Masayuki Ushio

Functional diversity of microbial decomposers facilitates plant coexistence in a plant–microbe–soil feedback model

Theory and empirical evidence suggest that plant–soil feedback (PSF) determines the structure of a plant community and nutrient cycling in terrestrial ecosystems. The plant community alters the nutrient pool size in soil by affecting litter decomposition processes, which in turn shapes the plant community, forming a PSF system. However, the role of microbial decomposers in PSF function is often overlooked, and it remains unclear whether decomposers reinforce or weaken litter-mediated plant control over nutrient cycling. Here, we present a theoretical model incorporating the functional diversity of both plants and microbial decomposers. Two fundamental microbial processes are included that control nutrient mineralization from plant litter: (i) assimilation of mineralized nutrient into the microbial biomass (microbial immobilization), and (ii) release of the microbial nutrients into the inorganic nutrient pool (net mineralization). With this model, we show that microbial diversity may act as a buffer that weakens plant control over the soil nutrient pool, reversing the sign of PSF from positive to negative and facilitating plant coexistence. This is explained by the decoupling of litter decomposability and nutrient pool size arising from a flexible change in the microbial community composition and decomposition processes in response to variations in plant litter decomposability. Our results suggest that the microbial community plays a central role in PSF function and the plant community structure. Furthermore, the results strongly imply that the plant-centered view of nutrient cycling should be changed to a plant–microbe–soil feedback system, by incorporating the community ecology of microbial decomposers and their functional diversity.

Effects of condensed tannins in conifer leaves on the composition and activity of the soil microbial community in a tropical montane forest

Background and aimsCondensed tannins, a dominant class of plant secondary metabolites, play potentially important roles in plant-soil feedbacks by influencing the soil microbial community. Effects of condensed tannins on the soil microbial community and activity were examined by a short-term tannin-addition experiment under field and laboratory conditions.MethodsCondensed tannins were extracted from the leaves of a dominant conifer (Dacrydium gracilis) in a tropical montane forest on Mt. Kinabalu, Borneo. The extracted tannins were added to soils beneath the conifer and a dominant broadleaf (Lithocarpus clementianus) to evaluate the dependence of the response to tannin addition on the initial composition of the soil microbial community.ResultsEnzyme activities in the field tannin-addition treatment were lower than in the deionized-water treatment. Carbon and nitrogen mineralization were also inhibited by tannin-addition. The fungi-to-bacteria ratio after tannin-addition was higher compared with the distilled-water treatment in the laboratory experiment.ConclusionsBased on our results, we suggest that the higher concentration of condensed tannins in the leaf tissues of Dacrydium than in those of Lithocarpus is a factor influencing the microbial community and activity. This may have influences on subsequent plant performance, which induces plant-soil feedback processes that can control dynamics of the tropical montane forest ecosystem.

Scale Dependence of Predator-Prey Mass Ratio. Determinants and Applications

Abstract Body size exerts a critical influence on predator–prey interactions and is therefore crucial for understanding the structure and dynamics of food webs. Currently, predator–prey mass ratio (PPMR) is regarded as the most promising modelling parameter for capturing the complex patterns of feeding links among species and individuals in a simplified way. While PPMR has been widely used in food-web modelling, its empirical estimation is more difficult, with the methodology remaining controversial. This is because PPMR (i) may be defined at different biological scales, such as from individuals to communities, and (ii) may also vary with biological factors, such as species identity and body mass, both of which conflict with the conventional model assumptions. In this chapter, we analyse recently compiled gut content data of marine food webs to address the two fundamental issues of scale-dependence and determinants of PPMR. We consider four definitions of PPMR: (i) species-averaged PPMR, (ii) link-averaged PPMR, (iii) individual-predator PPMR, and (iv) individual-link PPMR. First, we show that PPMR values have a complicated scale-dependence characterised by data elements, such as body mass and sample counts of predators and prey, due to averaging and sampling effects. We subsequently used AIC to systematically evaluate how the four types of PPMR are related to predator species identity and body mass. The results indicate that the model providing the best explanation for individual-predator and individual-link PPMRs incorporates both species identity and body mass. Meanwhile, the best model for species-averaged and link-averaged PPMRs was unclear, with different models being selected across sampling sites. These results imply that the size-based community-spectrum models describing individual-level interactions should include taxonomic dissimilarities. Based on the present study, we suggest that future research regarding PPMR must account for scale dependence and associated determinants to improve its utility as a widely applicable tool.

Microbial communities on flower surfaces act as signatures of pollinator visitation

Microbes are easily dispersed from one place to another, and immigrant microbes might contain information about the environments from which they came. We hypothesized that part of the microbial community on a flowers surface is transferred there from insect body surfaces and that this community can provide information to identify potential pollinator insects of that plant. We collected insect samples from the field, and found that an insect individual harbored an average of 12.2 × 105 microbial cells on its surface. A laboratory experiment showed that the microbial community composition on a flower surface changed after contact with an insect, suggesting that microbes are transferred from the insect to the flower. Comparison of the microbial fingerprint approach and direct visual observation under field condition suggested that the microbial community on a flower surface could to some extent indicate the structure of plant–pollinator interactions. In conclusion, species-specific insect microbial communities specific to insect species can be transferred from an insect body to a flower surface, and these microbes can serve as a “fingerprint” of the insect species, especially for large-bodied insects. Dispersal of microbes is a ubiquitous phenomenon that has unexpected and novel applications in many fields and disciplines.

Predator–prey body size relationships when predators can consume prey larger than themselves

As predator–prey interactions are inherently size-dependent, predator and prey body sizes are key to understanding their feeding relationships. To describe predator–prey size relationships (PPSRs) when predators can consume prey larger than themselves, we conducted field observations targeting three aquatic hemipteran bugs, and assessed their body masses and those of their prey for each hunting event. The data revealed that their PPSR varied with predator size and species identity, although the use of the averaged sizes masked these effects. Specifically, two predators had slightly decreased predator–prey mass ratios (PPMRs) during growth, whereas the other predator specialized on particular sizes of prey, thereby showing a clear positive size–PPMR relationship. We discussed how these patterns could be different from fish predators swallowing smaller prey whole.

In Situ Enzyme Activity in the Dissolved and Particulate Fraction of the Fluid from Four Pitcher Plant Species of the Genus Nepenthes

The genus Nepenthes, a carnivorous plant, has a pitcher to trap insects and digest them in the contained fluid to gain nutrient. A distinctive character of the pitcher fluid is the digestive enzyme activity that may be derived from plants and dwelling microbes. However, little is known about in situ digestive enzymes in the fluid. Here we examined the pitcher fluid from four species of Nepenthes. High bacterial density was observed within the fluids, ranging from 7×106 to 2.2×108 cells ml−1. We measured the activity of three common enzymes in the fluid: acid phosphatases, β-d-glucosidases, and β-d-glucosaminidases. All the tested enzymes detected in the liquid of all the pitcher species showed activity that considerably exceeded that observed in aquatic environments such as freshwater, seawater, and sediment. Our results indicate that high enzyme activity within a pitcher could assist in the rapid decomposition of prey to maximize efficient nutrient use. In addition, we filtered the fluid to distinguish between dissolved enzyme activity and particle-bound activity. As a result, filtration treatment significantly decreased the activity in all enzymes, while pH value and Nepenthes species did not affect the enzyme activity. It suggested that enzymes bound to bacteria and other organic particles also would significantly contribute to the total enzyme activity of the fluid. Since organic particles are themselves usually colonized by attached and highly active bacteria, it is possible that microbe-derived enzymes also play an important role in nutrient recycling within the fluid and affect the metabolism of the Nepenthes pitcher plant.

Environmental DNA enables detection of terrestrial mammals from forest pond water

Terrestrial animals must have frequent contact with water to survive, implying that environmental DNA (eDNA) originating from those animals should be detectable from places containing water in terrestrial ecosystems. Aiming to detect the presence of terrestrial mammals using forest water samples, we applied a set of universal PCR primers (MiMammal, a modified version of fish universal primers) for metabarcoding mammalian eDNA. The versatility of MiMammal primers was tested in silico and by amplifying DNAs extracted from tissues. The results suggested that MiMammal primers are capable of amplifying and distinguishing a diverse group of mammalian species. In addition, analyses of water samples from zoo cages of mammals with known species composition suggested that MiMammal primers could successfully detect mammalian species from water samples in the field. Then, we performed an experiment to detect mammals from natural ecosystems by collecting five 500‐ml water samples from ponds in two cool‐temperate forests in Hokkaido, northern Japan. MiMammal amplicon libraries were constructed using eDNA extracted from water samples, and sequences generated by Illumina MiSeq were subjected to data processing and taxonomic assignment. We thereby detected multiple species of mammals common to the sampling areas, including deer (Cervus nippon), mouse (Mus musculus), vole (Myodes rufocanus), raccoon (Procyon lotor), rat (Rattus norvegicus) and shrew (Sorex unguiculatus). Many previous applications of the eDNA metabarcoding approach have been limited to aquatic/semiaquatic systems, but the results presented here show that the approach is also promising even for forest mammal biodiversity surveys.

Core microbiomes for sustainable agroecosystems

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.Microbial communities are not only of great importance in the human gut, but also play irreplaceable roles in sustaining plant growth and functions. In this Perspective, strategies to optimize microbiome usage in agroecosystems are proposed.

A Coexisting Fungal-Bacterial Community Stabilizes Soil Decomposition Activity in a Microcosm Experiment

How diversity influences the stability of a community function is a major question in ecology. However, only limited empirical investigations of the diversity–stability relationship in soil microbial communities have been undertaken, despite the fundamental role of microbial communities in driving carbon and nutrient cycling in terrestrial ecosystems. In this study, we conducted a microcosm experiment to investigate the relationship between microbial diversity and stability of soil decomposition activities against changes in decomposition substrate quality by manipulating microbial community using selective biocides. We found that soil respiration rates and degradation enzyme activities by a coexisting fungal and bacterial community (a taxonomically diverse community) are more stable against changes in substrate quality (plant leaf materials) than those of a fungi-dominated or a bacteria-dominated community (less diverse community). Flexible changes in the microbial community composition and/or physiological state in the coexisting community against changes in substrate quality, as inferred by the soil lipid profile, may be the mechanism underlying this positive diversity–stability relationship. Our experiment demonstrated that the previously found positive diversity–stability relationship could also be valid in the soil microbial community. Our results also imply that the functional/taxonomic diversity and community ecology of soil microbes should be incorporated into the context of climate–ecosystem feedbacks. Changes in substrate quality, which could be induced by climate change, have impacts on decomposition process and carbon dioxide emission from soils, but such impacts may be attenuated by the functional diversity of soil microbial communities.

Water temperature-dependent degradation of environmental DNA and its relation to bacterial abundance

Environmental DNA (eDNA) is DNA shed by organisms into surrounding environments such as soil and water. The new methods using eDNA as a marker for species detection are being rapidly developed. Here we explore basic knowledge regarding the dependence of the eDNA degradation rate on time and water temperature, and the relationship between eDNA degradation and bacterial abundance. This subject has not been well clarified, even though it is essential for improving the reliability of eDNA analysis. To determine the time- and water temperature-dependent degradation of eDNA, river water was sampled and eDNA concentrations were determined for ayu sweetfish (Plecoglossus altivelis altivelis) and common carp (Cyprinus carpio) at seven time points, over a 48-h period, and at three different water temperatures. The degradation of eDNA was modeled for each species using an existing exponential decay model with an extension to include water temperature effects. The degradation models were constructed for ayu sweetfish as Nt = 229,901.2 × exp [− (0.01062 × k − 0.07081) × t] and for common carp as Nt = 2,558.0 × exp [− (0.01075 × k − 0.07372) × t]. Nt is the DNA concentration at time t (elapsed time in hours) and k is the water temperature (°C). We also measured the concentration of eDNA derived from purified genomic DNA of the common carp, which was spiked into aquarium water without the target species, and we measured the bacterial abundance in the sample water after 12 and 24 h of incubation. Environmental DNA degradation was accelerated at higher water temperatures (generalized linear model, GLM; p < 0.001), but bacterial abundance did not have a significant effect on eDNA degradation (GLM, p = 0.097). These results suggest that the proper treatment of this temperature effect in data interpretations and adjustments would increase the reliability of eDNA analysis in future studies.