Abstract Background Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N 2 -fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome. Results After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments). Conclusion Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling.
Elution of silicon (Si) from three types of slag fertilizers was tested in a paddy field. They were made from granulated blast furnace slag, dephosphorization slag and decarburization slag, respectively. Each fertilizer, embedded in epoxy resin to expose the cross section, was analyzed to get initial two-dimensional distribution images of Si, calcium (Ca), oxygen (O), magnesium (Mg), aluminum (Al), manganese (Mn) and iron (Fe) by electron probe micro-analyzer (EPMA). These resin specimens were set in a paddy field for 75 d. Then the second two-dimensional distribution images of Si, Ca, O, Mg, Al, Mn and Fe at the same site were analyzed again by EPMA. A comparison of the two-dimensional distribution images before and after setting in paddy field elucidated the following results: (1) Si eluted clearly from dephosphorization slag and decarburization slag; (2) Si, Ca, Mg and Al distributed homogeneously in granulated blast furnace slag. X-ray diffraction (XRD) clarified that granulated blast furnace slag was amorphous. The content of plant-available Si in each slag fertilizer was evaluated by the cation exchange resin extraction method. It was the highest in dephosphorization slag fertilizer. This result corresponded to Si elution from dephosphorization slag observed by EPMA. The content of plant-available Si was low in granulated blast furnace slag but high in air-cooled blast furnace slag. Although the content of plant-available Si in decarburization slag was low, the efficacy of Si elution was the highest in decarburization slag. From X-ray diffraction analyses, calcium silicate or larnite (Ca2SiO4) was considered to be the causative substance for efficient Si elution from decarburization slag and dephosphorization slag. Because of the high content of plant-available Si, dephosphorization slag and air-cooled blast furnace slag are recommended as silicate fertilizers in paddy fields.
Nitrous oxide (N2O), an ozone-depleting greenhouse gas, is generally produced by soil microbes, particularly NH3 oxidizers and denitrifiers, and emitted in large quantities after N fertilizer application in croplands. N2O can be produced via multiple processes, and reduced, with the involvement of more diverse microbes with different physiological constraints than previously thought; therefore, there is a lack of consensus on the production processes and microbes involved under different agricultural practices. In this study, multiple approaches were applied, including N2O isotopocule analyses, microbial gene transcript measurements, and selective inhibition assays, to revisit the involvement of NH3 oxidizers and denitrifiers, including the previously-overlooked taxa, in N2O emission from a cropland, and address the biological and environmental factors controlling the N2O production processes. Then, we synthesized the results from those approaches and revealed that the overlooked denitrifying bacteria and fungi were more involved in N2O production than the long-studied ones. We also demonstrated that the N2O production processes and soil microbes involved were different based on fertilization practices (plowing or surface application) and fertilization types (manure or urea). In particular, we identified the following intensified activities: (1) N2O production by overlooked denitrifying fungi after manure fertilization onto soil surface; (2) N2O production by overlooked denitrifying bacteria and N2O reduction by long-studied N2O-reducing bacteria after manure fertilization into the plowed layer; and (3) N2O production by NH3-oxidizing bacteria and overlooked denitrifying bacteria and fungi when urea fertilization was applied into the plowed layer. We finally propose the conceptual scheme of N flow after fertilization based on distinct physiological constraints among the diverse NH3 oxidizers and denitrifiers, which will help us understand the environmental context-dependent N2O emission processes.
In an attempt to clarify the genetic factors in alcoholism among the Japanese, polymorphism of alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) genes has been investigated. Genetic polymorphism of ADH2/ALDH2 in 66 cases of normal subjects, 90 cases of alcohol dependent, and 31 patients with alcoholic liver disease among Japanese has been analyzed using a polymerase chain reaction assay followed by a direct sequencing method, because ethanol is mainly catabolized by ADH and ALDH and less by cytochrome P450IIE1 and catalase. The incidence of both ADH2*1/*1 and ALDH2*1/*1 was significantly higher in patients with alcohol dependence and in patients with alcoholic liver disease when compared with that in control subjects. In addition, the incidence of ALDH2*1/*2 and ALDH2*2/*2 was significantly reduced in alcoholics compared with control subjects. Genetic polymorphism of ADH2/ALDH2 in patients with alcoholic liver disease was not different from that of alcohol dependents. According to these results, not only ALDH2 gene, often claimed to be responsible for alcohol dependence among Japanese, but also ADH2 gene polymorphism, which modulates the metabolism of ethanol, play important roles in habitual alcohol intake behavior in Japanese patients and in some patients leads to alcoholic liver diseases.
Anaeromyxobacter and Geobacter, iron-reducing bacteria belonging to Deltaproteobacteria, are newly discovered nitrogen-fixing bacteria predominant in paddy soils. We hypothesized that adding ferric iron oxide as an electron acceptor for respiration of the iron-reducing bacteria could enhance the nitrogen-fixing activity of Anaeromyxobacter and Geobacter in paddy soils. In the soil microcosm study, soil nitrogen-fixing activity significantly increased after adding ferrihydrite or Fe2O3, ferric iron oxides, to the soil. In these soils, gene transcripts of nifD from Anaeromyxobacter and Geobacter were detected, whereas those from other general diazotrophs were not detected. Anaeromyxobacter and Geobacter might be involved in the enhanced soil nitrogen-fixing activity. The application of iron powder to paddy field soils also enhanced the soil nitrogen-fixing activity. This study is the first to demonstrate that addition of iron compounds to paddy soil enhanced the soil nitrogen-fixing activity. The results of this study may lead to the development of novel paddy soil management strategies to increase soil nitrogen fertility and ensure rice yields with a reduced nitrogen fertilizer input and a lower environmental nitrogen burden.
