In an era of ecosystem degradation and climate change, maximizing microbial functions in agroecosystems has become a prerequisite for the future of global agriculture. However, managing species-rich communities of plant-associated microbiomes remains a major challenge. Here, we propose interdisciplinary research strategies to optimize microbiome functions in agroecosystems. Informatics now allows us to identify members and characteristics of 'core microbiomes', which may be deployed to organize otherwise uncontrollable dynamics of resident microbiomes. Integration of microfluidics, robotics and machine learning provides novel ways to capitalize on core microbiomes for increasing resource-efficiency and stress-resistance of agroecosystems.

Symbiotic microorganisms, such as mycorrhizal fungi, are known to associate with most plants; however members of the Cruciferae are an exception. We investigated nutrient exchange between a dark septate endophytic fungus, Heteroconium chaetospira, and Chinese cabbage plants (Cruciferae) in vitro. Chinese cabbage could not use some amino acids, while the fungus-treated plants were able to use all of the nitrogen forms provided. To demonstrate that nitrogen transfer occurs between the fungus and the host plant, we used a hydrophobic polytetrafluoroethylene (PTFE) membrane compartment system, which restricts diffusion and mass flow of ions and allows only fungal penetration. Our results strongly suggest that H. chaetospira provided nitrogen to the plant, rather than the plant mineralizing available organic nitrogen. In addition carbon transfer from the host plant to the fungus was demonstrated with HPLC and (l3)CO2-labeling experiments. When H. chaetospira colonized host plant roots under low glucose condition, ergosterol content in culture pot (as an index of fungal biomass) increased significantly compared to the fungal treatment without a host plant. Sucrose concentration in the host root significantly decreased as a result of fungal colonization, and mannitol (a specific carbon source to fungal cells) increased in the roots. Sucrose and mannitol in the host root treated with the fungus were labeled clearly by 13C after 1C-labeled CO2 was provided to the plant. These results suggest that the fungus obtained carbon, mainly as sucrose, from the host plant. We show for the first time the existence of a fungus establishing a mutualistic association with a nonmycorrhizal Cruciferae plant.

Root‐colonizing fungi were isolated from a total of 663 root segments of Chinese cabbage plants grown in soils collected from wheat, rape, Chinese cabbage, and napier grass fields. Most of the 322 isolates were from the wheat field soil and comprised 18 genera and two septate fungal groups. Hyaline and dark septate fungi accounted for approximately half the isolates from the wheat field soil. Sixteen isolates almost completely suppressed clubroot in sterile soil. Amongst these 16 isolates, two from Heteroconium chaetospira were also effective in nonsterile soil. Chinese cabbage seedlings from seed treated with these two isolates appeared healthy, and inoculation with one isolate promoted growth. Hyphae of the fungus covered the root surface and extensively colonized the inner cortical tissues.

Microscopic and molecular analyses showed the presence of endobacteria inside the mycelia of four out of twelve nitrous oxide (N 2 O)-producing fungal isolates identified as Mortierella elongata. The 16S rRNA gene was successfully amplified with DNA extracted directly from the endobacterium-containing fungal strains and all sequences were related to that of Candidatus Glomeribacter gigasporarum in the family Burkholderiaceae. Bacterial endotoxin was detected in the endobacterium-positive fungal strains but only trace levels were found in endobacterium-negative strains. No significant relationship was found between the fungal N 2 O-producing activity and the presence of endobacteria.Key words: endobacterium, N 2 O production, Mortierella elongata, soil fungusThe intracellular distribution of bacteria, or more specifically bacterial endosymbiosis, is known for numerous eukaryotic organisms including ciliate protozoa (25), various insects (11), a frenulata (marine invertebrate) (12), and wellknown legume roots. Concerning the association of bacteria with fungi, bacterial endosymbiosis has been reported in some strains of Glomeromycota [e.g. Geosiphon pyriform (22), and Gigaspora and Scutellospora species (4, 6, 7, 15)], Ascomycota [e.g. Tuber borchii (1)], Basidiomycota [e.g. Laccaria bicolor; (3)] and Zygomycota [e.g. Rhizopus species (10, 18)]. In our recent study, nitrous oxide (N 2 O)-producing fungal strains were isolated from upland soils and the intramycelial localization of bacterium (endobacterium) in the fungal isolates was found (Sato, Y., et al. 2008. Abstracts for the 12th International Symposium on Microbial Ecology, Cairns, Australia). The purpose of this study is to examine further the presence of endobacteria using fluorescence and electron microscopy, the amount of endotoxin, the 16S rRNA gene, and the relationship between the presence of endobacteria and fungal N 2 O-producing activity.Ten fungal strains used in this study were isolated from no-tilled, low-nitrogen input cropland soils at the Field Science Center, Ibaraki University College of Agriculture, located in the Kanto plains of Japan and were identified as phylum Zygomycota, Mortierella elongata from their morphological characteristics and their 18S-26S/28S internal transcribed spacer sequence (ITS). All of the M. elongata strains were examined for activity to produce N 2 O and found to have low activity levels during growth in cultures containing 10 mM nitrite but no activity in cultures with 10 mM nitrate (Y. Sato, T. Nishizawa, M. Umezu, K. Tsuruta, K. Narisawa, M. Komatsuzaki, N. Kaneko, H. Ohta, submitted for publication). Comparisons were made with herbarium materials, Mortierella elongata Linnemann NBRC 8570 and M. elongata MAFF 425591, obtained from the National Institute of Technology and Evaluation (NITE Biological Resource Center, Chiba, Japan), and National Institute of Agrobiological Sciences (NIAS Genebank, Ibaraki, Japan), respectively.The morphology of M. elongata strains was observed by fluorescence microscope. Briefly, ...

Chinese cabbage seedlings inoculated with an isolate of the hyphomycete, Heteroconium chaetospira, were transplanted to the field. After 3 months, they showed a 52-97% reduction in clubroot and a 49-67% reduction in Verticillium yellows compared with noninoculated controls. H. chaetospira colonized the cortical cells, especially in the root tip region. Infected plants showed no disease symptoms. The infection process involves the formation of appressoria on the cell surface and the subsequent growth of hyphae within cells. H. chaetospira colonized 18 plant species, indicating a wide range of hosts. It may have potential as a biocontrol agent for clubroot and Verticillium yellows.