Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural Relevance
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Title: Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural Relevance
Democratizing genomic data science, including bioinformatics, can diversify the STEM workforce and may, in turn, bring new perspectives into the space sciences. In this respect, the development of education and research programs that bridge genome science with “place” and world-views specific to a given region are valuable for Indigenous students and educators. Through a multi-institutional collaboration, we developed an ongoing education program and model that includes Illumina and Oxford Nanopore sequencing, free bioinformatic platforms, and teacher training workshops to address our research and education goals through a place-based science education lens. High school students and researchers cultivated, sequenced, assembled, and annotated the genomes of 13 bacteria from Mars analog sites with cultural relevance, 10 of which were novel species. Students, teachers, and community members assisted with the discovery of new, potentially chemolithotrophic bacteria relevant to astrobiology. This joint education-research program also led to the discovery of species from Mars analog sites capable of producing N-acyl homoserine lactones, which are quorum-sensing molecules used in bacterial communication. Whole genome sequencing was completed in high school classrooms, and connected students to funded space research, increased research output, and provided culturally relevant, place-based science education, with participants naming three novel species described here. Students at St. Andrew's School (Honolulu, Hawai‘i) proposed the name Bradyrhizobium prioritasuperba for the type strain, BL16AT, of the new species (DSM 112479T = NCTC 14602T). The nonprofit organization Kauluakalana proposed the name Brenneria ulupoensis for the type strain, K61T, of the new species (DSM 116657T = LMG = 33184T), and Hawai‘i Baptist Academy students proposed the name Paraflavitalea speifideiaquila for the type strain, BL16ET, of the new species (DSM 112478T = NCTC 14603T). more »« less
ABSTRACT Novel bacterial isolates with the capabilities of lignin depolymerization, catabolism, or both, could be pertinent to lignocellulosic biofuel applications. In this study, we aimed to identify anaerobic bacteria that could address the economic challenges faced with microbial-mediated biotechnologies, such as the need for aeration and mixing. Using a consortium seeded from temperate forest soil and enriched under anoxic conditions with organosolv lignin as the sole carbon source, we successfully isolated a novel bacterium, designated 159R. Based on the 16S rRNA gene, the isolate belongs to the genus Sodalis in the family Bruguierivoracaceae . Whole-genome sequencing revealed a genome size of 6.38 Mbp and a GC content of 55 mol%. To resolve the phylogenetic position of 159R, its phylogeny was reconstructed using (i) 16S rRNA genes of its closest relatives, (ii) multilocus sequence analysis (MLSA) of 100 genes, (iii) 49 clusters of orthologous groups (COG) domains, and (iv) 400 conserved proteins. Isolate 159R was closely related to the deadwood associated Sodalis guild rather than the tsetse fly and other insect endosymbiont guilds. Estimated genome-sequence-based digital DNA-DNA hybridization (dDDH), genome percentage of conserved proteins (POCP), and an alignment analysis between 159R and the Sodalis clade species further supported that isolate 159R was part of the Sodalis genus and a strain of Sodalis ligni . We proposed the name Sodalis ligni str. 159R (=DSM 110549 = ATCC TSD-177). IMPORTANCE Currently, in the paper industry, paper mill pulping relies on unsustainable and costly processes to remove lignin from lignocellulosic material. A greener approach is biopulping, which uses microbes and their enzymes to break down lignin. However, there are limitations to biopulping that prevent it from outcompeting other pulping processes, such as requiring constant aeration and mixing. Anaerobic bacteria are a promising alternative source for consolidated depolymerization of lignin and its conversion to valuable by-products. We presented Sodalis ligni str. 159R and its characteristics as another example of potential mechanisms that can be developed for lignocellulosic applications.
Updegraff, Tatum; Schiff-Clark, Grayson; Gossett, Hunter; Parsi, Sheila; Peterson, Rebecca; Whittaker, Robert; Dennison, Clare; Davis, Madison; Bray, James; Boden, Rich; et al(
, International Journal of Systematic and Evolutionary Microbiology)
Two sulphur-oxidizing, chemolithoautotrophic aerobes were isolated from the chemocline of an anchialine sinkhole located within the Weeki Wachee River of Florida. Gram-stain-negative cells of both strains were motile, chemotactic rods. Phylogenetic analysis of the 16S rRNA gene and predicted amino acid sequences of ribosomal proteins, average nucleotide identities, and alignment fractions suggest the strains HH1 T and HH3 T represent novel species belonging to the genus Thiomicrorhabdus . The genome G+C fraction of HH1 T is 47.8 mol% with a genome length of 2.61 Mb, whereas HH3 T has a G+C fraction of 52.4 mol% and 2.49 Mb genome length. Major fatty acids of the two strains included C 16 : 1 , C 18 : 1 and C 16 : 0 , with the addition of C 10:0 3-OH in HH1 T and C 12 : 0 in HH3 T . Chemolithoautotrophic growth of both strains was supported by elemental sulphur, sulphide, tetrathionate, and thiosulphate, and HH1 T was also able to use molecular hydrogen. Neither strain was capable of heterotrophic growth or use of nitrate as a terminal electron acceptor. Strain HH1 T grew from pH 6.5 to 8.5, with an optimum of pH 7.4, whereas strain HH3 T grew from pH 6 to 8 with an optimum of pH 7.5. Growth was observed between 15–35 °C with optima of 32.8 °C for HH1 T and 32 °C for HH3 T . HH1 T grew in media with [NaCl] 80–689 mM, with an optimum of 400 mM, while HH3 T grew at 80–517 mM, with an optimum of 80 mM. The name Thiomicrorhabdus heinhorstiae sp. nov. is proposed, and the type strain is HH1 T (=DSM 111584 T =ATCC TSD-240 T ). The name Thiomicrorhabdus cannonii sp. nov is proposed, and the type strain is HH3 T (=DSM 111593 T =ATCC TSD-241 T ).
A polyphasic taxonomic approach, incorporating analysis of phenotypic features, cellular fatty acid profiles, 16S rRNA gene sequences, and determination of average nucleotide identity (ANI) plus digital DNA–DNA hybridization (dDDH), was applied to characterize an anaerobic bacterial strain designated KD22Tisolated from human feces. 16S rRNA gene-based phylogenetic analysis showed that strain KD22Twas found to be most closely related to species of the genusGabonibacter.At the 16S rRNA gene level, the closest species from the strain KD22Tcorresponded withGabonibacter massiliensisGM7T, with a similarity of 97.58%. Cells of strain KD22T were Gram-negative coccobacillus, positive for indole and negative for catalase, nitrate reduction, oxidase, and urease activities. The fatty acid analysis demonstrated the presence of a high concentration of iso-C15: 0(51.65%). Next, the complete whole-genome sequence of strain KD22T was 3,368,578 bp long with 42 mol% of DNA G + C contents. The DDH and ANI values between KD22T and type strains of phylogenetically related species were 67.40% and 95.43%, respectively. These phylogenetic, phenotypic, and genomic results supported the affiliation of strain KD22Tas a novel bacterial species within the genusGabonibacter.The proposed name isGabonibacter chumensisand the type strain is KD22T(= CSUR Q8104T = DSM 115208 T).
Strain KD21T, isolated from the fecal sample of a healthy female volunteer, is a strictly anaerobic, non-motile, Gram-staining-positive, saccharolytic small rod that does not produce spores. Strain KD21T was able to grow in the range of temperature 28°C–37°C (optimum, 37 °C), pH 6.0–8.0 (optimum, pH 7.0), and with 0–5.0 g/l NaCl (optimum, 0 g/l NaCl). Bacteria cells reduced nitrates to nitrites. Its major fatty acids were C18:1ω9c, C16:0, C18:0, and summed in feature 8 (C18:1ω7c and/or C18:1ω6c). 16S rRNA gene phylogenetic analysis revealed that KD21T is a member of the genus Tractidigestivibacter and is distinct from any species with validly published names. The sequence showed 98.48% similarity with T. scatoligenes SK9K4T. The DNA G + C content of strain KD21T was 62.6 mol%. The DNA–DNA hybridization and OrthoANI values between strain KD21T and T. scatoligenes SK9K4T were 40.2% and 90.2%, respectively. Differences in phenotypic, phylogenetic, chemotaxonomic, and genomic characteristics indicated that strain KD21T represents a novel species within the genus Tractidigestivibacter. The name T. montrealensis sp. nov. is proposed and the type strain is KD21T (= CSUR Q8103T = DSM 115111T).
Berhane, B.; Dalal, M.; Klein-Gardner, S.; Carberry, A.; Reid, K.; Beauchamp, C.; Kouo, J.; Pines, D.(
, 3rd annual CoNECD – The Collaborative Network for Engineering and Computing Diversity Conference)
null
(Ed.)
As our nation’s need for engineering professionals grows, a sharp rise in P-12 engineering education programs and related research has taken place (Brophy, Klein, Portsmore, & Rogers, 2008; Purzer, Strobel, & Cardella, 2014). The associated research has focused primarily on students’ perceptions and motivations, teachers’ beliefs and knowledge, and curricula and program success. The existing research has expanded our understanding of new K-12 engineering curriculum development and teacher professional development efforts, but empirical data remain scarce on how racial and ethnic diversity of student population influences teaching methods, course content, and overall teachers’ experiences. In particular, Hynes et al. (2017) note in their systematic review of P-12 research that little attention has been paid to teachers’ experiences with respect to racially and ethnically diverse engineering classrooms. The growing attention and resources being committed to diversity and inclusion issues (Lichtenstein, Chen, Smith, & Maldonado, 2014; McKenna, Dalal, Anderson, & Ta, 2018; NRC, 2009) underscore the importance of understanding teachers’ experiences with complementary research-based recommendations for how to implement engineering curricula in racially diverse schools to engage all students.
Our work examines the experiences of three high school teachers as they teach an introductory engineering course in geographically and distinctly different racially diverse schools across the nation. The study is situated in the context of a new high school level engineering education initiative called Engineering for Us All (E4USA). The National Science Foundation (NSF) funded initiative was launched in 2018 as a partnership among five universities across the nation to ‘demystify’ engineering for high school students and teachers. The program aims to create an all-inclusive high school level engineering course(s), a professional development platform, and a learning community to support student pathways to higher education institutions.
An introductory engineering course was developed and professional development was provided to nine high school teachers to instruct and assess engineering learning during the first year of the project. This study investigates participating teachers’ implementation of the course in high schools across the nation to understand the extent to which their experiences vary as a function of student demographic (race, ethnicity, socioeconomic status) and resource level of the school itself. Analysis of these experiences was undertaken using a collective case-study approach (Creswell, 2013) involving in-depth analysis of a limited number of cases “to focus on fewer "subjects," but more "variables" within each subject” (Campbell & Ahrens, 1998, p. 541).
This study will document distinct experiences of high school teachers as they teach the E4USA curriculum. Participants were purposively sampled for the cases in order to gather an information-rich data set (Creswell, 2013). The study focuses on three of the nine teachers participating in the first cohort to implement the E4USA curriculum. Teachers were purposefully selected because of the demographic makeup of their students. The participating teachers teach in Arizona, Maryland and Tennessee with predominantly Hispanic, African-American, and Caucasian student bodies, respectively. To better understand similarities and differences among teaching experiences of these teachers, a rich data set is collected consisting of: 1) semi-structured interviews with teachers at multiple stages during the academic year, 2) reflective journal entries shared by the teachers, and 3) multiple observations of classrooms. The interview data will be analyzed with an inductive approach outlined by Miles, Huberman, and Saldaña (2014). All teachers’ interview transcripts will be coded together to identify common themes across participants. Participants’ reflections will be analyzed similarly, seeking to characterize their experiences. Observation notes will be used to triangulate the findings. Descriptions for each case will be written emphasizing the aspects that relate to the identified themes. Finally, we will look for commonalities and differences across cases. The results section will describe the cases at the individual participant level followed by a cross-case analysis.
This study takes into consideration how high school teachers’ experiences could be an important tool to gain insight into engineering education problems at the P-12 level. Each case will provide insights into how student body diversity impacts teachers’ pedagogy and experiences. The cases illustrate “multiple truths” (Arghode, 2012) with regard to high school level engineering teaching and embody diversity from the perspective of high school teachers. We will highlight themes across cases in the context of frameworks that represent teacher experience conceptualizing race, ethnicity, and diversity of students. We will also present salient features from each case that connect to potential recommendations for advancing P-12 engineering education efforts. These findings will impact how diversity support is practiced at the high school level and will demonstrate specific novel curricular and pedagogical approaches in engineering education to advance P-12 mentoring efforts.
Prescott, Rebecca D., Chan, Yvonne L., Tong, Eric J., Bunn, Fiona, Onouye, Chiyoko T., Handel, Christy, Lo, Chien-Chi, Davenport, Karen, Johnson, Shannon, Flynn, Mark, Saito, Jennifer A., Lee, Herb, Wong, Kaleomanuiwa, Lawson, Brittany N., Hiura, Kayla, Sager, Kailey, Sadones, Mia, Hill, Ethan C., Esibill, Derek, Cockell, Charles S., Santomartino, Rosa, Chain, Patrick S.G., Decho, Alan W., and Donachie, Stuart P. Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural Relevance. Retrieved from https://par.nsf.gov/biblio/10485781. Astrobiology 23.12 Web. doi:10.1089/ast.2023.0072.
Prescott, Rebecca D., Chan, Yvonne L., Tong, Eric J., Bunn, Fiona, Onouye, Chiyoko T., Handel, Christy, Lo, Chien-Chi, Davenport, Karen, Johnson, Shannon, Flynn, Mark, Saito, Jennifer A., Lee, Herb, Wong, Kaleomanuiwa, Lawson, Brittany N., Hiura, Kayla, Sager, Kailey, Sadones, Mia, Hill, Ethan C., Esibill, Derek, Cockell, Charles S., Santomartino, Rosa, Chain, Patrick S.G., Decho, Alan W., & Donachie, Stuart P. Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural Relevance. Astrobiology, 23 (12). Retrieved from https://par.nsf.gov/biblio/10485781. https://doi.org/10.1089/ast.2023.0072
Prescott, Rebecca D., Chan, Yvonne L., Tong, Eric J., Bunn, Fiona, Onouye, Chiyoko T., Handel, Christy, Lo, Chien-Chi, Davenport, Karen, Johnson, Shannon, Flynn, Mark, Saito, Jennifer A., Lee, Herb, Wong, Kaleomanuiwa, Lawson, Brittany N., Hiura, Kayla, Sager, Kailey, Sadones, Mia, Hill, Ethan C., Esibill, Derek, Cockell, Charles S., Santomartino, Rosa, Chain, Patrick S.G., Decho, Alan W., and Donachie, Stuart P.
"Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural Relevance". Astrobiology 23 (12). Country unknown/Code not available: Astrobiology. https://doi.org/10.1089/ast.2023.0072.https://par.nsf.gov/biblio/10485781.
@article{osti_10485781,
place = {Country unknown/Code not available},
title = {Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural Relevance},
url = {https://par.nsf.gov/biblio/10485781},
DOI = {10.1089/ast.2023.0072},
abstractNote = {Democratizing genomic data science, including bioinformatics, can diversify the STEM workforce and may, in turn, bring new perspectives into the space sciences. In this respect, the development of education and research programs that bridge genome science with “place” and world-views specific to a given region are valuable for Indigenous students and educators. Through a multi-institutional collaboration, we developed an ongoing education program and model that includes Illumina and Oxford Nanopore sequencing, free bioinformatic platforms, and teacher training workshops to address our research and education goals through a place-based science education lens. High school students and researchers cultivated, sequenced, assembled, and annotated the genomes of 13 bacteria from Mars analog sites with cultural relevance, 10 of which were novel species. Students, teachers, and community members assisted with the discovery of new, potentially chemolithotrophic bacteria relevant to astrobiology. This joint education-research program also led to the discovery of species from Mars analog sites capable of producing N-acyl homoserine lactones, which are quorum-sensing molecules used in bacterial communication. Whole genome sequencing was completed in high school classrooms, and connected students to funded space research, increased research output, and provided culturally relevant, place-based science education, with participants naming three novel species described here. Students at St. Andrew's School (Honolulu, Hawai‘i) proposed the name Bradyrhizobium prioritasuperba for the type strain, BL16AT, of the new species (DSM 112479T = NCTC 14602T). The nonprofit organization Kauluakalana proposed the name Brenneria ulupoensis for the type strain, K61T, of the new species (DSM 116657T = LMG = 33184T), and Hawai‘i Baptist Academy students proposed the name Paraflavitalea speifideiaquila for the type strain, BL16ET, of the new species (DSM 112478T = NCTC 14603T).},
journal = {Astrobiology},
volume = {23},
number = {12},
publisher = {Astrobiology},
author = {Prescott, Rebecca D. and Chan, Yvonne L. and Tong, Eric J. and Bunn, Fiona and Onouye, Chiyoko T. and Handel, Christy and Lo, Chien-Chi and Davenport, Karen and Johnson, Shannon and Flynn, Mark and Saito, Jennifer A. and Lee, Herb and Wong, Kaleomanuiwa and Lawson, Brittany N. and Hiura, Kayla and Sager, Kailey and Sadones, Mia and Hill, Ethan C. and Esibill, Derek and Cockell, Charles S. and Santomartino, Rosa and Chain, Patrick S.G. and Decho, Alan W. and Donachie, Stuart P.},
}
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