact of medically significant ISS bacteria that may have altered virulence on the immune response of the host. This study consists of two primary aims to assess this relationship. First, immune cells will be collected from healthy test subjects and cultured in static or in modeled microgravity conditions together with either control pathogens or with microgravity conditioned pathogens that were grown in bioreactors. Second, immune cells will be collected from astronauts before, during, and after flight and co-cultured with the control or the microgravity conditioned bacteria. Three pathogens were selected for this investigation: Pseudomonas aeruginosa , Salmonella enterica serovar Enteritidis and Burkholderia cepacia . Previously, the optimal cell to bacteria ratios that produce the greatest immune cell responses have been derived for these three bacteria. Cellular activation, as determined by the induction of cell surface activation markers and cytokine profiles, will be measured. Interactions between cells and bacteria will be assessed using fluorescent and electron microscopy techniques. This study will provide critical information to help understand how microgravity alters microbial virulence and the associated infectious disease risk to crewmembers during spaceflight missions. Over the past year, the Immunology and Microbiology laboratories at NASA Johnson Space Center have collaborated to process the astronaut subject samples to complete the last year of the flight portion of this study. This included the completion of four astronaut subjects full mission sampling sets. Sample processing included innate and adaptive cell flow cytometry as well as analysis of cytokine concentrations in the supernatant. The ground control segment of the study will take place during FY25 which involves parallel infections run under static and clinostat conditions. The acquired data sets over this 3-year study are now being analyzed to provide a comprehensive set of results and conclusions that will contribute to a more effective risk assessment for astronauts during spaceflight regarding this host-pathogen context.

Immunology↗
NASA NTRS1979

Studies on the Mechanisms of Microbial Adaptation to the Physical Environment

The environmental factors which affect humans and other animals also influence the microorganisms which are such an important part of our ecology. Some of the microorganisms are very closely associated with animals, living in the digestive tract and synthesizing essential nutrients for the host. For these microbes, most external physical changes are of little consequence, because they are well shielded by the animals' homeostatic systems. The vast majority of microorganisms, however, live free in nature, especially in the soil and oceans. It has been estimated that the upper 15 cm of a fertile soil may contain over 4000 kg of bacteria and fungi per hectare. These organisms are responsible for degrading the complex molecules of plants and animals when they die, eventually producing simple organics, carbon dioxide, and inorganics, which are then used for the next cycle of plant growth. It is believed that over 90 % of the biologically produced carbon dioxide results from the metabolic activity of bacteria and fungi. In addition to recycling plant nutrients, soil bacteria also provide new nutrients through 'fixation' of atmospheric nitrogen into ammonia and nitrate, the forms which can be used by plants. Microorganisms so have an enormous capacity for detoxifying both natural and man-made poisons. All of these functions of microorganisms are essential to the operation of the material cycles on Earth. This is true of all locations on the planet, regardless of the climate or other environmental factors. In fact, one of the most impressive attributes of microorganisms is their ability to adapt to every stable environment on Earth. These include such extremes as polar regions, hot springs, water saturated with salt, mountain tops, ocean depths, acid and alkaline waters, deserts, intense radioactivity, soil and water contaminated with toxic chemicals or petroleum, and areas devoid of oxygen.

Heinrich, M. R.↗
DOE OSTI2025

Diet outperforms microbial transplant to drive microbiome recovery in mice

A high-fat, low-fibre Western-style diet (WD) induces microbiome dysbiosis characterized by reduced taxonomic diversity and metabolic breadth, which in turn increases risk for a wide array of metabolic, immune and systemic pathologies. Recent work has established that WD can impair microbiome resilience to acute perturbations such as antibiotic treatment, although little is known about the mechanism of impairment and the specific consequences for the host of prolonged post-antibiotic dysbiosis. Here, in this study, we characterize the trajectory by which the gut microbiome recovers its taxonomic and functional profile after antibiotic treatment in mice on regular chow (RC) or WD, and find that only mice on RC undergo a rapid successional process of recovery. Metabolic modelling indicates that a RC diet promotes the development of syntrophic cross-feeding interactions, whereas in mice on WD, a dominant taxon monopolizes readily available resources without releasing syntrophic byproducts. Intervention experiments reveal that an appropriate dietary resource environment is both necessary and sufficient for rapid and robust microbiome recovery, whereas microbial transplant is neither. Furthermore, prolonged post-antibiotic dysbiosis in mice on WD renders them susceptible to infection by the intestinal pathogen Salmonella enterica serovar Typhimurium. Our data challenge widespread enthusiasm for faecal microbiota transplant (FMT) as a strategy to address dysbiosis, and demonstrate that specific dietary interventions are, at a minimum, an essential prerequisite for effective FMT, and may afford a safer, more natural and less invasive alternative.

Kennedy, M. S. [University of Chicago, IL (United ↗
DOE OSTI2024

RolyPoly (rp) v0.1.0

The Rolypoly pipeline is designed to process raw RNA-seq data and identify potential RNA viral sequences. It is split into several self contained steps: 1. input data filtering and QC, 2. Genome assembly and refinement, 3. Assembly filtering, 4. Mapping to known RNA viral genomes, 5. Searching for RNA viral marker genes. 6. Genome functional and structural annotation. 6. Report preparation and potential downstream analysis The last module, may include taxonomic assignment, host range estimation, and phenotypic prediction. There are many similar software, but they focus on human related viruses, and lack the downstream applications or differ in their sensitivity. The initial user base are non-computational microbial ecologists who wish to better understand the potential RNA viruses in their own generated samples.

Neri, Uri↗
DOE OSTI2026

Sampling Microbial Dynamics in the Salish Sea Estuary: Evaluating Methods to Capture Cyanobacteria and Cyanophage

Introduction: Picocyanobacteria from the genera Prochlorococcus and Synechococcus thrive across the globe in aquatic environments, have relatively small genomes, and have growth dynamics regulated by both viral interactions and abiotic conditions, making them excellent model organisms for exploring host-pathogencoevolution. Methods: We developed and refined methods to sample and sequence cyanobacteria, cyanophages, and measured features of their abiotic environment. Results: The protocol described herein can successfully discriminate large-cell eukaryotic organisms, but size fractionation of picocyanobacteria appears to be affected by the presence of free DNA, multicellular structures, and abundant tycheposons. Our preferred final protocol from this exploratory effort included a combination of in-line and single vacuum flask filtrations, which reduced filtration processing time by over threefold in some cases compared to other tested methods, such as a fully in-line sequence or in-site filtrations. We successfully extracted an average of approximately 400–1200 ng for all filter fractions, with some variations between kits. Discussion: The protocol described herein can successfully discriminate large-cell eukaryotic organisms, but size fractionation of picocyanobacteria appears to be affected by the presence of free DNA, multicellular structures, and abundant tycheposons.

Salish Sea↗
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 OSTI2024

Rapid Design and Engineering of Smart and Secure Microbiological Systems (Final Report)

The design and application of successfully engineered biosystems requires an understanding of how engineered microbes will interact with other organisms – either as one-on-one competitors or in the context of microbial consortia. Engineering microorganisms from first principles for non-laboratory, environmental applications is inherently challenging because: (1) engineered systems tend to quickly revert back to their wild-type behaviors; and (2) these systems typically pay a price in reduced fitness, making them uncompetitive against invasive contaminating species (i.e., metabolic burden). For this project, we used a synthetic biology-based strategy to investigate the organization, control, stabilization, and destabilization of natural and engineered microbes. This approach enabled development of (1) single-strain systems capable of detecting and responding to target organisms in the environment; (2) a pipeline for refining and engineering biological constructs in new, non-model host organisms; and (3) improved systems for rapidly designing, engineering, and assaying new biological modules. This coupled approach to safeguard system design is predictable and portable across bacterial species and is focused on microbes that are part of the beneficial plant microbiome. A long-term goal beyond the proposed research is to enable the rational engineering of microbial communities based on first principles of biological design that mimic the smart performance of microorganisms observed in natural systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Randomized control trial of moderate dose vitamin D alters microbiota stability and metabolite networks in healthy adults

ABSTRACT Evidence indicates that both vitamin D and the gut microbiome are involved in the process of colon carcinogenesis. However, it is unclear what effects supplemental vitamin D 3 has on the gut microbiome and its metabolites in healthy adults. We conducted a double-blind, randomized, placebo-controlled trial to identify the acute and long-term microbiota structural and metabolite changes that occur in response to a moderate dose (4,000 IU) of vitamin D 3 for 12 weeks in healthy adults. Our results demonstrated a significant increase in serum 25-hydroxy-vitamin D (25(OH)D) in the treatment group compared to placebo ( P < 0.0001). Vitamin D 3 significantly increased compositional similarity ( P < 0.0001) in the treatment group, and enriched members of the Bifidobacteriaceae family. We also identified a significant inverse relationship between the percent change in serum 25(OH)D and microbial stability in the treatment group ( R = −0.52, P < 0.019). Furthermore, vitamin D 3 supplementation resulted in notable metabolic shifts, in addition to resulting in a drastic rewiring of key gut microbial-metabolic associations. In conclusion, we show that a moderate dose of vitamin D 3 among healthy adults has unique acute and persistent effects on the fecal microbiota, and suggest novel mechanisms by which vitamin D may affect the host-microbiota relationship. IMPORTANCE Preventative measures to reduce the rise in early-onset colorectal cancer are of critical need. Both vitamin D, dietary and serum levels, and the gut microbiome are implicated in the etiology of colorectal cancer. By understanding the intimate relationship between vitamin D, the gut microbiome, and its metabolites, we may be able to identify key mechanisms that can be targeted for intervention, including inflammation and metabolic dysfunction. Furthermore, the similarity of vitamin D to cholesterol, which is metabolized by the gut microbiome, gives precedence to its ability to produce metabolites that can be further studied and leveraged for controlling colorectal cancer incidence and mortality.

Wyatt, Madhur↗
NASA NTRS2001

Space Station Biological Research Project Habitat: Incubator

Developed as part of the suite of Space Station Biological Research Project (SSBRP) hardware to support research aboard the International Space Station (ISS), the Incubator is a temperature-controlled chamber, for conducting life science research with small animal, plant and microbial specimens. The Incubator is designed for use only on the ISS and is transported to/from the ISS, unpowered and without specimens, in the Multi-Purpose Logistics Module (MPLM) of the Shuttle. The Incubator interfaces with the three SSBRP Host Systems; the Habitat Holding Racks (HHR), the Life Sciences Glovebox (LSG) and the 2.5 m Centrifuge Rotor (CR), providing investigators with the ability to conduct research in microgravity and at variable gravity levels of up to 2-g. The temperature within the Specimen Chamber can be controlled between 4 and 45 C. Cabin air is recirculated within the Specimen Chamber and can be exchanged with the ISS cabin at a rate of approximately equal 50 cc/min. The humidity of the Specimen Chamber is monitored. The Specimen Chamber has a usable volume of approximately equal 19 liters and contains two (2) connectors at 28v dc, (60W) for science equipment; 5 dedicated thermometers for science; ports to support analog and digital signals from experiment unique sensors or other equipment; an Ethernet port; and a video port. It is currently manifested for UF-3 and will be launched integrated within the first SSBRP Habitat Holding Rack.

Nakamura, G. J.↗
DOE OSTI2026

Divergent Rickettsia species exhibit distinct mechanisms of actin-based motility

Many Rickettsia species undergo actin-based motility to promote cell-cell spread during infection. Rickettsial genomes often encode two motility effectors, RickA and Sca2, which in the spotted fever group I species, Rickettsia parkeri act by activating the host Arp2/3 complex and by mimicking eukaryotic formins, respectively. The function of RickA and Sca2 orthologs in the distantly related species Rickettsia bellii was unclear. We report that R. bellii RickA activates the host Arp2/3 complex but has no discernible role in bacterial motility. The R. bellii Sca2 ortholog, Sca2/6, nucleates and elongates actin with a flexible structure and an unusual actin monomer-binding motif in a mechanism distinct from formins or other microbial actin nucleators. R. bellii motility is solely correlated with Sca2/6 localization and, compared with R. parkeri motility, is slow and meandering, generating distinctly organized actin tails. The evolutionary flexibility in the mechanism and regulation of rickettsial actin-based motility suggests similar adaptability for other microbes.

Bacher, Meghan C↗
NASA NTRS2005

Microbial Preservation in Sulfates in the Haughton Impact Structure Suggests Target in Search for Life on Mars

Microbes in Haughton Crater Sulfates: Impact craters are of high interest in planetary exploration because they are viewed as possible sites for evidence of life [1]. Hydrothermal systems in craters are particularly regarded as sites where primitive life could evolve. Evidence from the Miocene Haughton impact structure shows that crater hydrothermal deposits may also be a preferred site for subsequent colonization and hence possible extant life: Hydrothermal sulfates at Haughton are colonized by viable cyanobacteria [2]. The Haughton impact structure, Devon Island, Canadian High Arctic, is a 24 km-diameter crater of mid-Tertiary age. The structure preserves an exceptional record of impact-induced hydrothermal activity, including sulfide, and sulfate mineralization [3]. The target rocks excavated at the site included massive gypsum-bearing carbonate rocks of Ordovician age. Impact-remobilized sulfates occur as metre-scale masses of intergrown crystals of the clear form of gypsum selenite in veins and cavity fillings within the crater s impact melt breccia deposits [4]. The selenite is part of the hydrothermal assemblage as it was precipitated by cooling hot waters that were circulating as a result of the impact. Remobilization of the sulfate continues to the present day, such that it occurs in soil crusts (Fig. 1) including sandy beds with a gypsum cement. The sulfate-cemented beds make an interesting comparison with the sulfate-bearing sandy beds encountered by the Opportunity MER [5]. The selenite crystals are up to 0.3 m in width, of high purity, and transparent. They locally exhibit frayed margins where cleavage surfaces have separated. This exfoliation may be a response to freeze-thaw weathering. The selenite contains traces of rock detritus, newly precipitated gypsum, and microbial colonies. The rock detritus consists of sediment particles which penetrated the opened cleavages by up to 2cm from the crystal margins. Some of the detritus is cemented into place by gypsum, which must have been dissolved and reprecipitated from the host selenite.

Parnell, J.↗
NASA NTRS2023

Regulatory response to a hybrid ancestral nitrogenase in Azotobacter vinelandii

Biological nitrogen fixation, the microbial reduction of atmospheric nitrogen to bioavailable ammonia, represents both a major limitation on biological productivity and a highly desirable engineering target for synthetic biology. However, the engineering of nitrogen fixation requires an integrated understanding of how the gene regulatory dynamics of host diazotrophs respond across sequence-function space of its central catalytic metalloenzyme, nitrogenase. Here, we interrogate this relationship by analyzing the transcriptome of Azotobacter vinelandii engineered with a phylogenetically inferred ancestral nitrogenase protein variant. The engineered strain exhibits reduced cellular nitrogenase activity but recovers wild-type growth rates following an extended lag period. We find that expression of genes within the immediate nitrogen fixation network is resilient to the introduced nitrogenase sequence-level perturbations. Rather the sustained physiological compatibility with the ancestral nitrogenase variant is accompanied by reduced expression of genes that support trace metal and electron resource allocation to nitrogenase. Our results spotlight gene expression changes in cellular processes adjacent to nitrogen fixation as productive engineering considerations to improve compatibility between remodeled nitrogenase proteins and engineered host diazotrophs.

nitrogen fixation↗
DOE OSTI2025

Protecting honey bees through microbiome engineering

Honey bees are indispensable insects. Their pollination services support modern agriculture and natural ecosystems. Managed honey bee colonies face increasing threats to their survival, ranging from environmental stressors that include agrochemicals to infestations of arthropod pests and infections with microbial pathogens. Like humans, honey bees have a native gut microbiome that supports their health. However, the bee gut microbiome has a simpler composition than the gut microbiome of mammals, and its main constituent bacterial species can be easily cultured outside of the host. Furthermore, this experimental tractability and the need for new methods for protecting hive health have made honey bees a testbed for synthetic microbiomes augmented with probiotic bacteria and engineered DNA. Here, we discuss the natural benefits of bee gut bacteria, recent progress in genetically modifying these bacteria, and how symbiont-mediated RNA interference and other microbiome engineering approaches can boost bee immunity and suppress bee pathogens and parasites. Finally, we discuss how emerging methods for microbiome engineering and biocontainment could be applied to honey bees and used to address challenges in translating these proof-of-principle achievements into safe and effective technologies for field applications at scale.

Biological and medical sciences↗
DOE OSTI2024

Applying a polysaccharide lyase from Stenotrophomonas maltophilia to disrupt alginate exopolysaccharide produced by Pseudomonas aeruginosa clinical isolates

Pseudomonas aeruginosa is considered one of the most challenging, drug-resistant, opportunistic pathogens partly due to its ability to synthesize robust biofilms. Biofilm is a mixture of extracellular polymeric substances (EPS) that encapsulates microbial cells, leading to immune evasion, antibiotic resistance, and thus higher risk of infection. In the cystic fibrosis lung environment, P. aeruginosa undergoes a mucoid transition, defined by overproduction of the exopolysaccharide alginate. Alginate encapsulation results in bacterial resistance to antibiotics and the host immune system. Given its role in airway inflammation and chronic infection, alginate is an obvious target to improve treatment for P. aeruginosa infection. Previously, we demonstrated polysaccharide lyase Smlt1473 from Stenotrophomonas maltophilia strain k279a can catalyze the degradation of multiple polyuronides in vitro, including D-mannuronic acid (poly-ManA). Poly-ManA is a major constituent of P. aeruginosa alginate, suggesting that Smlt1473 could have potential application against multidrug-resistant P. aeruginosa and perhaps other microbes with related biofilm composition. In this study, we demonstrate that Smlt1473 can inhibit and degrade alginate from P. aeruginosa. Additionally, we show that tested P. aeruginosa strains are dominant in acetylated alginate and that all but one have similar M-to-G ratios. These results indicate that variation in enzyme efficacy among the isolates is not primarily due to differences in total EPS or alginate chemical composition. Overall, these results demonstrate Smlt1473 can inhibit and degrade P. aeruginosa alginate and suggest that other factors including rate of EPS production, alginate sequence/chain length, or non-EPS components may explain differences in enzyme efficacy.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2015

Human Factors and Habitability Challenges for Mars Missions

As NASA is planning to send humans deeper into space than ever before, adequate crew health and performance will be critical for mission success. Within the NASA Human Research Program (HRP), the Space Human Factors and Habitability (SHFH) team is responsible for characterizing the risks associated with human capabilities and limitations with respect to long-duration spaceflight, and for providing mitigations (e.g., guidelines, technologies, and tools) to promote safe, reliable and productive missions. SHFH research includes three domains: Advanced Environmental Health (AEH), Advanced Food Technology (AFT), and Space Human Factors Engineering (SHFE). The AEH portfolio focuses on understanding the risk of microbial contamination of the spacecraft and on the development of standards for exposure to potential toxins such as chemicals, bacteria, fungus, and lunar/Martian dust. The two risks that the environmental health project focuses on are adverse health effects due to changes in host-microbe interactions, and risks associated with exposure to dust in planetary surface habitats. This portfolio also proposes countermeasures to these risks by making recommendations that relate to requirements for environmental quality, foods, and crew health on spacecraft and space missions. The AFT portfolio focuses on reducing the mass, volume, and waste of the entire integrated food system to be used in exploration missions, and investigating processing methods to extend the shelf life of food items up to five years, while assuring that exploration crews will have nutritious and palatable foods. The portfolio also delivers improvements in both the food itself and the technologies for storing and preparing it. SHFE sponsors research to establish human factors and habitability standards and guidelines in five risk areas, and provides improved design concepts for advanced crew interfaces and habitability systems. These risk areas include: Incompatible vehicle/habitat design, inadequate human-computer interaction, inadequate critical task design, inadequate human-automation/robotic interaction, and performance errors due to training deficiencies. To address the identified research gaps within each risk, SHFH's research plan includes studies in the laboratory, in analogs, and on International Space Station (ISS). In addition to establishing and maintaining the risk-based research portfolio, SHFH is also implementing a qualitative approach to determine how we at NASA evaluate human performance. Via interviews with experts, such as trainers, flight controllers, and flight surgeons, we are collecting the metrics by which they assess human performance, evidence of performance issues, and potential or actual consequences. The Human Performance Data Project will determine what human performance data have been collected in the past at NASA, and what data should be collected in the future in order to complete our knowledgebase and reduce risks related to human factors and habitability.

Whitmore, Mihriban↗
DOE OSTI2024

The ancestral environment of teosinte populations shapes their root microbiome

Summary Background The composition of the root microbiome affects the host’s growth, with variation in the host genome associated with microbiome variation. However, it is not known whether this intra-specific variation of root microbiomes is a consequence of plants performing targeted manipulations of them to adapt to their local environment or varying passively with other traits. To explore the relationship between the genome, environment and microbiome, we sampled seeds from teosinte populations across its native range in Mexico. We then grew teosinte accessions alongside two modern maize lines in a common garden experiment. Metabarcoding was performed using universal bacterial and fungal primers to profile their root microbiomes. Results The root microbiome varied between the two modern maize lines and the teosinte accessions. We further found that variation of the teosinte genome, the ancestral environment (temperature/elevation) and root microbiome were all correlated. Multiple microbial groups significantly varied in relative abundance with temperature/elevation, with an increased abundance of bacteria associated with cold tolerance found in teosinte accessions taken from high elevations. Conclusions Our results suggest that variation in the root microbiome is pre-conditioned by the genome for the local environment (i.e. non-random). Ultimately, these claims would be strengthened by confirming that these differences in the root microbiome impact host phenotype, for example, by confirming that the root microbiomes of high-elevation teosinte populations enhance cold tolerance.

Genetics & Heredity↗
DOE OSTI2024

Identification and characterization of a skin microbiome on Caenorhabditis elegans suggests environmental microbes confer cuticle protection

ABSTRACT In the wild, C. elegans are emersed in environments teeming with a veritable menagerie of microorganisms. The C. elegans cuticular surface serves as a barrier and first point of contact with their microbial environments. In this study, we identify microbes from C. elegans natural habitats that associate with its cuticle, constituting a simple “skin microbiome.” We rear our animals on a modified CeMbio, mCeMbio, a consortium of ecologically relevant microbes. We first combine standard microbiological methods with an adapted micro skin-swabbing tool to describe the skin-resident bacteria on the C. elegans surface. Furthermore, we conduct 16S rRNA gene sequencing studies to identify relative shifts in the proportion of mCeMbio bacteria upon surface-sterilization, implying distinct skin- and gut-microbiomes. We find that some strains of bacteria, including Enterobacter sp. JUb101 , are primarily found on the nematode skin, while others like Stenotrophomonas indicatrix JUb19 and Ochrobactrum vermis MYb71 are predominantly found in the animal’s gut. Finally, we show that this skin microbiome promotes host cuticle integrity in harsh environments. Together, we identify a skin microbiome for the well-studied nematode model and propose its value in conferring host fitness advantages in naturalized contexts. IMPORTANCE The genetic model organism C. elegans has recently emerged as a tool for understanding host–microbiome interactions. Nearly all of these studies either focus on pathogenic or gut-resident microbes. Little is known about the existence of native, nonpathogenic skin microbes or their function. We demonstrate that members of a modified C. elegans model microbiome, mCeMbio, can adhere to the animal's cuticle and confer protection from noxious environments. We combine a novel micro-swab tool, the first 16S microbial sequencing data from relatively unperturbed C. elegans , and physiological assays to demonstrate microbially mediated protection of the skin. This work serves as a foundation to explore wild C. elegans skin microbiomes and use C. elegans as a model for skin research.

16S RNA↗
NASA NTRS2002

Distinguishing Indigenous from Contaminating Microorganisms in Rock Samples from a Deep Au Mine in South Africa

The concentration and distribution of microbial biomass within deep subsurface rock strata is not well known To date, most analyses are from water samples and a few cores. Hand samples, block samples and cores from an actively mined Carbon Leader ore zone at 3.2 kilometers depth were collected for microbial analyses. The Carbon Leader was comprised of quartz, S-bearing aromatic hydrocarbons, Fe(III) oxyhydroxides, sulfides, uraninite, Au and minor amounts of sulfate. The porosity of the ore was 1% and the maximum pore throat diameter was less than 0.1 microns; whereas, the porosity of the adjacent quartzite was .02 to .9% with a maximum pore throat diameter of 0.9 microns. Rhodamine dye, fluorescent microspheres, microbial enrichments, autoradiography, phospholipid fatty acid (PLEA) and 16S rDNA analyses were performed on these rock samples and the mining water. The date indicate that the levels of solute contamination less than 0.01% for pared rock samples. Despite this low level of contamination, PLEA, microbial enrichment, DNA and tracer analyses and calculations indicate that most of the viable microorganisms in the Carbon Leader represent gram negative aerobic heterotrophs and ammonia oxidizers that are phylogenetically identical or closely related to service water microorganisms. These microbial contaminants probably infiltrated the low permeability rock through mining-induced microfractures. Geochemical data also detected drilling water in a fault zone approx. 1 meter behind the rock face encountered during coring. The mining induced macrofractures that are common at these great depths act as pathways for the drilling water borne microorganisms into the lower temperature zone that extends several meters into rock strata from the rock face. Combined PLEA and T- RFLP analyses of the service water and Carbon Leader samples indicate that the concentration of indigenous microorganisms was less than 10(exp 2) cells/gram. Such a low concentrations result from the submicron pore throat diameters. PLFA. SO4-35 autoradiography and tracer analyses indicate that the bounding quartzite contains thermophilic sulfate reducing bacteria at 10(exp 3) cells/gram that are not attributable to drilling water contamination. The microorganisms may be surviving on sulfate generated by oxidation of sulfide by radiolytic reactions resulting from the high U concentration in the ore zone. The presence of up to 8,000 ppm of Fe(III) oxyhydroxides in the host rock will also act to recycle sulfide generated by the sulfate reducing bacteria into sulfate. The activity of these sulfate-reducing bacteria may be enhanced by mining induced fracturing which can propagate up to 40 meters into virgin rock where the temperatures are ca. 50 C, and decrepitate of sulfate rich fluid inclusions. In ultra deep mines, judicious application of tracers and multiple microbial characterization techniques can distinguish microbial contamination caused by the near field fracturing and drilling water migration from the indigenous microbial communities in rock strata. The importance of far field fracturing on indigenous microbial communities, however, remains unknown.

Onstott, T. C.↗