Current Lab Projects

Thaumarchaeota Involved in Ammonia-Oxidation in Terrestrial and Marine Environments

The first step of nitrification, oxidation of ammonia, long thought to be exclusive for the domain Bacteria, was recently tied to the archaeal domain. However, the contribution of AOA to nitrification of soil is still controversial. To date, only a limited number of AOA have been isolated and/or enriched in laboratory culture. This narrow field of characterized AOA has impaired our ability to advance understanding of AOA in soil environments. We obtained highly enriched cultures of ammonia-oxidizing archaea from terrestrial environments: Thaumarchaeota group I.1a, I.1b, and I.1a-associated. To obtain clues about the role of AOA in the nitrogen cycle for soil environments, ammonia oxidation properties of AOA could be investigated to compare with those of AOB.

Archaea are cosmopolitan members in planktonic prokaryotes in oceans. Several groups of planktonic Archaea were discovered in oceanic provinces: Thaumarchaeotal (Marine Group (MG) I and IA), Euryarchaeal (MGII, III, and IV). The only archaea cultivated in the laboratories were Marine Group I which was suggested as ammonia oxidizers. The importance of MGI as a major player in the global nitrogen cycle is well recognized based on recent evidence from North Sea and Atlantic Ocean. Since the marine Euryarchaeota (MGII) could not be cultivated in laboratory, knowledge on the function of the Euryarchaeota remains unknown yet. We have cultures of archaea affiliated with MGI and are characterizing them using metagenomics approaches to find factors stimulating planktonic archaea.

Anaerobic Archaea in Marine Sediments andin Hydrothermal Vents

Microorganisms in marine sediments contribute significantly to global cycles of organic and inorganic matters because of their abundance. Biogeochemistry of the anaerobic ecosystem in deep sea floor is enigmatic. Although MG I and II are the only major groups of archaea in ocean water column, a large variety of other crenarchaeotal and euryarchaeotal groups have been found in marine sediments. Despite of metagenomic studies on the anaerobic archaea, the roles of the archaea remained unknown. We are going to find clues for cultivation of the anaerobic archaea from marine sediments to understand their ecological roles.

Hydrothermalvent provide unique thermal ecosystems dependent on the primary production of chemoautotrophic microorganisms. Diverse anaerobic thermophiles (esp. Archaea) have been recovered from the environments. We are searching for novel biochemical reaction mediated by thermophilic microorganisms of hydrothermal vents such as thermophilic anaerobic methane oxidation and acetogenesis.

Anaerobic Bioremediation Coastal EnvironmentasAffected by Oil Spills

Contaminants of oil spill sites move to and stay in anoxic environments. Under anoxic conditions, activation reactions with oxygen are simply not possible and the pollutants frequently become recalcitrant. The anaerobic degradation pathway for a distinct compound is completely different from the respective aerobic degradation pathway due to absence of oxygen and many steps of anaerobic degradation should be bypassed under anoxic conditions. Many electron acceptors including nitrate, sulphate, iron, and bicarbonate could be used for anaerobic degradation. Due to difficulties to access to and understand anaerobic microbial world, many anaerobic microorganisms remained uncovered and the novel biochemical reactions has been frequently found to be involved. To understand anaerobic microbial processes of degradation of aromatic degradation, various technologies such as stable isotope probing, genome amplification, and next generation sequencing were employed. Currently, we are going to analyse diesel and gasoline-degrading microbial consortia under nitrate-/sulfate-/iron-reducing conditions.

Biogeochemical cycles of carbon andnitrogen in polynyas of Antarctic Sea

Pelagic oceans of polar region are regarded as important areas for biological carbon cycles. These high latitudes are especially sensitive to global climate changes. The resulting nutrient-rich seawater and insolation cause polynyas as one of the most biologically productive regions in the world's oceans and an ecological hotspot in Antarctic Ocean. The early blooming of algae is at the basis of the marine food chain. They are a source of heat and moisture to the atmosphere and a site of exchange of greenhouse (Ozone-depleting) gases (N₂O, CH₄, DMS etc.,), and so they modify the weather in surrounding areas. For understanding of activities and functional roles of cold-adapted procaryotes in the biogeochemical cycles in polynyas, the detailed revelation of diversity and abundance of procaryotes are pre-requisite. We have described the assemblage of bacteria and archaea in the polynya of Amundsen Sea which are highly productive areas of the Southern Antarctic Ocean using high-throughput next generation sequencing of 16S rRNA genes. Pelagibacter and Polaribacter were predominant in all layers and surface layers of Amundsen Sea, respectively. These bacteria might be the main players involved in remineralization of fixed carbons and thus, contritbute to the carbon pump in this region. Next, metagenomics tools will be applied for characterization of dominant bacterial (including Pelagibacter, Polaribacter, Oceanospirilla, and unclassified gammaproteobacteria JG1) and archaeal phylotypes.