The whole-genome sequences of eight fungal strains that were selected for exposure to microgravity at the International Space Station are presented here. These baseline sequences will help to understand the observed production of novel bioactive compounds.

This study presents the first global transcriptional profiling and phenotypic characterization of the major human opportunistic fungal pathogen, Candida albicans, grown in spaceflight conditions. Microarray analysis revealed that C. albicans subjected to short-term spaceflight culture differentially regulated 454 genes compared to synchronous ground controls, which represented 8.4% of the analyzed ORFs. Spaceflight-cultured C. albicans induced genes involved in cell aggregation (similar to flocculation), which was validated by microscopic and flow cytometry analysis. We also observed enhanced random budding of spaceflight-cultured cells as opposed to more normal bipolar budding patterns for ground samples, in accordance with the gene expression data. Furthermore, genes involved in antifungal agent and stress resistance were differentially regulated in spaceflight, including induction of ABC transporters and members of the major facilitator family, downregulation of ergosterol-encoding genes, and upregulation of genes involved in oxidative stress resistance. Finally, downregulation of genes involved in the actin cytoskeleton was observed. Interestingly, the transcriptional regulator Cap1 and over 30% of the Cap1 regulon was differentially expressed in spaceflight-cultured C. albicans. A potential role for Cap1 in the spaceflight response of C. albicans is suggested, as this regulator is involved in random budding, cell aggregation, actin cytoskeleton, and oxidative stress resistance; all related to observed spaceflight-associated changes of C. albicans. While culture of C. albicans in microgravity potentiates a global change in gene expression that could induce a virulence-related phenotype, no increased virulence in a murine intraperitoneal (i.p.) infection model was observed. This study represents an important basis for the assessment of the risk that commensal flora could play during spaceflight missions. Furthermore, since the low fluid-shear environment of microgravity is relevant to physical forces encountered by pathogens during the infection process, insights gained from this study could identify novel infectious disease mechanisms, with downstream benefits for the general public. Cells were grown for 24 hours on the space shuttle or as ground-based controls, preserved in RNALater, and stored at -80C. Four samples of each flight- and ground-based controls were harvested for microarray analysis. GAP is Group Activation Pack and each GAP contains 8 FPAs. The numbers represent the # assigned to the particular GAP and the number assigned to the specific FPA (1-8) within the indicated GAP. The same hardware is used for the flight samples and the ground samples.

Metagenome Assembled Genome (MAG) of Sphingomonas sanguinis from the International Space Station metagenome

Aspergillus fumigatus is a saprophytic filamentous fungus that is ubiquitous outdoors (soil decaying vegetation) and indoors (hospitals simulated closed habitats etc.). A. fumigatus can adapt to various environmental conditions and form airborne conidia that are the inoculum for a variety of diseases (e.g. non- and invasive pulmonary infections allergic bronchopulmonary aspergillosis etc.) in immunocompromised hosts. In an on-going Microbial Observatory Experiments on the International Space Station (ISS) molecular phylogeny of several fungal isolates were characterized. Two strains ISSF 21 and IF1SW-F4 were isolated from the HEPA filter and the surface of the Cupola of the ISS respectively. Using primers targeting the internal transcribed spacers ITS1 and 2 both isolates were identified as A. fumigatus. The whole genome sequence analysis of ISSF 21 revealed increased number of single nucleotide polymorphisms (SNPs) when compared to the reference A. fumigatus 293. Knowing that A. fumigatus is an opportunistic pathogen and microgravity highly influences the antibiotic susceptibility and pathogenicity of microorganisms we examined pathogenicity of both ISS isolates using the zebrafish larval model. The space station isolates (ISSF-021 and IF1SW-F4) were more virulent than two clinical strains (Af293 and CEA10) whose pathogenicity was highly characterized. Here the whole genome sequences of ISSF-021 strain are being deposited.

The environmental microbiome study was designed to decipher microbial diversity of the International Space Station surfaces in terms of spatial and temporal distributions using 16S and ITS iTag Illumina sequencing. We hypothesized that the microbial population of environmental surfaces changes in time due to astronauts xe2 x80 x99 activity and might be location specific. The environmental samples were collected with the polyester wipes from eight different locations in the ISS during two consecutive sampling sessions (three months apart). The specific objective was to unveil the viable microbial diversity of each location during two separate sessions in terms of abundance and richness of the communities. The International Space Station (ISS) as a closed built environment has its own environmental microbiome which is shaped by microgravity radiation and limited human presence. The microbial diversity associated with ISS environmental surfaces was investigated during this study. Polyester wipes and contact slides were used for sampling of eight various surface locations on the ISS at different time periods. The samples were retrieved and analyzed immediately upon the return to the Earth (via Soyuz TMA-14M or Dragon capsule from SpaceX). After surface sample collection contact slides containing nutrient media for the growth of bacteria and fungi were incubated at 25 xcb x9aC. The polyester wipes were processed to measure microbial burden (R2A Blood Agar and Potato Dextrose Agar) and recover cultivable bacteria as well as fungi. Subsequently viable microbial burden was assessed using Adenosine Triphosphate (ATP) assay and quantitative polymerase chain reaction (PCR) methods after propidium monoazide (PMA) treatment. The 16S-tag and metagenome analyses were used to elucidate viable microbial diversity. The cultivable bacterial population yield from the polyester wipes was very high (5 to 7-logs) when compared with the contact slides (102 to 103 CFU/m2). The PMA-qPCR analysis showed considerable variation of viable bacterial population (105 to 109 16S rDNA gene copies/m2) among locations sampled. Unlike contact slides polyester wipes cover much larger sample surface (~1 m2) and produce much more reliable results of the microbial diversity of the ISS covering both cultivable and non-cultivable species. The cultivable total and viable microbial diversity was determined utilizing state-of-the art molecular techniques. The implementation of the PMA assay before DNA extraction allowed distinguishing viable microorganisms which is crucial for determining their role to the crew health the ISS maintenance and the general knowledge of the closed environmentally controlled built systems.

Because of their ubiquity and resistance to spacecraft decontamination bacterial spores are considered likely potential forward contaminants on robotic missions to Mars. Thus it is important to understand their global responses to long-term exposure to space or Mars environments. As part of the PROTECT experiment spores of B. subtilis 168 were exposed to real space conditions and to simulated martian conditions for 559 days in low Earth orbit mounted on the EXPOSE-E exposure platform outside the European Columbus module on the International Space Station. Upon return spores were germinated total RNA extracted and fluorescently labeled and used to probe a custom Bacillus subtilis microarray to identify genes preferentially activated or repressed relative to ground control spores. Increased transcript levels were detected for a number of stress-related regulons responding to DNA damage (SOS response SP-beta prophage induction) protein damage (CtsR/Clp system) oxidative stress (PerR regulon) and cell envelope stress (SigV regulon). Spores exposed to space demonstrated a much broader and more severe stress response than spores exposed to simulated Mars conditions. The results are discussed in the context of planetary protection for a hypothetical journey of potential forward contaminant spores from Earth to Mars and their subsequent residence on Mars. Two-color microarrays were performed comparing germination of Space-exposed or Mars-exposed vs. ground-control (Earth) spores.

Genetic techniques were employed to investigate the archaeal, bacterial and eukaryotic communities associated with the Antarctic sponges Kirkpatrickia varialosa, Latrunculia apicalis, Homaxinella balfourensis, Mycale acerata and Sphaerotylus antarcticus. The sponges and seawater for the analyses were obtained from sites in McMurdo Sound: adjacent to McMurdo Station (MM), Scott Base (SB) and Cape Armitage (CA).Rarefaction analysis was performed to determine the number of unique bacterial clones as a proportion of the estimated total diversity.Archaeal PCR product was not detected from seawater, H. balfourensis or S. antarcticus samples. 150 archaeal clones (50 each from L. apicalis, K. varialosa, and M. acerata ) were screened by RFLP analysis, 4 unique operational taxonomic units (OTUs) wre observed. RFLP analysis screened 250 sponge-derived bacterial clones, 61 were unique OTUs not detected during examination of 160 seawater-derived clones and were subsequently sequenced for phylogenetic determination. Of the 160 seawater bacterial clones, 103 exhibited unique banding patterns, creating distinct seawater operational taxonomic units (OTUs).The phylogenetic affiliation of sponge-derived bacteria was assessed by 16S rRNA sequencing of cloned DNA fragments. Denaturing gradient gel electrophoresis (DGGE) was used to determine the profiles of 18S rRNA-defined eukaryotic populations from replicate sponge specimens at the 3 Antarctic sites. Samples analysed by DGGE were K. varialosa (K), L. apicalis (L), M. acerata (M) and seawater (SW). 2-4 replicates were used per sample type.Neighbour-joining phylogenetic trees were formed from analysis of: 889 bp of 16S rRNA gene sequence from Antarctic archaeal clones 1-4; 857 bp of 16S rRNA gene sequence from Antarctic bacterial clones; and 304 bp of bacterial 16S rRNA gene sequence retrieved from DGGE. Branches were also found using the Fitch-Margoliash or maximum parsimony methods.The bacterial communities associated with Antarctic sponges primarily clustered within the Gamma and Alpha proteobacteria and the Cytophaga/Flavobacterium of Bacteroidetes group.GenBank Accession Numbers were assigned to: 4 unique Antarctic archaeal sequences detected in M. acerata (AY320198, AY320199, AY320200, AY320201). The study aimed to describe the microbial species composition, the stability of the host-bacterium associations and the spatial variability in sponge-derived microbial communities. 54 sponge-derived unique bacterial clones which produced suitable sequence data for phylogenetic analysis, GenBank Accession Numbers in brackets (AY321378, AY321379, AY321380, AY321381, AY321382, AY321383, AY321384, AY321385, AY321386, AY321387, AY321388, AY321389, AY321390, AY321391, AY321392, AY321393, AY321394, AY321395, AY321396, AY321397, AY321398, AY321399, AY321400, AY321401, AY321402, AY321403, AY321404, AY321405, AY321406, AY321407, AY321408, AY321409, AY321410, AY321411, AY321412, AY321413, AY321414, AY321415, AY321416, AY321417, AY321418, AY321419, AY321420, AY321421, AY321422, AY321423, AY321424, AY321425, AY321426, AY321427, AY321428, AY321429, AY321430, AY321431, AY321432); 10 bands for which high quality eukaryotic sequence data was obtained (AY320202, AY320203, AY320204, AY320205, AY320206, AY320207, AY320208, AY320209, AY320210, AY320211); and high-quality sequences for 19 bacterial bands (AY320212, AY320213, AY320214, AY320215, AY320216, AY320217, AY320218, AY320219, AY320220, AY320221, AY320222, AY320223, AY320224, AY320225, AY320226, AY320227, AY320228, AY320229, AY320230).

Data were generated as part of a NASA-funded study (Turek F (PI) et al. Effects of Spaceflight on Gastrointestinal Microbiota in Mice: Mechanisms and Impact on Multi-System. NASA NRA: NRA NNH14ZTT002N). As part of the study, we requested and received samples from RR1. We generated 16S rRNA gene amplicon sequence data from DNA extracted from fecal samples, and compared these data to similar data generated on shuttle mission STS-135 and from ground-based studies of radiation. We assessed effect of flight conditions and radiation.

These data are bacterial 16S rRNA sequences and a taxonomic summary table for biofilm samples from the bio-reactors. The data may provide background/supporting information for other researchers who have a similar experimental plan with a microbial electrochemical cell reactor. This dataset is associated with the following publication: Santodomingo, J., H. Lee, B. Dhar, J. An, B. Rittmann, H. Ren, and J. Chae. The Roles of Biofilm Conductivity and Donor Substrate Kinetics in a Mixed-Culture Biofilm Anod. ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 50(23): 12799-12807, (2016).

The Sequence Read Archive (SRA) stores sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome Analyzer®, Life Technologies AB SOLiD System®, Helicos Biosciences Heliscope®, Complete Genomics®, and Pacific Biosciences SMRT®.