Dual inoculation of dark septate endophytes and Trichoderma viride drives plant performance and rhizosphere microbiome adaptations of Astragalus mongholicus to drought

SummaryRhizosphere microbes affect plant performance, including plant resistance against insect herbivores; yet, the relative influence of rhizosphere microbes vs. plant genotype on herbivory levels and on metabolites related to defense remains unclear.In Boechera stricta, we tested the effects of rhizosphere microbes and plant genotype on herbivore resistance, the primary metabolome, and select secondary metabolites.Plant populations differed significantly in the concentrations of 6 glucosinolates (GLS), secondary metabolites known to provide herbivore resistance in the Brassicaceae, and the population with lower GLS levels experienced ~60% higher levels of aphid (Aphis spp.) attack; no effect was observed of GLS on damage by a second herbivore, flea beetles (Altica spp.). Rhizosphere microbiome (intact vs. disrupted) had no effect on plant GLS concentrations. However, aphid number and flea beetle damage were respectively ~3-fold and 7-fold higher among plants grown in the disrupted rhizosphere microbiome treatment, and distinct (as estimated from 16s rRNA amplicon sequencing) intact native microbiomes also differed in their effects on herbivore damage. These differences may be attributable to shifts in primary metabolic pathways.The findings suggest that rhizosphere microbes can play a greater role than plant genotype in defense against insect herbivores, and act through mechanisms independent of plant genotype.

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Synergistic and offset effects of fungal species combinations on plant performance

10.1101/2021.05.09.443080 ◽

2021 ◽

Author(s):

Yoshie Hori ◽

Hiroaki Fujita ◽

Kei Hiruma ◽

Kazuhiko Narisawa ◽

Hirokazu Toju

Keyword(s):

Plant Growth ◽

Synergistic Effects ◽

Dry Weight ◽

Fungal Species ◽

Plant Performance ◽

Plant Growth Promoting Bacteria ◽

Microbial Species ◽

Plant Growth Promoting ◽

Growth Promoting ◽

Dual Inoculation

In natural and agricultural ecosystems, survival and growth of plants depend substantially on microbes in the endosphere and rhizosphere. Although numerous studies have reported the presence of plant-growth promoting bacteria and fungi in below-ground biomes, it remains a major challenge to understand how sets of microbial species positively or negatively affect plants' performance. By conducting a series of single- and dual-inoculation experiments of 13 endophytic and soil fungi targeting a Brassicaceae plant species, we here evaluated how microbial effects on plants depend on presence/absence of co-occurring microbes. The comparison of single- and dual-inoculation experiments showed that combinations of the fungal isolates with the highest plant-growth promoting effects in single inoculations did not yield highly positive impacts on plant performance traits (e.g., shoot dry weight). In contrast, pairs of fungi including small/moderate contributions to plants in single-inoculation contexts showed the greatest effects on plants among the 78 fungal pairs examined. These results on the offset and synergistic effects of pairs of microbes suggest that inoculation experiments of single microbial species/isolates can result in the overestimation or underestimation of microbial functions in multi-species contexts. Because keeping single-microbe systems in outdoor conditions is impractical, designing sets of microbes that can maximize performance of crop plants is an important step for the use of microbial functions in sustainable agriculture.

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Variation of soil microbiome in licorice rhizosphere driven with inoculating dark septate endophytes under drought stress

10.21203/rs.3.rs-87436/v1 ◽

2020 ◽

Author(s):

Chao He ◽

Wenquan Wang ◽

Junling Hou ◽

Xianen Li

Keyword(s):

Microbial Community ◽

Drought Stress ◽

Relative Abundance ◽

Water Regime ◽

Am Fungi ◽

Dark Septate Endophytes ◽

Rrna Genes ◽

Soil Microbial Community Structure ◽

Microbiome Composition ◽

Rhizosphere Microbiome

Abstract BackgroundDark septate endophytes (DSE) are facultative biotrophic ascomycetes that colonize plant roots either alone or with arbuscular mycorrhizal (AM) fungi. DSE may provide nutrients to their plant hosts and help them adapt to various abiotic and biotic stresses. DSE inoculation under drought stress increased the biomass, root exudates, and AM fungi in the licorice (Glycyrrhiza uralensis Fisch.) rhizosphere. We conducted a pot experiment to establish whether the responses of licorice to DSE inoculation under drought stress are caused by changes in the rhizosphere microbiome. Each pot was inoculated with either Acrocalymma vagum or Paraboeremia putaminum. One set of pots was inoculated with a sterile culture medium. All three DSE-treated and uninoculated pots were subjected either to a well-watered (70% field water capacity, FWC) or drought stress (30% FWC) water regime. Rhizosphere microbiome compositions were measured by Illumina MiSeq sequencing of the 16S and ITS2 rRNA genes.ResultsIn total, 1,278 fungal and 1,583 bacterial operational taxonomic units (OUTs) were obtained at a 97% sequence similarity level. Ascomycota were the predominant fungi and Proteobacteria, Actinobacteria, Chloroflexi and Firmicutes were the predominant bacteria. DSE inoculation and water regime significantly influenced the rhizosphere microbiome composition. However, the effects of DSE on the fungal community were greater than those on the bacterial community. Paraboeremia putaminum exerted a stronger impact on the licorice rhizosphere microbiome than Acrocalymma vagum under drought stress. The observed changes in edaphic factors (water condition, soil organic matter, available N, available P, and available K) caused by DSE inoculation could be explained by the variations in rhizosphere microbiome composition. A network analysis indicated that DSE inoculation augmented the relative abundance of beneficial symbiotrophic fungi and growth-promoting bacteria but diminished the relative abundance of pathogens in the licorice rhizosphere.ConclusionsThe present study showed that the licorice rhizosphere microbial community differed between the DSE-inoculated and uninoculated plants. DSE had a stronger influence on the fungal than on the bacterial rhizosphere community under drought stress. These give us the guidance to develop biofertilizers with DSE consortia to enhance the cultivation of medicinal plants by shaping soil microbial community structure in dryland agriculture.

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Antagonism potency of dark Septate endophytes against Pyricularia oryzae for improving health of rice plants

Jurnal Agro ◽

10.15575/9589 ◽

2020 ◽

Vol 7 (2) ◽

pp. 134-147

Author(s):

Dini Yuliani ◽

Bonny P W ◽

Soekarno Soekarno ◽

Abdul Munif ◽

Surono Surono

Keyword(s):

Growth Rate ◽

Dry Weight ◽

Colony Growth ◽

Pyricularia Oryzae ◽

Dark Septate Endophytes ◽

Blast Disease ◽

Plant Performance ◽

Dark Septate Endophyte ◽

Rice Plants ◽

Wet Weight

Blast disease caused by Pyricularia oryzae (Po) is the main disease affecting rice production. Dark septate endophytes (DSEs) is known to improve plant performance and suppress disease. This study evaluated DSEs antagonism potency against P. oryzae in improving the rice plant's health. The research stages consisted of: (1). DSE and Po growth rate; (2). Antagonism of DSEs against Po; (3). Chitinase; (4). DSEs Viability; (5). DSEs application to rice seeds in nurseries. The results showed the growth of APDS 3.2 colonies had fulfilled Petri (d = 9 cm) at three days after incubation (DAI), while 4.1 BTG and TKC 2.2.a at 7 DAI. Po had slow colony growth required 20 DAI. Inhibition of APDS 3.2 against Po was 43.75%, higher than of 4.1 BTG (38.60%) and of TKC 2.2.a (39.76%). The rice plants inoculated with APDS 3.2 had a relatively higher at seedling height, root length, wet weight, and dry weight than those inoculated with TKC 2.2.a and 4.1 BTG. The highest DSEs colonization was found in APDS 3.2 at 50.56%, followed by TKC 2.2.a (46.67%) and 4.1 BTG (40%). DSEs fungus has the potential to suppress rice blast pathogens by improving the health of rice plants, especially APDS 3.2.Key words: Colonization, Growth Rate, Viability Penyakit blas yang disebabkan oleh Pyricularia oryzae (Po) merupakan penyakit utama yang memengaruhi produksi padi. Dark septate endophyte (DSE) diketahui mampu meningkatkan performa tanaman dan menekan penyakit. Penelitian ini bertujuan untuk mengevaluasi potensi antagonisme DSE terhadap P. oryzae dalam meningkatkan kesehatan tanaman padi. Tahapan Penelitian terdiri atas: (1). Kecepatan tumbuh DSE dan Po; (2). Antagonisme DSE terhadap Po; (3). Kitinase; (4). Viabilitas DSE; (5). Aplikasi DSE pada benih padi di persemaian. Hasil penelitian menunjukkan pertumbuhan koloni APDS 3.2 telah memenuhi petri (d= 9 cm) pada 3 hari setelah inkubasi (HSI), sedangkan 4.1 BTG dan TKC 2.2.a pada 7 HSI. Pertumbuhan koloni Po lambat membutuhkan 20 HSI. Penghambatan APDS 3.2 terhadap Po sebesar 43,75% lebih tinggi dibandingkan 4.1 BTG (38,60%) maupun TKC 2.2.a (39,76%). Tanaman padi yang diinokulasi APDS 3.2 memiliki tinggi, panjang akar, bobot basah, dan bobot kering relatif lebih tinggi dibandingkan yang diinokulasi TKC 2.2.a dan 4.1 BTG. Kolonisasi DSE tertinggi dijumpai pada APDS 3.2 sebesar 50,56%, diikuti TKC 2.2.a (46,67%) dan 4.1 BTG (40%). Cendawan DSE memiliki potensi untuk menekan patogen blas padi dengan cara meningkatkan kesehatan tanaman padi, khususnya APDS 3.2.

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Rhizosphere protists are key determinants of plant health

Microbiome ◽

10.1186/s40168-020-00799-9 ◽

2020 ◽

Vol 8 (1) ◽

Cited By ~ 10

Author(s):

Wu Xiong ◽

Yuqi Song ◽

Keming Yang ◽

Yian Gu ◽

Zhong Wei ◽

...

Keyword(s):

Plant Growth ◽

Plant Health ◽

Plant Performance ◽

Disease Symptoms ◽

Predator Prey ◽

Rhizosphere Microbiome ◽

Pathogen Dynamics ◽

Microbial Eukaryotes ◽

Microbiome Research ◽

Bacteria And Fungi

Abstract Background Plant health is intimately influenced by the rhizosphere microbiome, a complex assembly of organisms that changes markedly across plant growth. However, most rhizosphere microbiome research has focused on fractions of this microbiome, particularly bacteria and fungi. It remains unknown how other microbial components, especially key microbiome predators—protists—are linked to plant health. Here, we investigated the holistic rhizosphere microbiome including bacteria, microbial eukaryotes (fungi and protists), as well as functional microbial metabolism genes. We investigated these communities and functional genes throughout the growth of tomato plants that either developed disease symptoms or remained healthy under field conditions. Results We found that pathogen dynamics across plant growth is best predicted by protists. More specifically, communities of microbial-feeding phagotrophic protists differed between later healthy and diseased plants at plant establishment. The relative abundance of these phagotrophs negatively correlated with pathogen abundance across plant growth, suggesting that predator-prey interactions influence pathogen performance. Furthermore, phagotrophic protists likely shifted bacterial functioning by enhancing pathogen-suppressing secondary metabolite genes involved in mitigating pathogen success. Conclusions We illustrate the importance of protists as top-down controllers of microbiome functioning linked to plant health. We propose that a holistic microbiome perspective, including bacteria and protists, provides the optimal next step in predicting plant performance.

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Effects of dark septate endophytes on tomato plant performance

Mycorrhiza ◽

10.1007/s00572-010-0351-1 ◽

2010 ◽

Vol 21 (5) ◽

pp. 413-422 ◽

Cited By ~ 46

Author(s):

Diana Rocio Andrade-Linares ◽

Rita Grosch ◽

Silvia Restrepo ◽

Angelika Krumbein ◽

Philipp Franken

Keyword(s):

Tomato Plant ◽

Dark Septate Endophytes ◽

Plant Performance

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Synergistic and Offset Effects of Fungal Species Combinations on Plant Performance

Frontiers in Microbiology ◽

10.3389/fmicb.2021.713180 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yoshie Hori ◽

Hiroaki Fujita ◽

Kei Hiruma ◽

Kazuhiko Narisawa ◽

Hirokazu Toju

Keyword(s):

Plant Growth ◽

Synergistic Effects ◽

Dry Weight ◽

Fungal Species ◽

Plant Performance ◽

Plant Growth Promoting Bacteria ◽

Microbial Species ◽

Plant Growth Promoting ◽

Growth Promoting ◽

Dual Inoculation

In natural and agricultural ecosystems, survival and growth of plants depend substantially on residing microbes in the endosphere and rhizosphere. Although numerous studies have reported the presence of plant-growth promoting bacteria and fungi in below-ground biomes, it remains a major challenge to understand how sets of microbial species positively or negatively affect plants’ performance. By conducting a series of single- and dual-inoculation experiments of 13 plant-associated fungi targeting a Brassicaceae plant species (Brassica rapa var. perviridis), we here systematically evaluated how microbial effects on plants depend on presence/absence of co-occurring microbes. The comparison of single- and dual-inoculation experiments showed that combinations of the fungal isolates with the highest plant-growth promoting effects in single inoculations did not have highly positive impacts on plant performance traits (e.g., shoot dry weight). In contrast, pairs of fungi with small/moderate contributions to plant growth in single-inoculation contexts showed the greatest effects on plants among the 78 fungal pairs examined. These results on the offset and synergistic effects of pairs of microbes suggest that inoculation experiments of single microbial species/isolates can result in the overestimation or underestimation of microbial functions in multi-species contexts. Because keeping single-microbe systems under outdoor conditions is impractical, designing sets of microbes that can maximize performance of crop plants is an important step for the use of microbial functions in sustainable agriculture.

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Plant performance of enhancing licorice with dual inoculating dark septate endophytes and Trichoderma viride mediated via effects on root development

10.21203/rs.2.23880/v1 ◽

2020 ◽

Author(s):

Chao He ◽

Wenquan Wang ◽

Junling Hou

Keyword(s):

Medicinal Plants ◽

Surface Area ◽

Root Morphology ◽

Root Biomass ◽

Trichoderma Viride ◽

Dark Septate Endophytes ◽

Root Surface Area ◽

Root:Shoot Ratio ◽

Phoma Herbarum ◽

Scytalidium Lignicola

Abstract This study aimed to assess whether licorice (Glycyrrhiza uralensis) can benefit from dual inoculation by Trichoderma viride and dark septate endophytes (DSE) isolated from other medicinal plants. We investigated the influences of three DSE (Paraboeremia putaminum, Scytalidium lignicola, and Phoma herbarum) isolated from other medicinal plants on the performance of licorice at different T. viride densities (1×106, 1×107, and 1×108 CFU/mL). Three DSE strains could colonize the roots of licorice, and they established a positive symbiosis with host plants depending on DSE species and T. viride densities. Inoculation of Paraboeremia putaminum increased the root biomass, length, surface area, and root:shoot ratio. Scytalidium lignicola increased the root length, diameter and surface area and decreased the root:shoot ratio. Phoma herbarum increased the root biomass and surface area. T. viride increased the root biomass, length, and surface area. Structural equation model (SEM) analysis showed that DSE associated with T. viride augmented plant biomass and height, shoot branching, and root surface area. Variations in root morphology and biomass were attributed to differences in DSE species and T. viride density among treatments. Paraboeremia putaminum or Phoma herbarum with low- or medium T. viride density and S. lignicola with low- or high T. viride density improved licorice root morphology and biomass. Our findings support the viewpoint that non-host DSE enhanced the root growth of the host plant under different densities T. viride conditions and may also be used to promote the cultivation of medicinal plants.

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Comparative Metagenomic Analysis of Rhizosphere Microbial Community Composition and Functional Potentials under Rehmannia glutinosa Consecutive Monoculture

International Journal of Molecular Sciences ◽

10.3390/ijms19082394 ◽

2018 ◽

Vol 19 (8) ◽

pp. 2394 ◽

Cited By ~ 11

Author(s):

Linkun Wu ◽

Juanying Wang ◽

Hongmiao Wu ◽

Jun Chen ◽

Zhigang Xiao ◽

...

Keyword(s):

Defense Mechanisms ◽

Microbial Community Composition ◽

Soil Health ◽

Genomic Diversity ◽

Plant Performance ◽

Rehmannia Glutinosa ◽

Microbial Structures ◽

Rhizosphere Microbiome ◽

Relative Abundances ◽

One Year

Consecutive monoculture of Rehmannia glutinosa, highly valued in traditional Chinese medicine, leads to a severe decline in both quality and yield. Rhizosphere microbiome was reported to be closely associated with the soil health and plant performance. In this study, comparative metagenomics was applied to investigate the shifts in rhizosphere microbial structures and functional potentials under consecutive monoculture. The results showed R. glutinosa monoculture significantly decreased the relative abundances of Pseudomonadaceae and Burkholderiaceae, but significantly increased the relative abundances of Sphingomonadaceae and Streptomycetaceae. Moreover, the abundances of genera Pseudomonas, Azotobacter, Burkholderia, and Lysobacter, among others, were significantly lower in two-year monocultured soil than in one-year cultured soil. For potentially harmful/indicator microorganisms, the percentages of reads categorized to defense mechanisms (i.e., ATP-binding cassette (ABC) transporters, efflux transporter, antibiotic resistance) and biological metabolism (i.e., lipid transport and metabolism, secondary metabolites biosynthesis, transport and catabolism, nucleotide transport and metabolism, transcription) were significantly higher in two-year monocultured soil than in one-year cultured soil, but the opposite was true for potentially beneficial microorganisms, which might disrupt the equilibrium between beneficial and harmful microbes. Collectively, our results provide important insights into the shifts in genomic diversity and functional potentials of rhizosphere microbiome in response to R. glutinosa consecutive monoculture.

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