Our new paper published in Nature Microbiology, which was a collaboration with the Ettema Lab (Upsalla Univ), and Teske Lab (UNC Chapel Hill), begins to resolve the metabolic capabilities of a group (class) of Archaea (referred to as SAGMEG) that are predominant in the subsurface and have not cultured.Two of the genomes were recovered from this hot spring in Yellowstone National Park (photo by Dan Coleman).
Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea
Press releases about this article.
A deeply-branched widespread new group of Archaea whose genome were recovered from estuary sediments, but are in sediments around the world. Read about their physiologies in this first paper in ISME J.
This paper was highlighted in Nature as well.
For the summer we have John working on assembling genomes of uncultured bacteria that were growing on oil from the Deep Water Horizon spill in the Gulf in 2010. He is about half way through his project and will soon have lot of genomes to look at their metabolisms!
Genomic resolution of linkages in carbon, nitrogen,and sulfur cycling among widespread estuary sediment bacteria
Brett J Baker, Cassandre Sara Lazar, Andreas P Teske, and Gregory J Dick
Background: Estuaries are among the most productive habitats on the planet. Bacteria in estuary sediments control the turnover of organic carbon and the cycling of nitrogen and sulfur. These communities are complex and primarily made up of uncultured lineages, thus little is known about how ecological and metabolic processes are partitioned in sediments.
Results: De novo assembly and binning resulted in the reconstruction of 82 bacterial genomes from different redox regimes of estuary sediments. These genomes belong to 23 bacterial groups, including uncultured candidate phyla (for example, KSB1, TA06, and KD3-62) and three newly described phyla (White Oak River (WOR)-1, WOR-2, and WOR-3). The uncultured phyla are generally most abundant in the sulfate-methane transition (SMTZ) and methane-rich zones, and genomic data predicts that they mediate essential biogeochemical processes of the estuarine environment, including organic carbon degradation and fermentation. Among the most abundant organisms in the sulfate-rich layer are novel Gammaproteobacteria that have genes for the oxidation of sulfur and the reduction of nitrate and nitrite. Interestingly, the terminal steps of denitrification (NO3 to N2O and then N2O to N2) are present in distinct bacterial populations.
Conclusions: This dataset extends our knowledge of the metabolic potential of several uncultured phyla. Within the sediments, there is redundancy in the genomic potential in different lineages, often distinct phyla, for essential biogeochemical processes. We were able to chart the flow of carbon and nutrients through the multiple geochemical layers of bacterial processing and reveal potential ecological interactions within the communities.
Figure1 – showing the phylogeny of bacteria based on multiple genes from the genomes
We are busy sorting through loads of genomic data from the Gulf of Mexico hypoxic dead zone and surrounding water. Here is the tetra nucleotide ESOM clustering map of the assembled genomes from that project. 55 genomes and counting!
Postdoctoral fellowship in marine microbial ecology
A postdoctoral fellowship in marine microbial ecology is available at the University of Texas, Marine Science Institute (https://utmsi.utexas.edu) located in the seaside community of Port Aransas, TX. The Baker lab (http://sites.utexas.edu/baker-lab/) is studying microbial biogeochemical cycling in a variety of marine and estuary habitats (namely sediments). The position will involve reconstruction of numerous (bacteria and archaea) genomes, and tracking gene activity in situ via transcriptomics, to understand how metabolic and ecological roles are partitioned in nature. Experience with metagenomic assembly of high-throughput (including transcriptomic) sequencing data, evidence of programming skills, and publication record are desirable. We are looking for a creative, independent scientist who can work and communicate effectively in an interdisciplinary, collaborative environment. A PhD and research experience in an appropriate discipline are required. The initial appointment will be for a two-year period, with the possibility of a yearly extension to up to three years based upon performance. To Apply, please submit a cover letter, CV, and contact information for 3 references via email to Brett Baker at email@example.com.
Kiley has been busy extracting DNA from some really interesting sediments samples from the Guaymas Basin in the Gulf of California. We have submitted them for metagenomic sequencing. We should be reconstructing some novel “hot-seep” bacteria and ANME archaea in the next few weeks!