Publications by authors named "Mayuko Jomura"

6 Publications

  • Page 1 of 1

Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition.

mSystems 2021 Jan 12;6(1). Epub 2021 Jan 12.

Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic

Forests accumulate and store large amounts of carbon (C), and a substantial fraction of this stock is contained in deadwood. This transient pool is subject to decomposition by deadwood-associated organisms, and in this process it contributes to CO emissions. Although fungi and bacteria are known to colonize deadwood, little is known about the microbial processes that mediate carbon and nitrogen (N) cycling in deadwood. In this study, using a combination of metagenomics, metatranscriptomics, and nutrient flux measurements, we demonstrate that the decomposition of deadwood reflects the complementary roles played by fungi and bacteria. Fungi were found to dominate the decomposition of deadwood and particularly its recalcitrant fractions, while several bacterial taxa participate in N accumulation in deadwood through N fixation, being dependent on fungal activity with respect to deadwood colonization and C supply. Conversely, bacterial N fixation helps to decrease the constraints of deadwood decomposition for fungi. Both the CO efflux and N accumulation that are a result of a joint action of deadwood bacteria and fungi may be significant for nutrient cycling at ecosystem levels. Especially in boreal forests with low N stocks, deadwood retention may help to improve the nutritional status and fertility of soils. Wood represents a globally important stock of C, and its mineralization importantly contributes to the global C cycle. Microorganisms play a key role in deadwood decomposition, since they possess enzymatic tools for the degradation of recalcitrant plant polymers. The present paradigm is that fungi accomplish degradation while commensalist bacteria exploit the products of fungal extracellular enzymatic cleavage, but this assumption was never backed by the analysis of microbial roles in deadwood. This study clearly identifies the roles of fungi and bacteria in the microbiome and demonstrates the importance of bacteria and their N fixation for the nutrient balance in deadwood as well as fluxes at the ecosystem level. Deadwood decomposition is shown as a process where fungi and bacteria play defined, complementary roles.
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http://dx.doi.org/10.1128/mSystems.01078-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7901482PMC
January 2021

GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies.

Sci Data 2020 07 13;7(1):228. Epub 2020 Jul 13.

Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.

Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com . The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.
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http://dx.doi.org/10.1038/s41597-020-0567-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7359306PMC
July 2020

Mycelial biomass estimation and metabolic quotient of Lentinula edodes using species-specific qPCR.

PLoS One 2020 18;15(5):e0232049. Epub 2020 May 18.

Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan.

Lentinula edodes, commonly known as shiitake, is an edible mushroom that is cultivated and consumed around the globe, especially in Asia. Monitoring mycelial growth inside a woody substrate is difficult, but it is essential for effective management of mushroom cultivation. Mycelial biomass also affects the rate of wood decomposition under natural conditions and must be known to determine the metabolic quotient, an important ecophysiological parameter of fungal growth. Therefore, developing a method to measure it inside a substrate would be very useful. In this study, as the first step in understanding species-specific rates of fungal decomposition of wood, we developed species-specific primers and qPCR procedures for L. edodes. We tested primer specificity using strains of L. edodes from Japan and Southeast Asia, as well as related species of fungi and plant species for cultivation of L. edodes, and generated a calibration curve for quantification of mycelial biomass in wood dust inoculated with L. edodes. The qPCR procedure we developed can specifically detect L. edodes and allowed us to quantify the increase in L. edodes biomass in wood dust substrate and calculate the metabolic quotient based on the mycelial biomass and respiration rate. Development of a species-specific method for biomass quantification will be useful for both estimation of mycelial biomass and determining the kinetics of fungal growth in decomposition processes.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0232049PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7233531PMC
July 2020

Biotic and Abiotic Factors Controlling Respiration Rates of Above- and Belowground Woody Debris of Fagus crenata and Quercus crispula in Japan.

PLoS One 2015 14;10(12):e0145113. Epub 2015 Dec 14.

Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan.

As a large, long-term pool and source of carbon and nutrients, woody litter is an important component of forest ecosystems. The objective of this study was to estimate the effect of the factors that regulate the rate of decomposition of coarse and fine woody debris (CFWD) of dominant tree species in a cool-temperate forest in Japan. Respiration rates of dead stems, branches, and coarse and fine roots of Fagus crenata and Quercus crispula felled 4 years prior obtained in situ ranged from 20.9 to 500.1 mg CO2 [kg dry wood](-1) h(-1) in a one-time measurement in summer. Respiration rate had a significant negative relationship with diameter; in particular, that of a sample of Q. crispula with a diameter of >15 cm and substantial heartwood was low. It also had a significant positive relationship with moisture content. The explanatory variables diameter, [N], wood density, and moisture content were interrelated. The most parsimonious path model showed 14 significant correlations among 8 factors and respiration. Diameter and [C] had large negative direct effects on CFWD respiration rate, and moisture content and species had medium positive direct effects. [N] and temperature did not have direct or indirect effects, and position and wood density had indirect effects. The model revealed some interrelationships between controlling factors. We discussed the influence of the direct effects of explanatory variables and the influence especially of species and position. We speculate that the small R2 value of the most parsimonious model was probably due to the omission of microbial biomass and activity. These direct and indirect effects and interrelationships between explanatory variables could be used to develop a process-based CFWD decomposition model.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0145113PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4682764PMC
July 2016

In situ CO2 efflux from leaf litter layer showed large temporal variation induced by rapid wetting and drying cycle.

PLoS One 2014 1;9(10):e108404. Epub 2014 Oct 1.

Laboratory of Forest Hydrology, Division of Environmental Science and Technology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.

We performed continuous and manual in situ measurements of CO2 efflux from the leaf litter layer (R(LL)) and water content of the leaf litter layer (LWC) in conjunction with measurements of soil respiration (RS) and soil water content (SWC) in a temperate forest; our objectives were to evaluate the response of R(LL) to rainfall events and to assess temporal variation in its contribution to R(S). We measured R(LL) in a treatment area from which all potential sources of CO2 except for the leaf litter layer were removed. Capacitance sensors were used to measure LWC. R(LL) increased immediately after wetting of the leaf litter layer; peak R(LL) values were observed during or one day after rainfall events and were up to 8.6-fold larger than R(LL) prior to rainfall. R(LL) declined to pre-wetting levels within 2-4 day after rainfall events and corresponded to decreasing LWC, indicating that annual R(LL) is strongly influenced by precipitation. Temporal variation in the observed contribution of R(LL) to RS varied from nearly zero to 51%. Continuous in situ measurements of LWC and CO2 efflux from leaf litter only, combined with measurements of RS, can provide robust data to clarify the response of R(LL) to rainfall events and its contribution to total R(S).
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0108404PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4182737PMC
June 2015