Minoru Ijichi

Heterotrophic bacteria as major nitrogen fixers in the euphotic zone of the Indian Ocean

Diazotrophy in the Indian Ocean is poorly understood compared to that in the Atlantic and Pacific Oceans. We first examined the basin-scale community structure of diazotrophs and their nitrogen fixation activity within the euphotic zone during the northeast monsoon period along about 69°E from 17°N to 20°S in the oligotrophic Indian Ocean, where a shallow nitracline (49–59 m) prevailed widely and the sea surface temperature (SST) was above 25°C. Phosphate was detectable at the surface throughout the study area. The dissolved iron concentration and the ratio of iron to nitrate + nitrite at the surface were significantly higher in the Arabian Sea than in the equatorial and southern Indian Ocean. Nitrogen fixation in the Arabian Sea (24.6–47.1 μmolN m−2 d−1) was also significantly greater than that in the equatorial and southern Indian Ocean (6.27–16.6 μmolN m−2 d−1), indicating that iron could control diazotrophy in the Indian Ocean. Phylogenetic analysis of nifH showed that most diazotrophs belonged to the Proteobacteria and that cyanobacterial diazotrophs were absent in the study area except in the Arabian Sea. Furthermore, nitrogen fixation was not associated with light intensity throughout the study area. These results are consistent with nitrogen fixation in the Indian Ocean, being largely performed by heterotrophic bacteria and not by cyanobacteria. The low cyanobacterial diazotrophy was attributed to the shallow nitracline, which is rarely observed in the Pacific and Atlantic oligotrophic oceans. Because the shallower nitracline favored enhanced upward nitrate flux, the competitive advantage of cyanobacterial diazotrophs over nondiazotrophic phytoplankton was not as significant as it is in other oligotrophic oceans.

Nitrification and its influence on biogeochemical cycles from the equatorial Pacific to the Arctic Ocean

We examined nitrification in the euphotic zone, its impact on the nitrogen cycles, and the controlling factors along a 7500 km transect from the equatorial Pacific Ocean to the Arctic Ocean. Ammonia oxidation occurred in the euphotic zone at most of the stations. The gene and transcript abundances for ammonia oxidation indicated that the shallow clade archaea were the major ammonia oxidizers throughout the study regions. Ammonia oxidation accounted for up to 87.4% (average 55.6%) of the rate of nitrate assimilation in the subtropical oligotrophic region. However, in the shallow Bering and Chukchi sea shelves (bottom ⩽67 m), the percentage was small (0–4.74%) because ammonia oxidation and the abundance of ammonia oxidizers were low, the light environment being one possible explanation for the low activity. With the exception of the shallow bottom stations, depth-integrated ammonia oxidation was positively correlated with depth-integrated primary production. Ammonia oxidation was low in the high-nutrient low-chlorophyll subarctic region and high in the Bering Sea Green Belt, and primary production in both was influenced by micronutrient supply. An ammonium kinetics experiment demonstrated that ammonia oxidation did not increase significantly with the addition of 31–1560 nm ammonium at most stations except in the Bering Sea Green Belt. Thus, the relationship between ammonia oxidation and primary production does not simply indicate that ammonia oxidation increased with ammonium supply through decomposition of organic matter produced by primary production but that ammonia oxidation might also be controlled by micronutrient availability as with primary production.

Abundance and Distribution of Dimethylsulfoniopropionate Degradation Genes and the Corresponding Bacterial Community Structure at Dimethyl Sulfide Hot Spots in the Tropical and Subtropical Pacific Ocean

ABSTRACT Dimethylsulfoniopropionate (DMSP) is mainly produced by marine phytoplankton but is released into the microbial food web and degraded by marine bacteria to dimethyl sulfide (DMS) and other products. To reveal the abundance and distribution of bacterial DMSP degradation genes and the corresponding bacterial communities in relation to DMS and DMSP concentrations in seawater, we collected surface seawater samples from DMS hot spot sites during a cruise across the Pacific Ocean. We analyzed the genes encoding DMSP lyase (dddP) and DMSP demethylase (dmdA), which are responsible for the transformation of DMSP to DMS and DMSP assimilation, respectively. The averaged abundance (±standard deviation) of these DMSP degradation genes relative to that of the 16S rRNA genes was 33% ± 12%. The abundances of these genes showed large spatial variations. dddP genes showed more variation in abundances than dmdA genes. Multidimensional analysis based on the abundances of DMSP degradation genes and environmental factors revealed that the distribution pattern of these genes was influenced by chlorophyll a concentrations and temperatures. dddP genes, dmdA subclade C/2 genes, and dmdA subclade D genes exhibited significant correlations with the marine Roseobacter clade, SAR11 subgroup Ib, and SAR11 subgroup Ia, respectively. SAR11 subgroups Ia and Ib, which possessed dmdA genes, were suggested to be the main potential DMSP consumers. The Roseobacter clade members possessing dddP genes in oligotrophic subtropical regions were possible DMS producers. These results suggest that DMSP degradation genes are abundant and widely distributed in the surface seawater and that the marine bacteria possessing these genes influence the degradation of DMSP and regulate the emissions of DMS in subtropical gyres of the Pacific Ocean.

Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunami

BackgroundThe Great East Japan Earthquake of 2011 triggered large tsunami waves, which flooded broad areas of land along the Pacific coast of eastern Japan and changed the soil environment drastically. However, the microbial characteristics of tsunami-affected soil at the genomic level remain largely unknown. In this study, we isolated microbes from a soil sample using general low-nutrient and seawater-based media to investigate microbial characteristics in tsunami-affected soil.ResultsAs expected, a greater proportion of strains isolated from the tsunami-affected soil than the unaffected soil grew in the seawater-based medium. Cultivable strains in both the general low-nutrient and seawater-based media were distributed in the genus Arthrobacter. Most importantly, whole-genome sequencing of four of the isolated Arthrobacter strains revealed independent losses of siderophore-synthesis genes from their genomes. Siderophores are low-molecular-weight, iron-chelating compounds that are secreted for iron uptake; thus, the loss of siderophore-synthesis genes indicates that these strains have adapted to environments with high-iron concentrations. Indeed, chemical analysis confirmed the investigated soil samples to be rich in iron, and culture experiments confirmed weak cultivability of some of these strains in iron-limited media. Furthermore, metagenomic analyses demonstrated over-representation of denitrification-related genes in the tsunami-affected soil sample, as well as the presence of pathogenic and marine-living genera and genes related to salt-tolerance.ConclusionsCollectively, the present results would provide an example of microbial characteristics of soil disturbed by the tsunami, which may give an insight into microbial adaptation to drastic environmental changes. Further analyses on microbial ecology after a tsunami are envisioned to develop a deeper understanding of the recovery processes of terrestrial microbial ecosystems.

Ammonia oxidizers in the sea-surface microlayer of a coastal marine inlet

Planktonic archaea are thought to play an important role in ammonia oxidation in marine environments. Data on the distribution, abundance, and diversity of ammonia oxidizers in the coastal sea-surface microlayer (SML) are lacking, despite previous reports of high abundance of Thaumarchaeota in the SML of estuaries and freshwater lakes. Here, we failed to detect the presence of ammonia-oxidizing bacteria in any of our samples taken from a semi-enclosed marine inlet in Japan. Therefore, we shifted our focus to examine the archaeal community composition as well as the Thaumarchaeota marine group I (MG-I) and ammonia monooxygenase subunit A (amoA) gene copy numbers and composition in the SML and corresponding underlying water (UW, 20 cm). amoA gene copy numbers obtained by quantitative PCR were consistent with the typical values observed in the surface waters of oceanic and coastal environments where nitrification activity has been detected, but the copy numbers were two- to three-fold less than those reported from the surface layers and UW of high mountain lakes. Both amoA and MG-I 16S rRNA gene copy numbers were significantly negatively correlated with chlorophyll-a and transparent exopolymer particle concentrations in the SML. Communities of archaea and ammonia-oxidizing archaea in SML samples collected during low wind conditions (≤5 m s–1) differed the most from those in UW samples, whereas the communities in SML samples collected during high wind conditions were similar to the UW communities. In the SML, low ratios of amoA to MG-I 16S rRNA genes were observed, implying that most of the SML Thaumarchaeota lacked amoA. To our knowledge, our results provide the first comparison of ammonia-oxidizing communities in the coastal SML with those in the UW.

The complete mitochondrial genome of the longfin dragonfish Tactostoma macropus (Stomiiformes: Stomiidae)

Abstract The complete mitochondrial genome (mitogenome) was determined for the longfin dragonfish Tactostoma macropus, which is the first for the genus and the third within the family Stomiidae. The mitogenome sequence is 17,690 bp in length containing 2 ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes, and a control region, as in most fishes. The gene order of T. macropus showed an unreported deviation from the typical vertebrate one. Phylogenetic reconstruction using the maximum likelihood method placed T. macropus in the monophyletic Stomiiformes. Three stomiid species were recovered as a moderately supported clade in the phylogenetic tree.

Habitability analyses of aquatic bacteria

Habitability is defined as an ability of an organism to inhabit different environments. Habitability of organisms, however, cannot be inferred from analyses such as a whole genome or community structures. A recently developed database, the MetaMetaDB, gives us information from what kind of environments one particular 16S rRNA sequence data has ever been obtained, and thus enables us to infer the habitability of the bacterium in question. In order to check the applicability of this database to study the habitability of aquatic bacteria, samples collected at two Naka River stations, one estuarine station from Naka River Estuary, two coastal stations at Oarai in Ibaraki Prefecture, Japan and one station in the Kuroshio Current of the western North Pacific were examined. The phylotypes were tracked against the MetaMetaDB and it was reasonably found that the low-salinity stations were dominated by sequences with “freshwater and groundwater”, “human” and “wastewater” habitat identities, while the high-salinity stations were dominated by those with a “marine” identity. The phylotypes of low-salinity stations with a particular habitat identity were absent or rare in the high-salinity stations and vice versa. The MetaMetaDB also showed that sequences of Cyanobacteria or related phylogenetic groups may be present in the human gut, as well as the probable distribution of the relatives (ancestors/descendants/siblings) of some bacteria. These overall findings proved that the MetaMetaDB is useful as a new tool to infer microbial habitability and it gives us new information on the possible origin and ecology of microorganisms in the environments.