- 著者
- Wataru Yazaki Tomohisa Shimasaki Yuichi Aoki Sachiko Masuda Arisa Shibata Wataru Suda Ken Shirasu Kazufumi Yazaki Akifumi Sugiyama
- 出版者
- Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles
- 雑誌
- Microbes and Environments (ISSN:13426311)
- 巻号頁・発行日
- vol.36, no.3, pp.ME21004, 2021 (Released:2021-07-06)
- 参考文献数
- 38
- 被引用文献数
- 3
Nitrogen deficiency affects soybean growth and physiology, such as symbiosis with rhizobia; however, its effects on the bacterial composition of the soybean root microbiota remain unclear. A bacterial community analysis by 16S rRNA gene amplicon sequencing showed nitrogen deficiency-induced bacterial community shifts in soybean roots with the marked enrichment of Methylobacteriaceae. The abundance of Methylobacteriaceae was low in the roots of field-grown soybean without symptoms of nitrogen deficiency. Although Methylobacteriaceae isolated from soybean roots under nitrogen deficiency did not promote growth or nodulation when inoculated into soybean roots, these results indicate that the enrichment of Methylobacteriaceae in soybean roots is triggered by nitrogen-deficiency stress.
- 著者
- Wataru Suda Michiei Oto Seigo Amachi Hirofumi Shinoyama Masahiro Shishido
- 出版者
- 日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会
- 雑誌
- Microbes and Environments (ISSN:13426311)
- 巻号頁・発行日
- vol.23, no.3, pp.248-252, 2008 (Released:2008-08-13)
- 参考文献数
- 29
- 被引用文献数
- 10 17
We developed a method for direct DNA isolation from phyllosphere microbial communities, designated Direct-DIP. This method comprises DNA extraction from non-shredded leaves with benzyl chloride, and DNA purification by gel filtration. Scanning electron microscopy showed that epiphytic microorganisms were completely removed from the leaf surface after benzyl chloride treatment, while microstructures of the leaf were not damaged. Clear DGGE profiles were obtained regardless of the plant species. Shannon diversity indices of DGGE profiles by Direct-DIP were higher than those by a conventional method. Our findings suggest that Direct-DIP is a rapid, simple, and cost-effective method of extracting DNA from phyllosphere microbial communities.
- 著者
- Annisa N. Lathifah Yong Guo Nobuo Sakagami Wataru Suda Masanobu Higuchi Tomoyasu Nishizawa Irfan D. Prijambada Hiroyuki Ohta
- 出版者
- Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology
- 雑誌
- Microbes and Environments (ISSN:13426311)
- 巻号頁・発行日
- pp.ME19041, (Released:2019-07-20)
- 被引用文献数
- 7
Microbial colonization, followed by succession, on newly exposed volcanic substrates represents the beginning of the development of an early ecosystem. During early succession, colonization by mosses or plants significantly alters the pioneer microbial community composition through the photosynthetic carbon input. To provide further insights into this process, we investigated the three-year-old volcanic deposits of Mount Merapi, Indonesia. Samples were collected from unvegetated (BRD) and moss-covered (BRUD) sites. Forest site soil (FRS) near the volcanic deposit-covered area was also collected for reference. An analysis of BRD and BRUD revealed high culturable cell densities (1.7–8.5×105 CFU g–1) despite their low total C (<0.01%). FRS possessed high CFU (3×106 g–1); however, its relative value per unit of total C (2.6%) was lower than that of the deposit samples. Based on the tag pyrosequencing of 16S rRNA genes, the BRD bacterial community was characterized by a higher number of betaproteobacterial families (or genus), represented by chemolithotrophic Methylophilaceae, Leptothrix, and Sulfuricellaceae. In contrast, BRUD was predominated by different betaproteobacterial families, such as Oxalobacteraceae, Comamonadaceae, and Rhodocyclaceae. Some bacterial (Oxalobacteraceae) sequences were phylogenetically related to those of known moss-associated bacteria. Within the FRS community, Proteobacteria was the most abundant phylum, followed by Acidobacteria, whereas Burkholderiaceae was the most dominant bacterial family within FRS. These results suggest that an inter-family succession of Betaproteobacteria occurred in response to colonization by mosses, followed by plants.
- 著者
- Wataru Suda Asami Nagasaki Masahiro Shishido
- 出版者
- 日本微生物生態学会 / 日本土壌微生物学会 / Taiwan Society of Microbial Ecology / 植物微生物研究会
- 雑誌
- Microbes and Environments (ISSN:13426311)
- 巻号頁・発行日
- vol.24, no.3, pp.217-223, 2009 (Released:2009-09-04)
- 参考文献数
- 40
- 被引用文献数
- 20 45
To investigate changes in bacterial communities associated with a fungal foliar disease, epiphytic bacteria from powdery mildew-infected and uninfected leaves of cucumber and Japanese spindle were analyzed using both culture-dependent and -independent methods. Dilution plate counting suggested that powdery mildew-infected leaves likely accommodated larger populations of phyllosphere bacteria than uninfected leaves. Community-level physiological profiles (CLPP) also indicated that functional diversity, richness, and evenness of bacterial communities were significantly greater in the phyllosphere of powdery mildew-infected leaves. Genotype diversity and richness based on band patterns of denaturing gradient gel electrophoresis (DGGE) of the phyllosphere bacterial community were greater for leaves infected by powdery mildew. A principle component analysis of CLPP and DGGE patterns revealed a clear difference between infected and uninfected leaves of both plant species. These results suggest that powdery mildew-infection results in larger bacterial populations, and greater diversity and richness, and also changes the structure of the phyllosphere bacterial community. Furthermore, DNA sequences of the DGGE bands that showed greater intensity in the infected than uninfected leaves, differed between cucumber and Japanese spindle. This suggests that specific bacteria are associated with the plant species accompanying this fungal infection.