Project Name Microbial Community Genomics at the HOT/ALOHA 
Domain (1) bacteria
Investigators (2)
Institution Center for Microbial Oceanography: Research and Education
Project Code CAM_PROJ_HOT
Project Type metagenome
Publications (1)

Microbial plankton are central mediators of matter and energy flux in the sea. These tiny creatures can derive energy from sunlight or inorganic chemicals (including hydrogen, sulfur or reduced metals), and harness it to produce organic matter from simple gases like CO2 and N2. By virtue of these photosynthetic and chemosynthetic abilities, microbes can form the basis for complex food webs in a wide variety of habitats. They are also prodigious consumers of organic matter, and thereby perform important recycling functions in many environments. Additionally, microbial species both produce and consume greenhouse gases. As the primary metabolic engines of the biosphere, they drive the major cycles of the elements, including carbon, nitrogen, and sulfur. Microbial activities are also intimately intertwined with those of other species, in competition for nutrients, as parasites or predators, and as mutualistic symbionts without whom many other plant and animal species could not exist.

Figure 1: Temperature versus salinity (T-S) relations for the North Pacific Subtropical Gyre at station ALOHA Click on the image for more information. Despite their ubiquity, abundance, and biogeochemical importance, the vertical distribution and functional variability of microbes in the ocean's interior is still only poorly known. By contrast, vertical zonation of marine eukaryotic phytoplankton and zooplankton has been well documented for over a century. Upper depth strata are characterized by steep gradients in light quality and intensity, temperature, and macronutrient and trace metal concentrations. At greater depths, low temperature, increasing hydrostatic pressure, the disappearance of light, and dwindling energy supplies largely influence oceanic biota. In this new age of environmental genomics, we now have the opportunity to better define, at the genome level, the spatial and temporal variability of genes, genomes, populations, communities, ecology and evolution of microbes in the ocean (2). Our longterm project aims to relate the taxonomic, genomic, and metabolic diversity of native oceanic microbial species, to the dynamic processes in which they participate, at the ecosystem level. This first genomic depth profile we have collected represents only a beginning - a nascent database that we fully expect will grow and expand over time. The ordered clone libraries additionally provide a resource for full fosmid sequencing, and further metabolic gene expression and biochemical study. This nascent database provides a starting point for further in depth studies of ocean microbial community genomics in time and space, to be conducted at the newly created NSF Science and Technology center, C-MORE, The Center for Microbial Oceanography: Research and Education.

Click on the image for more information. C-MORE is based at the University of Hawaii Manoa, and led by Director Dr. David Karl. The C-MORE team is composed of experts in microbial biology and oceanography from a variety of Institutions. C-MORE research themes are organized around four interconnected themes microbial biodiversity, metabolism and C-N-P-energy flow, remote and continuous sensing and links to climate variability, and ecosystem modeling, simulation and prediction. One of C-MORE's overaching goals is to link "microbial genome space" in the ocean, to its expression, function and interconnections with the totality of the ecosystem: In a phrase, one of our larger aims is to link genomes to biomes. Databases such as this nascent genomic depth series, linked to ongoing oceanographic time series data, serve as a foundation, resource, and springboard for further study of microbial biodiversity and function in the ocean ecosystem.

No assemblies.

Sample Name PI Desc
HF_SMPL_BATS216_20M_SG NA BATS216_20m_Shotgun
HF_SMPL_BATS216_50M_SG NA BATS216_50m_Shotgun
HF_SMPL_HOT179_125M_SG NA HOT179_125m_Shotgun
HF_SMPL_HOT179_25M_SG NA HOT179_25m_Shotgun
HF_SMPL_HOT179_500M_SG NA HOT179_500m_Shotgun
HF_SMPL_HOT179_75M_SG NA HOT179_75m_Shotgun
HF_SMPL_HOT186_110M_GDNA NA HOT186_110m_gDNA
HF_SMPL_HOT186_500M_GDNA NA HOT186_500m_gDNA
HF10_10-07-02 NA HF10_10-07-02 - HOT station ALOHA, 10 m
HF130_10-06-02 NA HF130_10-06-02 - HOT station ALOHA, 130 m
HF200_10-06-02 NA HF200_10-06-02 - HOT station ALOHA, 200 m
HF4000_12-21-03 NA HF4000_12-21-03 - HOT station ALOHA, 4000 m
HF500_10-06-02 NA HF500_10-06-02 - HOT station ALOHA, 500 m
HF70_10-07-02 NA HF70_10-07-02 - HOT station ALOHA, 70 m
HF770_12-21-03 NA HF770_12-21-03 - HOT station ALOHA, 770 m

Type Location
Meta  /iplant/home/shared/imicrobe/projects/31/CAM_PROJ_HOT.csv
Meta  /iplant/home/shared/imicrobe/projects/31/
Read Peptide  /iplant/home/shared/imicrobe/projects/31/CAM_PROJ_HOT.read_pep.fa
Reads  /iplant/home/shared/imicrobe/projects/31/
Reads  /iplant/home/shared/imicrobe/projects/31/samples/685/HF_SMPL_BATS216_20M_SG.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/686/HF_SMPL_BATS216_50M_SG.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/687/HF_SMPL_HOT179_125M_CDNA.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/688/HF_SMPL_HOT179_125M_GDNA.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/689/HF_SMPL_HOT179_125M_SG.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/690/HF_SMPL_HOT179_25M_CDNA.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/691/HF_SMPL_HOT179_25M_GDNA.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/692/HF_SMPL_HOT179_25M_SG.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/693/HF_SMPL_HOT179_500M_CDNA.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/694/HF_SMPL_HOT179_500M_GDNA.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/695/HF_SMPL_HOT179_500M_SG.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/696/HF_SMPL_HOT179_75M_CDNA.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/697/HF_SMPL_HOT179_75M_GDNA.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/698/HF_SMPL_HOT179_75M_SG.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/699/HF_SMPL_HOT186_110M_GDNA.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/700/HF_SMPL_HOT186_25M_GDNA.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/701/HF_SMPL_HOT186_500M_GDNA.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/702/HF_SMPL_HOT186_75M_GDNA.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/703/JGI_SMPL_HF10_10-07-02.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/704/JGI_SMPL_HF130_10-06-02.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/705/JGI_SMPL_HF200_10-06-02.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/706/JGI_SMPL_HF4000_12-21-03.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/707/JGI_SMPL_HF500_10-06-02.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/708/JGI_SMPL_HF70_10-07-02.fa
Reads  /iplant/home/shared/imicrobe/projects/31/samples/709/JGI_SMPL_HF770_12-21-03.fa