Root endophytic bacterial and fungal communities in a natural hot desert are differentially regulated in dry and wet seasons by stochastic processes and functional traits

Taniguchi, Takeshi*; Isobe, Kazuo*; Imada, Shogo*; Eltayeb, M. M.*; Akaji, Yasuaki*; Nakayama, Masataka; Allen, M. F.*; Aronson, E. L.*

Science of the Total Environment, 899, p.165524_1 - 165524_13, 2023/11

https://doi.org/10.1016/j.scitotenv.2023.165524

Dryland ecosystems experience seasonal cycles of severe drought and moderate precipitation. Desert plants typically have patchy distributions, and many may develop symbiotic relationships with root endophytic microbes to survive under the repeated wet and extremely dry conditions. Although community coalescence has been found in many systems, the colonization by functional microbes and its relationship to seasonal transitions in arid regions are not well understood. Here we examined root endophytic microbial taxa, and their traits in relation to their root colonization, during the dry and wet seasons in a hot desert of the southwestern United States. We used high-throughput DNA sequencing of 16S rRNA and ITS gene profiling of five desert shrubs, and analyzed the seasonal change in endophytic microbial lineages. In summer, Actinobacteria increased, although this was not genus-specific. For fungi, Glomeraceae selectively increased in summer. In winter, Gram-negative bacterial genera, including those capable of nitrogen fixation and plant growth promotion, increased. Neutral model analysis revealed a strong stochastic influence on endophytic bacteria but a weak effect for fungi, especially in summer. The taxa with higher frequency than that predicted by the neutral model shared environmental adaptability and symbiotic traits, whereas the frequency of pathogenic fungi was at or under the predicted value. These results suggest that community assembly of bacteria and fungi is regulated differently. The bacterial community was affected by stochastic and deterministic processes via the bacterial response to drought (response trait) and beneficial effect on plants (effect trait). For fungi, mycorrhizal fungi were selected by plants in summer. The regulation of beneficial microbes by plants in both dry and wet seasons suggests the presence of plant-soil positive feedback in this natural desert ecosystem.

Shift in the rhizosphere microbial communities between growing- and low-temperature dormant seasons in a northern hardwood forest

Nakayama, Masataka; Tateno, Ryunosuke*

Plant and Soil, 17 Pages, 2023/00

https://doi.org/10.1007/s11104-023-06391-y

Microbial communities within the soil surrounding plant roots (rhizosphere) are distinct from those in the non-rhizosphere soil because of root exudation and symbiosis with plant roots and play important roles in plant growth. However, seasonal variations in these rhizosphere microbial communities are not well known, especially during the plant's dormant season in cool temperate forests. We investigated the rhizosphere microbial communities in a cool-temperate deciduous broad-leaved forest at the growing season (mid-summer) and at the beginning and end of the plant's dormant season (early winter and early spring) using metabarcoding of prokaryotic 16S rRNA genes and fungal ITS region, microbial functional prediction, and co-occurrence network analysis. The rhizosphere dominant prokaryotic subgroup (occupying 19.4 3.2% of relative read counts) had non-significant seasonal fluctuations, and their relative read counts were correlated with physicochemical properties, including pH and water content. In contrast, the relative read count of ectomycorrhizal fungi was 1.4 times higher in the rhizosphere than that in the bulk soil in mid-summer. However, the relative read counts of ectomycorrhizal fungi within rhizospheres in winter and spring (28.5 18.9% and 20.8 13.8%, respectively) were similar to that in bulk soil (25.8 18.7% and 22.4 17.1%, respectively). Ectomycorrhizal fungi reduced their occupancy within the rhizosphere during the plant's dormant seasons, whereas rhizosphere-dominant prokaryotic communities were stable during the seasonal change, implying the importance of prokaryotic rather than ectomycorrhizal fungal communities in the processes occurring within the rhizosphere during dormant seasons.

Rapid measurement of the chloride diffusion coefficient in concrete from combination of non-steady-state migration experiment and EPMA

Ogino, Masataka*; Owaki, Eiji*; Shirase, Mitsuyasu*; Nakayama, Masashi

Konkurito Kogaku Nenji Rombunshu (DVD-ROM), 39(1), p.703 - 708, 2017/07

no abstracts in English

A Measurement method for diffusivity coefficient of concrete by application of EPMA to an electrophoretic test of non-static state

Ogino, Masataka*; Owaki, Eiji*; Shirase, Mitsuyasu*; Nakayama, Masashi

no journal, , 

no abstracts in English

Does spatially heterogeneous nitrogen deposition affect nitrogen and carbon dynamics in a decidous broad-leaved forest?

Katata, Genki*; Fukushima, Keitaro*; Koarashi, Jun; Yamaguchi, Takashi*; Watanabe, Makoto*; Nagano, Hirohiko; Nakayama, Masataka*; Tateno, Ryunosuke*

no journal, , 

no abstracts in English

Nitrate contamination via groundwater of the pasture and farmland beyond the watershed boundary in the forest streamwater

Fukushima, Keitaro*; Iwasaki, Kenta*; Oda, Yoshiya*; Sakai, Masaru*; Katata, Genki*; Yamaguchi, Takashi*; Nakayama, Masataka*; Kubota, Tomohiro*; Nagano, Hirohiko; Watanabe, Makoto*; et al.

no journal, , 

no abstracts in English

Characterizations of formed biofilms and microbial communities on microplastics in coastal rivers of Japan

Battulga, B.; Nakayama, Masataka; Atarashi-Andoh, Mariko; Koarashi, Jun

no journal, , 

Plastic debris in the aquatic environment has become a growing concern due to their long-term ecological consequences. The current study is focused on microbial community composition on microplastics (MPs; sizes 5 mm) and characteristics of MP-associated biofilms in coastal river environments of Japan in order to understand the impact of MP-associated biofilms on aquatic organic matter cycling. The aims of the current study are i) extraction and characterization of microbial biofilms on MPs and ii) identification of diversity and composition of microbial communities on MP surfaces and in surrounding surface waters and sediments. The samples were collected from two coastal rivers during 2021-2022 on a seasonal basis. In this study, we proposed a new method to extract biofilms from MPs using ultrasound-assisted syringe treatment for isotopic analysis. Morphotypes of MPs and associated specific microbial taxa as well as seasonal differences were also observed.

Effect of artificial root exudates on the forest soil microbial community and nitrogen dynamics

Nakayama, Masataka; Tateno, Ryunosuke*

no journal, , 

Root exudates, carbon compounds secreted from plant fine roots, enhance nutrient cycles within root surrounding soil (rhizosphere) by stimulating microbial activities and growth. However, there is a lack of knowledge about the effect of the differences in the chemical composition of root exudates and the diversity of root exudates on the nitrogen cycle within the rhizosphere. Here, we investigated the impact of the differences in root exudates on the nitrogen cycles and microbial community using artificial root exudates (ARE). We added ARE from the simulated fine root and changed their diversity from 1 to 3 per incubation system. Soil microbial gene abundances varied among ARE types and diversity, but the differences were not statistically significant. In addition, there was a non-significant effect of ARE on nitrogen cycling processes. These results indicated that the diversity and compositions of root exudates did not affect the microbial community and nitrogen cycle for at least a short time.

Microbial life on plastics and its implication on elemental cycling in the aquatic environment

Battulga, B.; Nakayama, Masataka; Atarashi-Andoh, Mariko; Koarashi, Jun

no journal, , 

A growing attention has been addressed on microbial attachment and biofilm formation on plastic debris especially on microplastics (MPs; sizes: 5 mm) in the aquatic environment. The current study is focused on bacterial and fungal community composition, diversity, and structure in MP-associated biofilms to emphasize potential alteration of elemental cycling by the presence of MPs in the coastal aquatic environment. We collected MP, surface water, bottom sediment, and coastal sand samples from two contrasting coastal areas of Japan on a seasonal basis. Surface morphology and attached microorganisms on MPs were visually inspected by scanning electron microscopy (SEM). A high-throughput sequencing using Illumina MiSeq was performed in the collected samples to investigate the microbial community composition and diversity among different samples.

Soil microbial fluctuation and CO release increase under dry-wet cycles

Suzuki, Yuri*; Nagano, Hirohiko*; Hiradate, Shuntaro*; Atarashi-Andoh, Mariko; Abe, Yukiko; Koarashi, Jun; Nakayama, Masataka

no journal, ,