How long have you collaborated with the JGI and on which projects?
I’ve been working with the JGI for about ten years now. To date, all of our work has focused on some aspect of life in terrestrial geothermal springs, mostly Great Boiling Spring in northeast Nevada. These projects have included work on both microbial isolates and on whole communities and yet-uncultivated microorganisms. We have sequenced a number of genomes from novel thermophiles, including novel species of Thermocrinis, Thermus, and Rhodothermus, as well as three new lineages of Chloroflexi, together representing two new classes, Thermoflexi and “Planoflexi”, and a new order, Kallotenuales. We have followed up with the novel Chloroflexi strains some functional genomics studies. That work involves the separation and identification of media components before and after cultivation (the exometabolome), which gives us a very detailed look at what compounds are utilized and produced. The exometabolomics work has been a great complement to our genomics work and standard cultivation studies and has led to some very interesting surprises that weren’t predicted from the annotated genomes. This work gives us a much better understanding of the metabolisms of these organisms and may give us better insights into media components necessary to cultivate Chloroflexi and/or difficult-to- cultivate microorganisms in general.
Additionally, we have also collaborated on microbial community work and yet-uncultivated microorganisms. The community work has led to, to our knowledge, the first quantitative relationships between microbial diversity and temperature. Additionally, that work has given us much-needed genomic insights into natural microbial communities in natural geothermal systems as well as systems degrading biofuels substrates. Arguably the most impactful work has been on the genomic exploration of novel, deep branches on the phylogenetic tree through both metagenomics and single-cell genomics. This work has been part of the Genomic Encyclopedia of Bacteria and Archaea-Microbial Dark Matter (GEBA-MDM) project.
Why is this research important?
I’m proud to say that our work is significantly contributing to our knowledge of biodiversity on Earth, which is the central goal of the GEBA-MDM project and its predecessor, the GEBA project, which focused on microbial isolate genomes. Humans have always had a knack for exploration and we are exploring biodiversity here on Earth the best way we know how. This information makes its way into the textbooks and changes the way students think about life. The data we generate are also very important baseline data for biotechnology applications and hopefully biofuels applications.
What do you value about JGI’s contributions?
JGI has greatly expanded the scope of my lab’s research. I can honestly say that working with JGI has transformed my career. JGI has fantastic facilities and bright, collaborative, and forward-thinking scientists. This combination, along with JGI’s experience planning and executing bold and aggressive projects has moved my science way beyond it would be without JGI. Plus, they’re all great people!
- Cole JK, Peacock JP, Dodsworth JA, Williams AJ, Thompson DB, Dong H, Wu G, Hedlund BP. 2013. Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities. ISME Journal 7:718-729.
- Dodsworth JA, Blainey PC, Murugapiran SK, Swingley WD, Ross CA, Tringe SG, Chain PS, Scholz MB, Lo CC, Raymond J, Quake SR, Hedlund BP. 2013. Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nature Communications. 4:1854.
- Hedlund BP, Murugapiran SK, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TB, Ngan CY, Daum C, Duffy K, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Williams AJ, Cole JK, Dodsworth JA, Woyke T. 2015. High-quality draft genome sequence of Kallotenue papyrolyticum JKG1T reveals broad heterotrophic capacity focused on carbohydrate and amino acid metabolism. Genome Announcements. 3:e01410-15.
- Hedlund BP, Dodsworth JA, Murugapiran SK, Rinke C, Woyke T. 2014. Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter”. Extremophiles. 18:865-875.
- Nobu M, Dodsworth J, Murugapiran S, Rinke C, Gies E, Webster G, Schwientek P, Kille P, Parkes J, Sass H, Jorgensen B, Weightman A, Liu W, Hallam S, Tsiamis G, Woyke T, Hedlund BP. 2015. Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics. ISME Journal. 10:273-286.
- Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature. 499:431-437.