Deep Trench Single-cell Genomics

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Microbial diversity in deep-sea environments is high, where microbial evolution and distribution have been influenced by extreme factors such as high pressure, low temperature, low carbon and no light. Scientists from the University of California San Diego and University of Puerto Rico-Mayaguez will explore the biodiversity of microorganisms of particularly extreme deep-sea environments - deep-sea trenches - by focusing on one site, the Puerto Rico Trench, the deepest part of the Atlantic Ocean. Deep trench prokaryotes (bacteria and archaea) are expected to possess novel enzymes and cell properties which allow them to survive and grow under these extreme conditions. One major goal of this project is to study the genomes of these microorganisms to understand what capabilities they have evolved to live in this harsh environment. Another goal is to evaluate the extent and diversity of novel protein families in the genomes of these deep trench microbes. Water samples collected from the trench and maintained under very high pressure (80 MPa or 11,000 psi), will be examined using single-cell genomic technology. A careful sorting procedure will be developed to avoid contamination, chimeras (hybridization of two or more different genomes) and other artifacts of sample handling. These researchers will collect two hundred individual cells from the water sample by micromanipulation and amplify their genomic DNA in nanoliter volume microfluidic chambers. They will perform 16S rDNA (universal marker gene) sequencing on each sample as an independent genetic identifier. They will then select genomic DNA candidates with novel phylogenetic characteristics for further full genome sequencing. The closed and assembled genome sequences will be annotated to assign gene function. These researchers will compare these genome sequences with sequences from various marine metagenomic datasets and will also compare the extent and diversity of novel protein families in these genomes to the large number of protein families identified in the Global Ocean Survey dataset. These researchers expect to discover anticipated as well as unexpected properties of deep sea microorganisms in this manner. Their outreach activities will include multiple workshops with the deep sea microbiology community and the development of an international conference on High Pressure Bioscience and Biotechnology. The genome sequences will also become a rare community resource since microbial samples from deep sea trenches are very difficult to obtain.