Interaction with Soil Bacteria Affects the Growth and Amino Acid Content of Piriformospora indica

Interaction studies of Serendipita indica and Zhihengliuella sp. ISTPL4 and their synergistic role in growth promotion in rice

Rapid urbanization and globalization demand increasing agricultural productivity. Soil nutrient supply capacity is continuously decreasing due to soil erosion, degradation, salt deposition, undesired element, metal deposition, water scarcity, and an uneven nutrient delivery system. Rice cultivation requires a large amount of water which is becoming detrimental due to these activities. There is a need to increase its productivity. Microbial inoculants are becoming increasingly important in achieving sustainable agricultural production systems. The current study was conducted to investigate the interaction between the root endophytic fungus Serendipita indica (S. indica) and the actinobacterium Zhihengliuella sp. ISTPL4 (Z. sp. ISTPL4) and their synergistic effects on the growth of rice (Oryza sativa L). Both S. indica and Z. sp. ISTPL4 showed positive interactions. Growth of S. indica was observed at different days after Z. sp. ISTPL4 inoculation, and stimulated growth of S. indica was observed when Z. sp. ISTPL4 was inoculated at 5 dafi (days after fungal inoculation). Z. sp. ISTPL4 promoted the growth of S. indica as it increased spore germination. Furthermore, confocal and scanning electron microscopy (SEM) analyses showed a 27% increase in the spore size of S. indica in the presence of Z. sp. ISTPL4. In a liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis increased production of alanine and glutamic acid was observed in their sequential co-culture as compared with individual cultures. Sequential inoculation of S. indica and Z. sp. ISTPL4 significantly increased the biochemical and physical characteristics of rice as compared with their individual inoculum. Biochemical parameters such as chlorophyll content, total soluble sugar, and flavonoid content in the rice increased by up to 57%, 47%, and 39%, respectively, in the presence of the combined inoculum of S. indica and Z. sp. ISTPL4. This will be the first study, to the best of our knowledge, which shows the fungus and actinobacterium interaction and their synergistic roles in the growth promotion of rice. Furthermore, this novel combination can also be used to boost the growth of other crops to increase the agricultural yield.

Bacillus amyloliquefaciens Increases the GABA in Rice Seed for Upregulation of Type I Collagen in the Skin

Biosynthesis of gamma-aminobutyric acid (GABA) can be achieved by naturally occurring microorganisms with the advantages of cost-effectiveness and safety. In this study, Bacillus amyloliquefaciens EH-9 strain (B. amyloliquefaciens EH-9), a soil bacterium, was used to promote the accumulation of GABA in germinated rice seed. Further, the topical application of supernatant from rice seed co-cultivated with soil B. amyloliquefaciens EH-9 can significantly increase the production of type I collagen (COL1) in the dorsal skin of mice. The knocking down of the GABA-A receptor (GABA_A) significantly reduced the production of COL1 in the NIH/3T3 cells and in the dorsal skin of mice. This result suggests that topical application of GABA can promote the biosynthesis of COL1 via its interaction with the GABA_A receptor in the dorsal skin of mice. In summary, our findings illustrate for the first time that soil B. amyloliquefaciens EH-9 elicits GABA production in germinated rice seed to upregulate the formation of COL1 in the dorsal skin of mice. This study is translational because the result shows a potential remedy for skin aging by stimulating COL1 synthesis using biosynthetic GABA associated with B. amyloliquefaciens EH-9.

Isolation and identification of mycorrhizal helper bacteria of Vaccinium uliginosum and their interaction with mycorrhizal fungi

Mycorrhizal helper bacteria (MHB) can promote mycorrhizal fungal colonization and form mycorrhizal symbiosis structures. To investigate the effect of interactions between mycorrhizal beneficial microorganisms on the growth of blueberry, 45 strains of bacteria isolated from the rhizosphere soil of Vaccinium uliginosum were screened for potential MHB strains using the dry-plate confrontation assay and the bacterial extracellular metabolite promotion method. The results showed that the growth rate of mycelium of Oidiodendron maius 143, an ericoid mycorrhizal fungal strain, was increased by 33.33 and 77.77% for bacterial strains L6 and LM3, respectively, compared with the control in the dry-plate confrontation assay. In addition, the extracellular metabolites of L6 and LM3 significantly promoted the growth of O. maius 143 mycelium with an average growth rate of 40.9 and 57.1%, respectively, the cell wall-degrading enzyme activities and genes of O. maius 143 was significantly increased. Therefore, L6 and LM3 were preliminarily identified as potential MHB strains. In addition, the co-inoculated treatments significantly increased blueberry growth; increased the nitrate reductase, glutamate dehydrogenase, glutamine synthetase, and glutamate synthase activities in the leaves; and promoted nutrient uptake in blueberry. Based on the physiological, and 16S rDNA gene molecular analyses, we initially identified strain L6 as Paenarthrobacter nicotinovorans and LM3 as Bacillus circulans. Metabolomic analysis revealed that mycelial exudates contain large amounts of sugars, organic acids and amino acids, which can be used as substrates to stimulate the growth of MHB. In conclusion, L6 and LM3 and O. maius 143 promote each other's growth, while co-inoculation of L6 and LM3 with O. maius 143 can promote the growth of blueberry seedlings, providing a theoretical basis for further studies on the mechanism of ericoid mycorrhizal fungi-MHB-blueberry interactions. It laid the technical foundation for the exploitation of biocontrol strain resources and the development of biological fertilizer.

Responses of Bacterial Community Structure, Diversity, and Chemical Properties in the Rhizosphere Soil on Fruiting-Body Formation of Suillus luteus

Mycorrhiza helper bacteria (MHB) play an important role in driving mycorrhizal formation. There are few reports on the relationship between bacteria and fruiting growths. Taking mycorrhizal rhizosphere soil from sporocarps of the S. luteus and non-mycorrhizal rhizosphere soil of the host plant (Larix gmelinii), we measured the bacterial community structure and diversity and chemical properties to clarify the effect of bacteria on fruiting-body formation. The bacterial diversity was significantly higher in mycorrhizal rhizosphere soil (p < 0.05) than that in non-mycorrhizal rhizosphere soil. The relative abundance of Burkholderia, Bradyrhizobium, Pseudomonas, and Rhizobium was significantly higher (p < 0.05) in mycorrhizal rhizosphere soil than in non-mycorrhizal rhizosphere soil. The soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), total potassium (TK), ammonium nitrogen (AN), available phosphorus (AP), available potassium (AK), and the activity of catalase, urease, and phosphatase in mycorrhizal rhizosphere soil were significantly higher (p < 0.05) than those in non-mycorrhizal rhizosphere soil. A redundancy analysis (RDA) showed that dominant bacteria are closely related to soil enzyme activity and physicochemical properties (p < 0.05). The boletus recruits a large number of bacteria around the plant roots that speed up nutrient transformation and increase the soil nutrient content, providing an important guarantee for mycelium culture and fruiting-body formation. These findings provide ideas for the nutritional supply of boletus sporocarps and lay the theoretical foundation for the efficient artificial cultivation of boletus.

Comparative fungal diversity and dynamics in plant compartments at different developmental stages under root-zone restricted grapevines

BACKGROUND

The root-zone restriction cultivation technique is used to achieve superior fruit quality at the cost of limited vegetative and enhanced reproductive development of grapevines. Fungal interactions and diversity in grapevines are well established; however, our knowledge about fungal diversity under the root-zone restriction technique is still unexplored. To provide insights into the role of mycobiota in the regulation of growth and fruit quality of grapevine under root-zone restriction, DNA from rhizosphere and plant compartments, including white roots (new roots), leaves, flowers, and berries of root-zone restricted (treatment) and conventionally grown plants (control), was extracted at three growth stages (full bloom, veraison, and maturity).

RESULTS

Diversity analysis based on the ITS1 region was performed using QIIME2. We observed that the root-zone restriction technique primarily affected the fungal communities of the soil and plant compartments at different growth stages. Interestingly, Fusarium, Ilyonectria, Cladosporium and Aspergillus spp observed in the rhizosphere overlapped with the phyllosphere at all phenological stages, having distinctive abundance in grapevine habitats. Peak richness and diversity were observed in the rhizosphere at the full bloom stage of control plants, white roots at the veraison stage of treatment, leaves at the maturity stage of treatment, flowers at the full bloom stage and berries at the veraison stage of control plants. Except for white roots, the diversity of soil and plant compartments of treated plants tended to increase until maturity. At the maturity stage of the treated and control plants, the abundance of Aspergillus spp. was 25.99 and 29.48%, respectively. Moreover, the total soluble sugar content of berries was 19.03 obrix and 16 obrix in treated and control plants, respectively, at the maturity stage.

CONCLUSIONS

This is the first elucidative study targeting the fungal diversity of conventional and root-restricted cultivation techniques in a single vineyard. Species richness and diversity are affected by stressful cultivation known as root zone restriction. There is an association between the abundance of Aspergillus spp. and fruit quality because despite causing stress to the grapevine, superior quality of fruit is retrieved in root-zone restricted plants.

Plant-Microbe Interaction: Aboveground to Belowground, from the Good to the Bad

Soil health and fertility issues are constantly addressed in the agricultural industry. Through the continuous and prolonged use of chemical heavy agricultural systems, most agricultural lands have been impacted, resulting in plateaued or reduced productivity. As such, to invigorate the agricultural industry, we would have to resort to alternative practices that will restore soil health and fertility. Therefore, in recent decades, studies have been directed towards taking a Magellan voyage of the soil rhizosphere region, to identify the diversity, density, and microbial population structure of the soil, and predict possible ways to restore soil health. Microbes that inhabit this region possess niche functions, such as the stimulation or promotion of plant growth, disease suppression, management of toxicity, and the cycling and utilization of nutrients. Therefore, studies should be conducted to identify microbes or groups of organisms that have assigned niche functions. Based on the above, this article reviews the aboveground and below-ground microbiomes, their roles in plant immunity, physiological functions, and challenges and tools available in studying these organisms. The information collected over the years may contribute toward future applications, and in designing sustainable agriculture.

The Free-Living Stage Growth Conditions of the Endophytic Fungus Serendipita indica May Regulate Its Potential as Plant Growth Promoting Microbe

Serendipita indica (former Piriformospora indica) is a non-obligate endophytic fungus and generally a plant growth and defence promoter with high potential to be used in agriculture. However, S. indica may switch from biotrophy to saprotrophy losing its plant growth promoting traits. Our aim was to understand if the free-living stage growth conditions (namely C availability) regulate S. indica’s phenotype, and its potential as plant-growth-promoting-microbe (PGPM). We grew S. indica in its free-living stage under increasing C availabilities (2–20 g L^–1 of glucose or sucrose). We first characterised the effect of C availability during free-living stage growth on fungal phenotype: colonies growth and physiology (plasma membrane proton pumps, stable isotopic signatures, and potential extracellular decomposing enzymes). The effect of the C availability during the free-living stage of the PGPM was evaluated on wheat. We observed that C availability during the free-living stage regulated S. indica’s growth, ultrastructure and physiology, resulting in two distinct colony phenotypes: compact and explorer. The compact phenotype developed at low C, used peptone as the major C and N source, and displayed higher decomposing potential for C providing substrates; while the explorer phenotype developed at high C, used glucose and sucrose as major C sources and casein and yeast extract as major N sources, and displayed higher decomposing potential for N and P providing substrates. The C availability, or the C/N ratio, during the free-living stage left a legacy to the symbiosis stage, regulating S. indica’s potential to promote plant growth: wheat growth promotion by the explorer phenotype was ± 40% higher than that by the compact phenotype. Our study highlights the importance of considering microbial ecology in designing PGPM/biofertilizers. Further studies are needed to test the phenotypes under more extreme conditions, and to understand if the in vitro acquired characteristics persist under field conditions.