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20 results for “Microbial Observatory”
Microbial Observatory at North Temperate Lakes LTER High-resolution temporal and spatial dynamics of microbial community structure in freshwater bog lakes 2005 - 2009 original format (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-ntl/349/4. The abstract below was extracted from the Level 0 data package and is included for context: The North Temperate Lakes - Microbial Observatory seeks to study freshwater microbes over long time scales (10+ years). Observing microbial communities over multiple years using DNA sequencing allows in-depth assessment of diversity, variability, gene content, and seasonal/annual drivers of community composition. Combining information obtained from DNA sequencing with additional experiments, such as investigating the biochemical properties of specific compounds, gene expression, or nutrient concentrations, provides insight into the functions of microbial taxa. Our 16S rRNA gene amplicon datasets were collected from bog lakes in Vilas County, WI, and from Lake Mendota in Madison, WI. Ribosomal RNA gene amplicon sequencing of freshwater environmental DNA was performed on samples from Crystal Bog, North Sparkling Bog, West Sparkling Bog, Trout Bog, South Sparkling Bog, Hell’s Kitchen, and Mary Lake. These microbial time series are valuable both for microbial ecologists seeking to understand the properties of microbial communities and for ecologists seeking to better understand how microbes contribute to ecosystem functioning in freshwater.
Lake Mendota Microbial Observatory Temperature, Dissolved Oxygen, pH, and conductivity data, 2006-present.
The Lake Mendota Microbial Observatory collects routine water physical and chemical measurements alongside their microbial samples. This dataset includes measurements of water temperature, dissolved oxygen, pH, and conductivity collected at the central Deep Hole, collocated with a weather buoy (43°05'58.2"N 89°24'16.2"W). All measurements were collected with handheld probes. Data from 2006-2014 was compiled from multiple sources and includes only water temperature and dissolved oxygen. Data from 2014-2019 is from the same probe, a YSI Pro Plus instrument, and also includes pH and specific conductance. Routine microbial observatory sampling continues into the present.
Lake Mendota Microbial Observatory Secchi Disk Measurements 2012-present
The Lake Mendota Microbial Observatory collects routine water clarity measurements alongside their microbial samples. This dataset includes measurements of water clarity collected at the central Deep Hole, collocated with a weather buoy (43°05'58.2"N 89°24'16.2"W). All measurements were collected with handheld Secchi discs. When multiple personnel performed the Secchi disc measurements, the average and standard deviation are reported. To take the Secchi depth, sunglasses are removed and the disc is lowered on the shaded side of the boat. The Secchi depth is the average between where the Secchi disc disappears while lowering it and where it reappears while raising it. Routine microbial observatory sampling continues into the present.
Microbial Observatory at North Temperate Lakes LTER Time series of bacterial community dynamics in Lake Mendota 2000 - 2009
With an unprecedented decade-long time series from a temperate eutrophic lake, we analyzed bacterial and environmental co-occurrence networks to gain insight into seasonal dynamics at the community level. We found that (1) bacterial co-occurrence networks were non-random, (2) season explained the network complexity and (3) co-occurrence network complexity was negatively correlated with the underlying community diversity across different seasons. Network complexity was not related to the variance of associated environmental factors. Temperature and productivity may drive changes in diversity across seasons in temperate aquatic systems, much as they control diversity across latitude. While the implications of bacterioplankton network structure on ecosystem function are still largely unknown, network analysis, in conjunction with traditional multivariate techniques, continues to increase our understanding of bacterioplankton temporal dynamics.
Microbial Observatory at North Temperate Lakes LTER Spatial and temporal cyanobacterial population dynamics in Lake Mendota 2009 - 2011
Toxic cyanobacterial blooms threaten freshwaters worldwide but have proven difficult to predict because the mechanisms of bloom formation and toxin production are unknown, especially on weekly time scales. Water quality management continues to focus on aggregated metrics, such as chlorophyll and total nutrients, which may not be sufficient to explain complex community changes and functions such as toxin production. For example, nitrogen (N) speciation and cycling play an important role, on daily time scales, in shaping cyanobacterial communities because declining N has been shown to select for N fixers. In addition, subsequent N pulses from N2 fixation may stimulate and sustain toxic cyanobacterial growth. Herein, we describe how rapid early summer declines in N followed by bursts of N fixation have shaped cyanobacterial communities in a eutrophic lake (Lake Mendota, Wisconsin, USA), possibly driving toxic Microcystis blooms throughout the growing season. On weekly time scales in 2010 and *2011, we monitored the cyanobacterial community in a eutrophic lake using the phycocyanin intergenic spacer (PC-IGS) region to determine population dynamics. In parallel, we measured microcystin concentrations, N2 fixation rates, and potential environmental drivers that contribute to structuring the community.
Microbial Observatory at North Temperate Lakes LTER High-resolution temporal and spatial dynamics of microbial community structure in freshwater bog lakes 2005 - 2009 original format
The North Temperate Lakes - Microbial Observatory seeks to study freshwater microbes over long time scales (10+ years). Observing microbial communities over multiple years using DNA sequencing allows in-depth assessment of diversity, variability, gene content, and seasonal/annual drivers of community composition. Combining information obtained from DNA sequencing with additional experiments, such as investigating the biochemical properties of specific compounds, gene expression, or nutrient concentrations, provides insight into the functions of microbial taxa. Our 16S rRNA gene amplicon datasets were collected from bog lakes in Vilas County, WI, and from Lake Mendota in Madison, WI. Ribosomal RNA gene amplicon sequencing of freshwater environmental DNA was performed on samples from Crystal Bog, North Sparkling Bog, West Sparkling Bog, Trout Bog, South Sparkling Bog, Hell’s Kitchen, and Mary Lake. These microbial time series are valuable both for microbial ecologists seeking to understand the properties of microbial communities and for ecologists seeking to better understand how microbes contribute to ecosystem functioning in freshwater.
Lake Mendota Microbial Observatory Nutrient Data 2013-2018
Pelagic water samples were collected from Lake Mendota as part of routine microbial observatory sampling and analyzed for total and dissolved nitrogen and phosphorus, as well as inorganic nitrogen compounds. On a typical sampling trip, a 12m tube approximating the depth of the epilimnion layer was used to collected an integrated epilimnion water sample from the central, deepest location in the lake. Two separate water grabs, which we refer to here as biological replicates, were typically taken from different sides of the small motor boat and processed separately. Water samples were stored frozen at -20 C until nutrient analysis was performed using a segmented flow analyzer. These samples differ in several key ways from the other routine NTL-LTER nutrient measurements, namely in that they reflect a mixed water column sample rather than a discrete depth, that the dissolved fraction is collected using the microbial observatory's 0.22 um filter instead of 0.45 um, and that the nitrate/nitrite speciation is included by repeating the analysis with and without the standard reducing column. This nutrient data is collected from the same water samples used for microbial analysis, and the collection site is also co-located with the Lake Mendota weather buoy.
Microbial Observatory at North Temperate Lakes LTER High-resolution temporal and spatial dynamics of microbial community structure in freshwater bog lakes 2005 - 2009 original format (Reformatted to a Darwin Core Archive)
This data package is formatted as a Darwin Core Archive (DwC-A, event core). For more information on Darwin Core see https://www.tdwg.org/standards/dwc/. This Level 2 data package was derived from the Level 1 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-ntl/344/6, which was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-ntl/349/4. The abstract below was extracted from the Level 0 data package and is included for context: The North Temperate Lakes - Microbial Observatory seeks to study freshwater microbes over long time scales (10+ years). Observing microbial communities over multiple years using DNA sequencing allows in-depth assessment of diversity, variability, gene content, and seasonal/annual drivers of community composition. Combining information obtained from DNA sequencing with additional experiments, such as investigating the biochemical properties of specific compounds, gene expression, or nutrient concentrations, provides insight into the functions of microbial taxa. Our 16S rRNA gene amplicon datasets were collected from bog lakes in Vilas County, WI, and from Lake Mendota in Madison, WI. Ribosomal RNA gene amplicon sequencing of freshwater environmental DNA was performed on samples from Crystal Bog, North Sparkling Bog, West Sparkling Bog, Trout Bog, South Sparkling Bog, Hell’s Kitchen, and Mary Lake. These microbial time series are valuable both for microbial ecologists seeking to understand the properties of microbial communities and for ecologists seeking to better understand how microbes contribute to ecosystem functioning in freshwater.
Measurements of Methanethiol (MeSH) and dimethyl sulfide (DMS) in surface seawater during 2022 at the monthly sampling observatory of Blanes Bay Microbial Observatory.
<p><span>Global emissions of methanethiol are highly uncertain and the drivers influencing its seawater concentrations are quasi unexplored. Here we try to address this gap in our understanding by contributing new seasonally resolved seawater measurements. Mediterranean surface seawater sampling at the Blanes Bay Microbial Observatory was carried out monthly during 2022. January, March and April were not sampled due to technical difficulties. Seawater was hand-collected in glass sampling bottles around 11:00 am each day. The samples were kept in the dark and analysed at the ICM-CSIC for MeSH and DMS with the Vocus-PTR coupled to SFCE within 3 h of sample collection. This dataset contains MeSH and DMS surface seawater concentrations and relevant auxiliary data (chlorophyll a, sea surface temperature and sea surface salinity). Sea surface temperature and salinity were determined using a CTD profiler Model SD204 (SAIV A/S). The chlorophyll from the Blanes 2022 timeseries was measured on a fluorometer (10AU Turner fluorometer).</span></p> <p><span>Details on the measurement methodology can be found here:</span></p> <p><span>Wohl, C.; Güell-Bujons, Q.; Castillo, Y.M.; Calbet, A.; Simó, R. Volatile Organic Compounds Released by Oxyrrhis marina Grazing on Isochrysis galbana. Oceans 2023, 4, 151-169. https://doi.org/10.3390/oceans4020011</span></p> <p><span> </span></p> <p><span>Definitions of acronyms, site abbreviations, or other project-specific designations:</span></p> <p><span>Lat=latitude (negative indicates south)</span></p> <p><span>Lon=longitude (negative indicates west )</span></p> <p><span>Hourlybin = The mean measured concentration during each hour is shown, 30 min either side of the listed time. The timestamp indicates sampling time in UTC, expressed as DD/MM/YYYY HH:MM</span></p> <p><span>MeSH_nM= methanethiol surface seawater concentration in nM, defined as nmol dm^(-3)</span></p> <p><span>DMS_nM= dimethyl sulfide surface seawater concentration in nM, defined as nmol dm^(-3)</span></p> <p><span>fluo = chlorophyll a concentration in mg m^(-3)</span></p> <p><span>SST= sea surface temperature in degrees Celsius </span></p> <p><span>SSS= sea surface salinity in practical salinity units (PSU)</span></p>
International Space Station - Microbial Observatory of Pathogenic Virus Bacteria and Fungi project
This study investigated the interplay between the microbial community of the International Space Station and its crew. Environmental samples were collected from 8 habitable locations around the ISS. The microbial composition was measured using shotgun metagenomic sequencing and procesed using the Livermore Metagenomics Analysis Toolkit.
Microbial Observatory (ISS-MO): Molecular characterization of Bacillus issensis sp. nov. isolated from various quarters of the International Space Station
As part of an ongoing effort to catalogue microbial communities inhabiting the International Space Station (ISS) crew-associated environmental samples were collected from the Japanese Kibo Russian and US research modules. Initial analysis based on 16S rRNA gene sequencing identified 11 Bacillus isolates (two from Kibo Japanese Experiment Module (JEM) four from US Segment Harmony Node 2 and five from Russian Segment Zvezda module sites) all belonging to the Bacillus anthracis-B. cereus-B. thuringiensis group. Isolates were further characterized by whole genome comparative analysis. Each isolate was sequenced assembled and aligned against all members of the B. cereus sensu lato group. Based on genome size estimates (5.2 - 5.3 Mbp) strain nucleotide identity (>99.99%) and maximum likelihood phylogenetic placement all isolates were found to exhibit a very high level of similarity. With respect to gene content all isolates were inspected for cry proteins common to B. thuringiensis as well as toxins specific to B. cereus. No significant hits were found to any known cry genes while full-length matches were found for multiple B. cereus toxin genes. Finally the isolates were closely screened against B. anthracis genomes and no B. anthracis signatures were identified. Notably all isolates contained the plcR ancestral C allele and lacked significant hits to pXO1 and pXO2 plasmids and toxins. The collective results from the analysis confirm that these strains belong to a previously uncharacterized Bacillus species hereafter referred to as Bacillus issensis. The type strain is ISSFR-003T (=NRRL B-65389T= DSMZ 101676T).
Microbial Observatory (ISS-MO): Antimicrobial resistance genes
The environmental samples were collected with the polyester wipes from eight different locations in the International Space Station (ISS) during two consecutive sampling sessions (three months apart) within the ISS Microbial Observatory Experiment. DNA extracted from each of the samples was used to create amplicon libraries based on customized panel of 500 antimicrobial resistance genes followed by next-generation sequencing. This is the first study of that shows the reservoir of antimicrobial genes in the ISS. 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.
International Space Station - Microbial Observatory of Pathogenic Virus, Bacteria, and Fungi project
This study investigated the interplay between the microbial community of the International Space Station and its crew. Environmental samples were collected from 8 habitable locations around the ISS. The microbial composition was measured using shotgun metagenomic sequencing and procesed using the Livermore Metagenomics Analysis Toolkit.
Microbial Observatory (ISS-MO): Indoor microbiome study of the International Space Station surfaces
Presented here is the environmental microbiome study of the International Space Station surfaces. 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 pool of genes for each location during two separate sessions to learn of functional and metabolic diversity of microorganisms in the ISS. 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 25C. 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 (10^2 to 10^3 CFU/m2). The PMA-qPCR analysis showed considerable variation of viable bacterial population (10^5 to 10^9 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.
Microbial Observatory (ISS-MO): Microbial diversity
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' 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 25C. 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.
Microbial Observatory (ISS-MO): Study of BSL-2 bacterial isolates from the International Space Station
In an on-going Microbial Observatory experimental investigation on the International Space Station (ISS) multiple bacterial isolates of Biosafety Level 2 (BSL-2) were isolated and identified. The antibiotic susceptibility pattern was tested in these BSL-2 isolates for the following antibiotics: cefazolin ciprofloxacin cefoxitin erythromycin gentamycin oxacillin penicillin rifampin tobramycin and many of the BSL-2 isolates showed multiple drug resistance. Among these isolates 21 strains were chosen for whole genome sequencing (WGS) for a possible lead to develop appropriate countermeasures. In addition the genomic data would enable to determine the influence of microgravity on the pathogenicity and virulence in the BSL-2 microorganisms.
Microbial Observatory (ISS-MO): Draft Genome Sequence of two Aspergillus fumigatus Strains Isolated from the International Space Station
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.
Microbial Observatory (ISS-MO): Molecular characterization of Bacillus issensis sp. nov. isolated from various quarters of the International Space Station
As part of an ongoing effort to catalogue microbial communities inhabiting the International Space Station (ISS) crew-associated environmental samples were collected from the Japanese Kibo Russian and US research modules. Initial analysis based on 16S rRNA gene sequencing identified 11 Bacillus isolates (two from Kibo Japanese Experiment Module (JEM) four from US Segment Harmony Node 2 and five from Russian Segment Zvezda module sites) all belonging to the Bacillus anthracis-B. cereus-B. thuringiensis group. Isolates were further characterized by whole genome comparative analysis. Each isolate was sequenced assembled and aligned against all members of the B. cereus sensu lato group. Based on genome size estimates (5.2 - 5.3 Mbp) strain nucleotide identity (>99.99%) and maximum likelihood phylogenetic placement all isolates were found to exhibit a very high level of similarity. With respect to gene content all isolates were inspected for cry proteins common to B. thuringiensis as well as toxins specific to B. cereus. No significant hits were found to any known cry genes while full-length matches were found for multiple B. cereus toxin genes. Finally the isolates were closely screened against B. anthracis genomes and no B. anthracis signatures were identified. Notably all isolates contained the plcR ancestral C allele and lacked significant hits to pXO1 and pXO2 plasmids and toxins. The collective results from the analysis confirm that these strains belong to a previously uncharacterized Bacillus species hereafter referred to as Bacillus issensis. The type strain is ISSFR-003T (=NRRL B-65389T= DSMZ 101676T).
Microbial Observatory (ISS-MO): Molecular characterization of Bacillus issensis, sp. nov., isolated from various quarters of the International Space Station
As part of an ongoing effort to catalogue microbial communities inhabiting the International Space Station (ISS) crew-associated environmental samples were collected from the Japanese Kibo Russian and US research modules. Initial analysis based on 16S rRNA gene sequencing identified 11 Bacillus isolates (two from Kibo Japanese Experiment Module (JEM) four from US Segment Harmony Node 2 and five from Russian Segment Zvezda module sites) all belonging to the Bacillus anthracis-B. cereus-B. thuringiensis group. Isolates were further characterized by whole genome comparative analysis. Each isolate was sequenced assembled and aligned against all members of the B. cereus sensu lato group. Based on genome size estimates (5.2 - 5.3 Mbp) strain nucleotide identity (>99.99%) and maximum likelihood phylogenetic placement all isolates were found to exhibit a very high level of similarity. With respect to gene content all isolates were inspected for cry proteins common to B. thuringiensis as well as toxins specific to B. cereus. No significant hits were found to any known cry genes while full-length matches were found for multiple B. cereus toxin genes. Finally the isolates were closely screened against B. anthracis genomes and no B. anthracis signatures were identified. Notably all isolates contained the plcR ancestral C allele and lacked significant hits to pXO1 and pXO2 plasmids and toxins. The collective results from the analysis confirm that these strains belong to a previously uncharacterized Bacillus species hereafter referred to as Bacillus issensis. The type strain is ISSFR-003T (=NRRL B-65389T= DSMZ 101676T).
Microbial Observatory (ISS-MO): Molecular characterization of Bacillus issensis sp. nov. isolated from various quarters of the International Space Station
As part of an ongoing effort to catalogue microbial communities inhabiting the International Space Station (ISS) crew-associated environmental samples were collected from the Japanese Kibo Russian and US research modules. Initial analysis based on 16S rRNA gene sequencing identified 11 Bacillus isolates (two from Kibo Japanese Experiment Module (JEM) four from US Segment Harmony Node 2 and five from Russian Segment Zvezda module sites) all belonging to the Bacillus anthracis-B. cereus-B. thuringiensis group. Isolates were further characterized by whole genome comparative analysis. Each isolate was sequenced assembled and aligned against all members of the B. cereus sensu lato group. Based on genome size estimates (5.2 - 5.3 Mbp) strain nucleotide identity (>99.99%) and maximum likelihood phylogenetic placement all isolates were found to exhibit a very high level of similarity. With respect to gene content all isolates were inspected for cry proteins common to B. thuringiensis as well as toxins specific to B. cereus. No significant hits were found to any known cry genes while full-length matches were found for multiple B. cereus toxin genes. Finally the isolates were closely screened against B. anthracis genomes and no B. anthracis signatures were identified. Notably all isolates contained the plcR ancestral C allele and lacked significant hits to pXO1 and pXO2 plasmids and toxins. The collective results from the analysis confirm that these strains belong to a previously uncharacterized Bacillus species hereafter referred to as Bacillus issensis. The type strain is ISSFR-003T (=NRRL B-65389T= DSMZ 101676T).
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