Eiko Kuramae

Netherlands Institute of Ecology (NIOO-KNAW) | NIOO-KNAW · Microbial Ecology

The rhizosphere, or the area immediately surrounding plant roots, contains many microbes vital to a plant’s health. Recently researchers examined this ‘rhizomicrobiome’ of Oryza rufipogon to understand the core microbial groups found under differing conditions. The sampled rice was a mix of populations growing in natural reserves and populations th...

Although rice cultivation holds potential for restoring unproductive saline-alkali soils and increasing food production, the mechanisms underlying the relationship between microbial functions and soil element turnover remain unclear. To clarify this relationship, this study investigated the soil physicochemical properties and microbial functions du...

The bacteria that dominate and become enriched in the rhizosphere during continuous cropping are of increasing interest, as they can greatly adapt to the rhizosphere. However, there are still little knowledge about the general composition and function of these bacteria. In this study, we planted tomatoes in three different soils for three planting...

To excavate a complex co-degradation system for decomposing cellulose more efficiently, cellulose-degrading bacteria, including Bacillus subtilis WF-8, Bacillus licheniformis WF-11, Bacillus Cereus WS-1 and Streptomyces Nogalater WF-10 were added during maize straw and cattle manure aerobic composting. Bacillus and Streptomyces successfully coloniz...

The challenges of nitrogen (N) management in agricultural fields include minimizing N losses while maximizing profitability and soil health. Crop residues can alter N and carbon (C) cycle processes in the soil and modulate the responses of the subsequent crop and soil- microbe-plant interactions. Here, we aim to understand how organic amendments wi...

Sorghum production is seriously threatened by the root parasitic weeds (RPWs) Striga hermonthica and Striga asiatica in sub-Saharan Africa. Research has shown that Striga control depends on eliminating its seed reserves in soil. Several species of the genus Fusarium (Nectriaceae, Hypocreales), which have been isolated from diseased Striga plants ha...

An alarming and increasing deforestation rate threatens Amazon tropical ecosystems and subsequent degradation due to frequent fires. Agroforestry systems (AFS) may offer a sustainable alternative, reportedly mimicking the plant‐soil interactions of the natural mature forest. However, the role of microbial community in tropical AFS remains largely u...

Background The assembly of the rhizomicrobiome, i.e., the microbiome in the soil adhering to the root, is influenced by soil conditions. Here, we investigated the core rhizomicrobiome of a wild plant species transplanted to an identical soil type with small differences in chemical factors and the impact of these soil chemistry differences on the co...

Sorghum bicolor is one of the most important cereals in the world and a staple crop for smallholder famers in sub Saharan Africa. However approximately 20% of sorghum yield is annually lost on the African continent due to infestation with the root parasitic weed Striga hermonthica . Existing Striga management strategies often show an inconsistent t...

Introducing probiotics to soil is a sustainable way to stimulate the production of plant metabolites. However, the soil-resident microbes may compromise the efficiency of probiotics. To date, it remains challenging to integrate the effects of probiotics on plant performance with soil microbiome changes. Using Cyclocarya paliurus (Batal.) Iljinsk as...

Cover crops are a potential pathway for ecological cultivation in agricultural systems. In tropical no-till agricultural systems, the maintenance of residues on the soil surface and the addition of nitrogen (N) benefit the growth and grain yield of cash crops as well as the chemical and physical properties of the soil. However, the effects of these...

Soil microbial communities are essential components of agroecological ecosystems that influence soil fertility, nutrient turnover, and plant productivity. Metagenomics data are increasingly easy to obtain, but studies of soil metagenomics face three key challenges: (1) accounting for soil physicochemical properties; (2) incorporating untreated cont...

In the process of aerobic nitrification, nitrite-oxidizing bacteria together with ammonia-oxidizing microorganisms convert mineral nitrogen from its most reduced appearance, i.e., ammonium, into its most oxidized form, i.e., nitrate. Because the form of mineral nitrogen has large environmental implications, nitrite-oxidizing bacteria such as Nitrob...

High-throughput sequencing, culture-dependent workflows, and microbiome transfer experiments reveal whether potassium phosphite (KP), an environmentally acceptable agricultural chemical, could specifically enrich the antagonistic bacterial community that inhibited the growth of the pathogen Ralstonia solanacearum. The application of KP enriched the...

This study focused on the effects of vinasse (V), a by-product of the sugar-ethanol industry, combined with mineral nitrogen fertilizer (N) and straw retention on the fungal community diversity, composition, and structure in a sugarcane-cultivated soil. The experiment consisted of a combination of V, mineral N and sugarcane-straw blanket. Soil samp...

The rhizosphere-associated microbiome impacts plant performance and tolerance to abiotic and biotic stresses. Despite increasing recognition of the enormous functional role of the rhizomicrobiome on the survival of wild plant species growing under harsh environmental conditions, such as nutrient, water, temperature, and pathogen stresses, the utili...

The increase in sequencing capacity has amplified the number of taxonomically unclassified sequences in most databases. The classification of such sequences demands phylogenetic tree construction and comparison to currently classified sequences, a process that demands the processing of large amounts of data and use of several different software. He...

Rhizosphere microbial community composition is strongly influenced by plant species and cultivar. However, our understanding of the impact of plant cultivar genetic variability on microbial assembly composition remains limited. Here, we took advantage of vegetatively propagated chrysanthemum (Chrysanthemum indicum L.) as a plant model and induced r...

Soil phosphorus (P) availability may limit plant growth and alter root-soil interactions and rhizosphere microbial community composition. The composition of the rhizosphere microbial community can also be shaped by plant genotype. In this study, we examined the rhizosphere microbial communities of young plants of 24 species of eucalypts (22 Eucalyp...

Early nitrogen (N) application on live cover crops or their residues is a potential alternative for supplying N demand while enhancing the yield of subsequent cash crops in tropical regions. The objective of applying N on live forage grasses or their residues to no-till (NT) systems is to promote the gradual release of N via straw decomposition to...

Rice paddy ecosystems support nearly half of the global population and harbor remarkably diverse microbiomes and functions in a variety of soil types. Diazotrophs provide significant bioavailable nitrogen in paddy soil, priming nitrogen transformation and other biogeochemical processes.

Dead wood quantity and quality is important for forest biodiversity, by determining wood inhabiting fungal assemblages. We therefore evaluated how fungal communities were regulated by stem traits and compartments (i.e., bark, outer‐ and inner wood) of 14 common temperate tree species. Fresh logs were incubated in a common garden experiment in a for...

Strigolactones are endogenous plant hormones regulating plant development and are exuded into the rhizosphere when plants experience nutrient deficiency. There, they promote the mutualistic association of plants with arbuscular mycorrhizal fungi that help the plant with the uptake of nutrients from the soil. This shows that plants actively establis...

Nitrous oxide (N2O) production in tropical soils cultivated with sugarcane is associated with ammonia-oxidizing bacteria (AOB) and fungal denitrifiers. However, the taxonomic identities and the community diversities, compositions, and structures of AOB and fungal denitrifiers in these soils are not known. Here, we examined the effects of applying d...

Residues of cover crop grasses release nitrogen (N) to subsequent crops, which can contribute to sustainable agricultural management and prevent increases in N-loss-related microorganisms. Moreover, applying N fertilizer to cover crops can enhance the N-use efficiency and yields of subsequent cash crops and tighten the N cycle in the soil. However,...

Forage grasses used in cropping no-till systems in tropical regions alter soil chemical properties, but their long-term impact on soil microbial processes of the nitrogen (N) cycle and microbial community abundance, composition and structure are unknown. Here, microbial functions related to nitrogen fixation, nitrification and denitrification as we...

A common agricultural practice of combining organic fertilizer vinasse (a liquid residue from sugarcane ethanol production) with mineral nitrogen (N) fertilizer promotes N losses such as greenhouse gas emissions due to the effects of physicochemical changes in soil on the microbiota inhabiting this environment. In this study, we applied microarray...

Bacterial wilt caused by Ralstonia solanacearum is a distributed and worldwide soil-borne disease. The application of biocontrol microbes or agricultural chemicals has been widely used to manage tomato bacterial wilt. However, whether and how agricultural chemicals affect the antagonistic ability of biocontrol microbes is still unknown. Here, we co...

AimsSpecific soil bacteria can sense and respond to the selective rhizosphere recruitment of root exudates using unique systems of chemotaxis that mediate plant-microbe and microbe-microbe interactions. This study investigates how the bacterial chemotaxis systems have been impacted by selection during the domestication of rice (Oryza species).Metho...

Optimizing agronomic efficiency (AE) of nitrogen (N) fertilizer use by crops and enhancing crop yields are challenges for tropical no-tillage systems since maintaining crop residues on the soil surface alters the nutrient supply to the system. Cover crops receiving N fertilizer can provide superior biomass, N cycling to the soil and plant residue m...

Microbial communities from rhizosphere (rhizomicrobiomes) have been significantly impacted by domestication as evidenced by a comparison of the rhizomicrobiomes of wild and related cultivated rice accessions. While there have been many published studies focusing on the structure of the rhizomicrobiome, studies comparing the functional traits of the...

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distin...

The development and productivity of plants are governed by their genetic background, nutrient input, and the microbial communities they host, i.e. the holobiont. Accordingly, engineering beneficial root microbiomes has emerged as a novel and sustainable approach to crop production with reduced nutrient input. Here, we tested the effects of six bact...

Short dry spells are an important grain yield constraint in tropical regions. Plant growth-promoting bacteria (PGPB) and their metabolites can mitigate the impact of drought stress by promoting changes in plant metabolism, physiology, and biochemistry. However, the effects of PGPB on soybean [Glycine max (L.) Merril] under drought stress in tropica...

Branched glycerol dialkyl glycerol tetraethers (BrGDGTs) are a suite of orphan bacterial membrane lipids commonly used as paleo-environmental proxies for mean annual air temperature (MAT) and pH. Recent calibrations between the Methylation of Branched Tetraethers index (MBT’5ME) and MAT, based on modern surface soils (including peats), show a consi...

The demand for the increased productivity of sugarcane crops has required changes in its production chain, such as the use of pre-sprouted seedlings (PSS) of sugarcane into the chain. In this system, the inoculation of beneficial microorganisms, such as plant growth-promoting bacteria (PGPB) and arbuscular mycorrhizal fungi (AMF), can improve seedl...

Unsustainable agricultural management practices such as non-conservationist tillage and overuse of fertilizers result in soil acidity and, in turn, soil degradation due to reduced carbon (C) concentrations and nutrient availability and increased aluminum toxicity. Application of lime (L) and phosphogypsum (PG) can overcome these constraints and imp...

To maintain the beneficial effects of microbial inoculants on plant and soil, repeated inoculation represents a promising option. Until now, the impacts of one-off inoculation on the native microbiome have been explored, but it remains unclear how long and to what extent the periodic inoculations would affect the succession of the resident microbio...

Beneficial plant–microbe interactions lead to physiological and biochemical changes that may result in plant-growth promotion. This study evaluated the effect of the interaction between sugarcane and endophytic bacterial strains on plant physiological and biochemical responses under two levels of nitrogen (N) fertilization. Six strains of endophyti...

The rhizosphere fungal community affects the ability of crops to acquire nutrients and their susceptibility to pathogen invasion. However, the effects of rice domestication on the diversity and interactions of rhizosphere fungal community still remain largely unknown. Here, internal transcribed spacer amplicon sequencing was used to systematically...

Cyclocarya paliurus (Batal.) Iljinsk is an important medicinal plant for treating chronic diseases, but it is difficult to obtain high yields when growing on low-fertility soil. Inoculation with soil beneficial microorganism has suggested an effective means of stimulating plant growth and secondary metabolite production, but effect on plant perform...

Background The soil microbiome drives soil ecosystem function, and soil microbial functionality is directly linked to interactions between microbes and the soil environment. However, the context-dependent interactions in the soil microbiome remain largely unknown. Results Using latent variable models (LVMs), we disentangle the biotic and abiotic i...

Acidobacteriota are highly abundant in soils, however, few cultured representatives are available. The purity of the reagents can influence microbial growth in laboratory conditions and successful isolation. Here we investigated the impact of different agar brands in culture medium and advocate that agar origin should be carefully considered for Ac...

The rhizomicrobial community is influenced by plant genotype. However, the potential differences in the co-assembly of bacterial and fungal communities between parental lines and different generations of rice progenies have not been examined. Here we compared the bacterial and fungal communities in the rhizomicrobiomes of female parent Oryza rufipo...

Background: Application of certain agricultural chemicals could modulate the soil microbiome and induce potential antagonistic microbes. However, the specific selective effects of agricultural chemicals on soil bacterial functions and their co-occurrences are not well understood, and no studies have verified that the enriched potential antagonistic...

Wastewater is considered a renewable resource water and energy. An advantage of decentralized sanitation systems is the separation of the blackwater (BW) stream, contaminated with human pathogens, from the remaining household water. However, the composition and functions of the microbial community in BW are not known. In this study, we used shotgun...

Plant growth-promoting bacteria (PGPB) are claimed to not only improve plant fitness but also alleviate plant stress. In this study, we evaluated the effect of five PGPB strains on plantlet growth and nutrient and aluminum (Al) uptake under acid soil conditions characterized by low P and K nutrient availability and high metal and aluminum (Al) bioa...

Here we describe a suite of methods to identify potential taxonomic and functional soil microbial indicators of soil quality and plant health in biofuel crops in various areas and land types. This approach draws on tools to assess microbial diversity, greenhouse gas fluxes, and soil physicochemical properties in bioenergy cropping systems. Integrat...

High grain yields of upland rice (Oryza sativa L.) can be achieved in no-tillage systems. However, managing nitrogen (N) fertilization for rice in succession to forage grasses is a challenge because forage residues change N cycling and increase microbial immobilization of N, thereby reducing N availability to the subsequent cash crop. In the presen...

Biofilms are the slimy cities some microbes form when they invade a surface. Conventional cleaning products are generally good at breaking up biofilms. But they tend to be harsh on the environment. And while natural products are a good alternative, it takes multiple enzymes to break up the strong polymers that make bacteria stick. But researchers a...

Background: Soil microbiota exert fundamental functions in maintaining ecosystem functioning and services, including pedogenesis, biogeochemical processes and plant productivity, especially for agriculture system. Despite their ubiquitousness from the epipedon to deep soil, the vertical characteristics of microbiomes (especially for functional micr...

Soil microbial community data produced by next-generation sequencing platforms has introduced a new era in microbial ecology studies but poses a challenge for data analysis: huge tables with highly sparse data combined with methodological limitations leading to biased analyses. Methodological studies have attempted to improve data interpretation vi...

Liming is widely used to decrease soil acidity, and the application of lime alone or in combination with other amendments, such as gypsum, is a viable agricultural practice to improve soil nutrient status and crop yield. However, the effects of applying lime and gypsum alone or in combination on the microbial population and N cycle in intercropped...

Microalgae are highly effective in nutrient recovery and have strong potential as a sustainable wastewater treatment technology. For this experiment, we obtained microalgae cultivated in pilot-scale tubular photobioreactor (PBR) located in a glass greenhouse of the Netherlands Institute of Ecology (NIOO-KNAW), in Wageningen, the Netherlands. The cu...

The presence of genes for glycosyl hydrolases in many Acidobacteria genomes indicates an important role in the degradation of plant cell wall material. Acidobacteria bacterium AB60 was obtained from Cerrado oligotrophic soil in Brazil, where this phylum is abundant. The 16S rRNA gene analyses showed that AB60 was closely related to the genera Occal...

Background: Wastewater is considered as a renewable resource water and energy. An advantage of decentralized sanitation systems is the separation of the blackwater (BW) stream, which is highly contaminated with human pathogens, from the remaining household water. However, the composition and functions of the microbial community in BW are not known....

Acidobacteria are one of the most abundant and ubiquitous bacterial phyla in soil, but the mechanisms underpinning their ecological success remain unknown. Acidobacteria produce copious amounts of extracellular polymeric substances (EPS) with unique sugar composition that can be used as a nutrient source for other microorganisms. Here, we investiga...

The quality of the vineyard soils has a direct impact on grapes and wine quality and represents a key component of the “Terroir concept.” However, information on the impact of soil microbiota on grapevine plants and wine quality are generally lacking. In fact, over the last few years most of the attempts made to correlate soil microbial communities...

In tropical regions, intercropping systems under no-tillage improve biomass quantity, soil conservation, and cash crop productivity. However, the optimal sowing time for forage species in these cropping systems is unknown. The objective of this study was to evaluate the effects of two sowing times of palisade and guinea grass on forage production a...

Background: Cultivation-independent methods, including metagenomics, are tools for the exploration and discovery of biotechnological compounds produced by microbes in natural environments. Glycoside hydrolases (GHs) enzymes are extremely desired and important in the industry of production for goods and biofuel and removal of problematic biofilms a...

Acidobacteria represents one of the most dominant bacterial groups across diverse ecosystems. However, insight into their ecology and physiology has been hampered by difficulties in cultivating members of this phylum. Previous cultivation efforts have suggested an important role of trace elements for the proliferation of Acidobacteria, however,