Plant-Associated Microbes: From Rhizobia To Plant Microbiomes

Wasai, Sawa; Minamisawa, Kiwamu

doi:10.1264/jsme2.me3301rh

Cited by 28 publications

(30 citation statements)

References 55 publications

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“…The root microbiome is vital for plant health and productivity (9, 76). Arbuscular mycorrhizal (AM) fungi are important members of this microbiome due to their ability to enhance plant nutrient uptake, particularly that of phosphorus (P) (68).…”

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Impact of Introduction of Arbuscular Mycorrhizal Fungi on the Root Microbial Community in Agricultural Fields

et al. 2019

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Arbuscular mycorrhizal (AM) fungi are important members of the root microbiome and may be used as biofertilizers for sustainable agriculture. To elucidate the impact of AM fungal inoculation on indigenous root microbial communities, we used high-throughput sequencing and an analytical pipeline providing fixed operational taxonomic units (OTUs) as an output to investigate the bacterial and fungal communities of roots treated with a commercial AM fungal inoculum in six agricultural fields. AM fungal inoculation significantly influenced the root microbial community structure in all fields. Inoculation changed the abundance of indigenous AM fungi and other fungal members in a field-dependent manner. Inoculation consistently enriched several bacterial OTUs by changing the abundance of indigenous bacteria and introducing new bacteria. Some inoculum-associated bacteria closely interacted with the introduced AM fungi, some of which belonged to the genera Burkholderia , Cellulomonas , Microbacterium , Sphingomonas , and Streptomyces and may be candidate mycorrhizospheric bacteria that contribute to the establishment and/or function of the introduced AM fungi. Inoculated AM fungi also co-occurred with several indigenous bacteria with putative beneficial traits, suggesting that inoculated AM fungi may recruit specific taxa to confer better plant performance. The bacterial families Methylobacteriaceae , Acetobacteraceae , Armatimonadaceae , and Alicyclobacillaceae were consistently reduced by the inoculation, possibly due to changes in the host plant status caused by the inoculum. To the best of our knowledge, this is the first large-scale study to investigate interactions between AM fungal inoculation and indigenous root microbial communities in agricultural fields.

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Impact of Introduction of Arbuscular Mycorrhizal Fungi on the Root Microbial Community in Agricultural Fields

et al. 2019

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“…The nitrogen (N) input of soils is based on symbiotic biological N 2 fixation (BNF), which may also be the main source in organic farming (77). Although research on the plant microbiome is increasing due to novel molecular and analytical methods (85), limited information is currently available on the long-term changes in natural bacterial populations in relation to host plant diversity and the abundance of rhizobia (28, 73).…”

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Density and Diversity of Microbial Symbionts under Organic and Conventional Agricultural Management

et al. 2019

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The influence of organic and conventional farming and agroecology on the diversity and functioning of indigenous soil microbial communities was examined using a multifactorial analysis based on an extended minimum data set of classical status and functional tests. Main soil physicochemical properties and selected microbiological indicators, the quantity of heterotrophic or aerobic spore-forming bacteria, basal and substrate-induced respiration, catabolic activity with MicroResp™, and fluorescein diacetate enzyme activity were characterized. A pot experiment applying the most probable number method was designed with soil dilution series using Pisum sativum L. and Triticum spelta L. to assess the symbiotic infectivity and genetic diversity of key indicator groups of the plant microbiome, e.g. nitrogen-fixing bacteria (rhizobia) and arbuscular mycorrhizal fungi. Soil pH, humus content, CFU, enzyme activity, and soil respiration were significantly higher in organic soils. The activity of soil microorganisms was mainly related to clay, humus, calcium, and magnesium parameters. A redundancy analysis test of catabolic activities showed that samples were grouped according to different substrate utilization patterns and land uses were also clearly separated from each other. Farming practice influenced the abundance and diversity of microbial populations. Dark septate endophytic fungi were only found in conventional soils. In addition to confirming soil health improvements by organic management, our results highlight the importance of a complex evaluation including both classical status and functional parameters of soil microbiota, which may more reliably indicate a shift in the quality status of soils.

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“…Nitrogen fixation is a significant factor influencing the development of macro- and microbial communities, particularly in environments in which the supply of nitrogen compounds is less than that of carbon, e.g. , photosynthesis-driven (76), chemolithotroph-dominated (35, 49, 55), and plant-associated (53, 57, 60, 75) microbial communities and gut microflora in wood-feeding termites (52).…”

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Phylogenetic Diversity of Nitrogenase Reductase Genes and Possible Nitrogen-Fixing Bacteria in Thermophilic Chemosynthetic Microbial Communities in Nakabusa Hot Springs

Nishihara

Thiel

Matsuura

et al. 2018

Microbes and environments

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Chemosynthetic microbial communities develop and form dense cell aggregates in slightly alkaline sulfidic hot springs in the temperature range of 70–86°C at Nakabusa, Japan. Nitrogenase activity has recently been detected in the microbial communities collected. To identify possible members capable of nitrogen fixation, we examined the diversities of 16S rRNA and nitrogenase reductase (NifH) gene sequences in four types of chemosynthetic communities with visually different colors and thicknesses. The results of a 16S rRNA gene analysis indicated that all four microbial communities had similar bacterial constituents; the phylum Aquificae was the dominant member, followed in abundance by Thermodesulfobacteria, Firmicutes, and Thermotogae. Most of the NifH sequences were related to sequences reported in hydrothermal vents and terrestrial hot springs. The results of a phylogenetic analysis of NifH sequences revealed diversity in this gene among the communities collected, distributed within 7 phylogenetic groups. NifH sequences affiliated with Aquificae (Hydrogenobacter/Thermocrinis) and Firmicutes (Caldicellulosiruptor) were abundant. At least two different energy metabolic pathways appeared to be related to nitrogen fixation in the communities analyzed; aerobic sulfur/hydrogen-oxidizing bacteria in Aquificae and fermentative bacteria in Firmicutes. The metabolic characteristics of these two dominant phyla differed from those previously inferred from nitrogenase activity assays on chemosynthetic communities, which were associated with hydrogen-dependent autotrophic sulfate reduction. These assays may correspond to the observed NifH sequences that are distantly related to the known species of Thermodesulfovibrio sp. (Nitrospirae) detected in the present study. The activities of nitrogen-fixing organisms in communities may depend on redox states as well as the availability of electron donors, acceptors, and carbon sources.

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Plant-Associated Microbes: From Rhizobia To Plant Microbiomes

Cited by 28 publications

References 55 publications

Impact of Introduction of Arbuscular Mycorrhizal Fungi on the Root Microbial Community in Agricultural Fields

Impact of Introduction of Arbuscular Mycorrhizal Fungi on the Root Microbial Community in Agricultural Fields

Density and Diversity of Microbial Symbionts under Organic and Conventional Agricultural Management

Phylogenetic Diversity of Nitrogenase Reductase Genes and Possible Nitrogen-Fixing Bacteria in Thermophilic Chemosynthetic Microbial Communities in Nakabusa Hot Springs

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