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日本語

The United Nations (UN) declaration of 2015 as the ‘International Year of Soil’, was symptomatic of a worldwide push to raise awareness of the vital role played by the soil that covers our Earth, and the need to preserve it. Diverse groups of organisms such as bacteria, fungi, protists, and small soil animals inhabit the soil, and together they form the soil ecosystem. Nematodes are a representative soil animal; they are a few millimeters long and have a shape resembling a worm. They play an important role in the cycling of soil materials.

Many soil nematodes are bacteria feeders, but they have a wide variety of feeding habits, such as feeding on fungi, plant parasitism, or being omnivorous. In particular, plant parasitic nematodes often cause devastating damage to crops. Therefore, the classification and identification of nematodes is also important from an agricultural standpoint. However, nematodes are diverse, and there are over 30,000 species. Additionally, because nematodes resemble one another, morphological identification of nematodes is difficult for anyone but experts.

The research team focused on "DNA barcoding" to identify the species based on their unique nucleotide sequences of a barcode gene, and they established a method using a next-generation sequencer that can decode huge numbers of nucleotide sequences. They used this method to analyze nematode communities from different soil environments. Initially, four DNA barcode regions were set for the 18S ribosomal RNA genes shared by eukaryotes.

The soil nematodes used for analysis were isolated from an uncultivated field, a copse and a zucchini-cultivated home garden. The PCR was used to amplify the four gene fragments from the DNA of the nematodes and determine the nucleotide sequences. Additionally, the nematode-derived sequence variants (SVs) representing independent nematode species were identified, and after taxonomical classification and analysis of the SVs, it was revealed that plant parasitizing nematodes were more prevalent in the copse soil whereas bacteria feeders were more prevalent in the garden soil. It was also determined that predatory nematodes and omnivorous nematodes were abundant in the uncultivated field, in addition to bacteria feeders.

This DNA barcoding method using a next-generation sequencer is widely used for the analysis of intestinal microbiota, etc., but analyses of eukaryotes such as nematodes are still in the research stage. This research provides an example of its usefulness for the taxonomic profiling of soil nematodes.

Research team leader Professor Toshihiko Eki stated,
"In my work on genetic research, I have been dealing with nematodes (mainly C. elegans) for around 20 years. I came up with this theme as a suitable candidate for agriculture based research on behalf of our university's Research Center for Agrotechnology and Biotechnology. As a test, we isolated nematodes from the university's soybean field and an unmanaged flowerbed and analyzed the DNA barcode for each nematode. I found that in contrast to the soybean fields, which were dominated by bacterivorous nematodes, the flower beds were dominated by plant-parasitic nematodes that parasitize weeds and nematodes that prey on them.

This discovery was the start of our research (Morise et al., PLoS ONE, 2012). If we consider this method of using one-by-one DNA sequencing as being the first generation, the current method of using the next-generation sequencer can be considered as the second generation. With this method we were successfully able to clarify the characteristics of the nematode communities from each of the three soil environments."

Rather than isolating and analyzing soil nematodes, the research team is now developing a third-generation DNA barcoding method that directly extracts DNA from the soil and analyzes the entire organism inhabiting the soil. We are currently analyzing the soil biota of cabbage fields, and other areas. Our goal is to analyze how soil biota, including microorganisms, change with the growth of crops with a high degree of accuracy, to elucidate the relationship between crops and soil biota, and to clarify the effects of cultivated plants on soil biota and the biota associated with plant diseases at the genetic level.

If this research progresses, it will enable rational crop cultivation and management based on the results of soil organism analysis, which will contribute to the promotion of smart agriculture in Japan and overseas, including the Higashimikawa region, one of the most important agricultural areas in Japan.

This research was performed with the support of the Takahashi Industrial and Economic Research Foundation.