scholarly journals Rhizobium Symbiotic Capacity Shapes Root-Associated Microbiomes in Soybean

2021 ◽  
Vol 12 ◽  
Author(s):  
Yuanhui Liu ◽  
Bin Ma ◽  
Wenfeng Chen ◽  
Klaus Schlaeppi ◽  
Matthias Erb ◽  
...  
Keyword(s):  
Root Exudates ◽  
Root Exudation ◽  
Amplicon Sequencing ◽  
Vital Role ◽  
Plant Performance ◽  
Physiochemical Properties ◽  
Nod Factor ◽  
Community Shift ◽  
Soybean Roots ◽  
Microbiome Assembly

Root-microbiome interactions are of central importance for plant performance and yield. A distinctive feature of legumes is that they engage in symbiosis with N2-fixing rhizobia. If and how the rhizobial symbiotic capacity modulates root-associated microbiomes are still not yet well understood. We determined root-associated microbiomes of soybean inoculated with wild type (WT) or a noeI mutant of Bradyrhizobium diazoefficiens USDA 110 by amplicon sequencing. UPLC-MS/MS was used to analyze root exudates. The noeI gene is responsible for fucose-methylation of Nod factor secreted by USDA 110 WT strain. Soybean roots inoculated with the noeI mutant showed a significant decrease in nodulation and root-flavonoid exudation compared to roots inoculated with WT strain. The noeI mutant-inoculated roots exhibited strong changes in microbiome assembly in the rhizosphere and rhizoplane, including reduced diversity, changed co-occurrence interactions and a substantial depletion of root microbes. Root exudates and soil physiochemical properties were significantly correlated with microbial community shift in the rhizosphere between different rhizobial treatments. These results illustrate that rhizobial symbiotic capacity dramatically alters root-associated microbiomes, in which root exudation and edaphic patterns play a vital role. This study has important implications for understanding the evolution of plant-microbiome interactions.

The symbiotic capacity of rhizobium shapes root-associated microbiomes

2020 ◽  
Author(s):  
Yuanhui Liu ◽  
Bin Ma ◽  
Wenfeng Chen ◽  
Klaus Schlaeppi ◽  
Matthias Erb ◽  
...  
Keyword(s):  
Root Exudation ◽  
Plant Performance ◽  
Wild Type ◽  
Bacterial Strains ◽  
Central Importance ◽  
Nod Factor ◽  
Beneficial Microbes ◽  
Soybean Plants ◽  
Microbial Symbiosis ◽  
Microbiome Assembly

Abstract Background: Root-microbiome interactions are of central importance for plant performance and yield. A distinctive feature of legumes in this context is that they engage in symbiosis with rhizobia, which are abundant in soils and include both symbiotic and non-symbiotic bacterial strains. If and how the capacity of rhizobia to form symbiosis modulates root-associated microbiomes are not well understood. Results: We address this question by inoculating soybean (Glycine max) plants with wild type (WT) or a noeI mutant of Bradyrhizobium diazoefficiens. The noeI mutant produces a defective Nod factor and is thus compromised in its ability to establish functional symbiosis. Compared to soybean plants inoculated with WT rhizobia, plants inoculated with the noeI mutant showed a significant decrease in nodulation and root-flavonoid exudation, and exhibited strong changes in microbiome assembly in the rhizosphere and the rhizoplane. NoeI mutant-inoculated roots exhibited reduced diversity, co-occurrence interactions and a substantial depletion of beneficial microbes on the roots. The effects of the noeI mutation were absent in soils without plants, demonstrating that they are plant dependent. Complementation experiments showed that flavonoid supplementation is sufficient to restore recruitment of beneficial microbes. Conclusion: The results illustrate that the capacity of a rhizobium to form microbial symbiosis dramatically alters root-associated microbiomes, most likely by changing root exudation patterns. The results of this study have important implications for our understanding of the evolution of plant-microbiome interactions in the context of plant-bacterial symbioses.

Natural variation in root exudation of GABA and DIMBOA impacts the maize root endosphere and rhizosphere microbiomes

2021 ◽  
Author(s):  
Peng Wang ◽  
Lucas Dantes Lopez ◽  
Sophie Alvarez ◽  
Martha Lopez-Guerrero ◽  
Karin van Dijk ◽  
...  
Keyword(s):  
Root Exudates ◽  
Natural Variation ◽  
Root Exudation ◽  
Amplicon Sequencing ◽  
Hydroponic System ◽  
Kegg Pathways ◽  
16S Rrna Amplicon Sequencing ◽  
Maize Genotypes ◽  
Powerful Approach ◽  
The Impact

Root exudates are important for shaping root-associated microbiomes. However, studies on a wider range of metabolites in exudates are required for a comprehensive understanding about their influence on microbial communities. We identified maize inbred lines that differ in exudate concentrations of DIMBOA and GABA using a semi-hydroponic system. These lines were grown in the field to determine the changes in microbial diversity and gene expression due to varying concentrations of DIMBOA and GABA in exudates using 16S rRNA amplicon sequencing and metatranscriptomics. Results showed individual and interaction effects of DIMBOA and GABA on the rhizosphere and root endosphere beta-diversity, most strongly at the V10 growth stage. The main bacterial families affected by both compounds were Ktedonobacteraceae and Xanthomonadaceae. Higher concentrations of DIMBOA in exudates affected the rhizosphere metatranscriptome, enriching for KEGG pathways associated with plant disease. This study validated the use of natural variation within plant species as a powerful approach for understanding the role of root exudates on microbiome selection. We also showed that a semi-hydroponic system can be used to identify maize genotypes that differ in GABA and DIMBOA exudate concentrations under field conditions. The impact of GABA exudation on root-associated microbiomes was shown for the first time.

scholarly journals Multiple bacteria associated with the more dysbiotic genitourinary microbiomes in patients with type 2 diabetes mellitus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hua Zha ◽  
Fengping Liu ◽  
Zongxin Ling ◽  
Kevin Chang ◽  
Jiezuan Yang ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Type 2 Diabetes ◽  
Type 2 Diabetes Mellitus ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Diversity Indices ◽  
Vital Role ◽  
Rrna Gene ◽  
Beta Glucosidase

AbstractType 2 diabetes mellitus (T2DM) influences the human health and can cause significant illnesses. The genitourinary microbiome profiles in the T2DM patients remain poorly understood. In the current study, a series of bioinformatic and statistical analyses were carried out to determine the multiple bacteria associated with the more dysbiotic genitourinary microbiomes (i.e., those with lower dysbiosis ratio) in T2DM patients, which were sequenced by Illumina-based 16S rRNA gene amplicon sequencing. All the genitourinary microbiomes from 70 patients with T2DM were clustered into three clusters of microbiome profiles, i.e., Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, with Cluster_3_T2DM at the most dysbiotic genitourinary microbial status. The three clustered T2DM microbiomes were determined with different levels of alpha diversity indices, and driven by distinct urinalysis variables. OTU12_Clostridiales and OTU28_Oscillospira were likely to drive the T2DM microbiomes to more dysbiotic status, while OTU34_Finegoldia could play a vital role in maintaining the least dysbiotic T2DM microbiome (i.e., Cluster_1_T2DM). The functional metabolites K08300_ribonuclease E, K01223_6-phospho-beta-glucosidase and K00029_malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) were most associated with Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, respectively. The characteristics and multiple bacteria associated with the more dysbiotic genitourinary microbiomes in T2DM patients may help with the better diagnosis and management of genitourinary dysbiosis in T2DM patients.

scholarly journals Stoichiometry constrains microbial response to root exudation- insights from a model and a field experiment in a temperate forest

2013 ◽  
Vol 10 (2) ◽  
pp. 821-838 ◽  
Author(s):  
J. E. Drake ◽  
B. A. Darby ◽  
M.-A. Giasson ◽  
M. A. Kramer ◽  
R. P. Phillips ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Microbial Biomass ◽  
Field Experiment ◽  
Microbial Activity ◽  
Root Exudates ◽  
Microbial Respiration ◽  
Root Exudation ◽  
N Availability ◽  
Rhizosphere Soils ◽  
Wide Range

Abstract. Plant roots release a wide range of chemicals into soils. This process, termed root exudation, is thought to increase the activity of microbes and the exoenzymes they synthesize, leading to accelerated rates of carbon (C) mineralization and nutrient cycling in rhizosphere soils relative to bulk soils. The nitrogen (N) content of microbial biomass and exoenzymes may introduce a stoichiometric constraint on the ability of microbes to effectively utilize the root exudates, particularly if the exudates are rich in C but low in N. We combined a theoretical model of microbial activity with an exudation experiment to test the hypothesis that the ability of soil microbes to utilize root exudates for the synthesis of additional biomass and exoenzymes is constrained by N availability. The field experiment simulated exudation by automatically pumping solutions of chemicals often found in root exudates ("exudate mimics") containing C alone or C in combination with N (C : N ratio of 10) through microlysimeter "root simulators" into intact forest soils in two 50-day experiments. The delivery of C-only exudate mimics increased microbial respiration but had no effect on microbial biomass or exoenzyme activities. By contrast, experimental delivery of exudate mimics containing both C and N significantly increased microbial respiration, microbial biomass, and the activity of exoenzymes that decompose low molecular weight components of soil organic matter (SOM, e.g., cellulose, amino sugars), while decreasing the activity of exoenzymes that degrade high molecular weight SOM (e.g., polyphenols, lignin). The modeling results were consistent with the experiments; simulated delivery of C-only exudates induced microbial N-limitation, which constrained the synthesis of microbial biomass and exoenzymes. Exuding N as well as C alleviated this stoichiometric constraint in the model, allowing for increased exoenzyme production, the priming of decomposition, and a net release of N from SOM (i.e., mineralization). The quantity of N released from SOM in the model simulations was, under most circumstances, in excess of the N in the exudate pulse, suggesting that the exudation of N-containing compounds can be a viable strategy for plant-N acquisition via a priming effect. The experimental and modeling results were consistent with our hypothesis that N-containing compounds in root exudates affect rhizosphere processes by providing substrates for the synthesis of N-rich microbial biomass and exoenzymes. This study suggests that exudate stoichiometry is an important and underappreciated driver of microbial activity in rhizosphere soils.

Plants colonized by AM fungi regulate further root colonization by AM fungi through altered root exudation

1999 ◽  
Vol 77 (6) ◽  
pp. 891-897 ◽  
Author(s):  
Alexandra Pinior ◽  
Urs Wyss ◽  
Yves Piché ◽  
Horst Vierheilig
Keyword(s):  
Root Exudates ◽  
Glomus Mosseae ◽  
Glomus Intraradices ◽  
Root Colonization ◽  
Root Exudation ◽  
Axenic Culture ◽  
Am Fungi ◽  
Hyphal Growth ◽  
Gigaspora Rosea ◽  
Stimulation Of

The effect of root exudates from non-mycorrhizal and mycorrhizal cucumber (Cucumis sativus L.) plants colonized by one of three arbuscular mycorrhizal fungi (Gigaspora rosea Nicolson & Schenck, Glomus intraradices Smith & Schenck, or Glomus mosseae (Nicolson & Gerdemann) Gerd. & Trappe) on hyphal growth of Gi. rosea and G. intraradices in axenic culture and on root colonization by G. mosseae in soil was investigated. Root exudates from non-mycorrhizal cucumber plants clearly stimulated hyphal growth, whereas root exudates from all mycorrhizal cucumber plants tested showed no stimulation of the hyphal growth of Gi. rosea and only a slight stimulation of the hyphal growth of G. intraradices. Moreover, root exudates from all mycorrhizal cucumber plants inhibited root colonization by G. mosseae compared with the water-treated controls. These results suggest that plants colonized by AM fungi regulate further mycorrhization via their root exudates.Key words: Glomales, Gigaspora rosea, Glomus intraradices, Glomus mosseae, root exudates, regulation.

Optimal Design of a Heat Exchanger for an Externally-Fired Microturbine in Combined Heat and Power Generation

2008 ◽  
Author(s):  
Juha Kaikko ◽  
Lasse Koskelainen ◽  
Jari L. H. Backman ◽  
Jaakko Larjola
Keyword(s):  
Heat Exchanger ◽  
Net Present Value ◽  
Vital Role ◽  
Hot Water ◽  
Plant Performance ◽  
Energy Prices ◽  
Direct Combustion ◽  
Heat Engines ◽  
Economical Optimization ◽  
The Cost

Biofuels have a vital role in emerging distributed energy systems. Special interest is focused on heat engines that can utilize biomass by direct combustion, such as externally-fired microturbines (EFMT). This paper considers a case where a natural gas-fired microturbine is converted into an EFMT. In the application the combustion chamber is replaced by a metallic heat exchanger retrofitted into a large biomass-fueled hot water boiler. The hot air that leaves the microturbine is directed into the furnace as preheated combustion air. In the paper, techno-economical optimization is performed for the selected heat exchanger configuration. The optimization is based on maximizing the net present value of the investment. The optimum depends on the cost of the new components and the resulting effect on the overall plant performance. The results show that the energy prices have only a mild impact on the optimum dimensions, although the feasibility of the investment itself depends strongly on the economy parameters. Using the optimized heat exchanger, the performance of the EFMT is predicted under part-load conditions of the boiler.

scholarly journals Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing

PLoS ONE ◽  
2012 ◽  
Vol 7 (8) ◽  
pp. e41606 ◽  
Author(s):  
Sebastian Jünemann ◽  
Karola Prior ◽  
Rafael Szczepanowski ◽  
Inga Harks ◽  
Benjamin Ehmke ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Ion Torrent ◽  
Community Shift

scholarly journals Rhizosphere microbes and host plant genotype influence the plant metabolome and reduce insect herbivory

2018 ◽  
Author(s):  
Charley J. Hubbard ◽  
Baohua Li ◽  
Robby McMinn ◽  
Marcus T. Brock ◽  
Lois Maignien ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Flea Beetle ◽  
Insect Herbivory ◽  
Amplicon Sequencing ◽  
Plant Performance ◽  
Insect Herbivores ◽  
List Type ◽  
Plant Genotype ◽  
Herbivore Resistance ◽  
Rhizosphere Microbiome

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.

scholarly journals Fusarium Oxysporum Disrupts Microbiome-Metabolome Networks in Arabidopsis Thaliana Roots

2021 ◽  
Author(s):  
Enoch Narh Kudjordjie ◽  
Kourosh Hooshmand ◽  
Rumakanta Sapkota ◽  
Inge S. Fomsgaard ◽  
Mogens Nicolaisen
Keyword(s):  
Arabidopsis Thaliana ◽  
Fusarium Oxysporum ◽  
Fungal Pathogen ◽  
Plant Disease ◽  
Differential Resistance ◽  
Amplicon Sequencing ◽  
Interactive Effects ◽  
Pathogen Invasion ◽  
Plant Disease Control ◽  
Microbiome Assembly

Abstract BackgroundAlthough it is well established that plant metabolomes mediate microbiome assembly, the question of how metabolome-microbiome interactions may prevent pathogen invasion remains to be answered. To address this question, we studied microbiome and metabolome profiles of two Arabidopsis thaliana accessions, Columbia-0 (Col-0) and Landsberg erecta (Ler-0) with differential resistance profiles to the fungal pathogen Fusarium oxysporum f.sp. mathioli (FOM). We used amplicon sequencing to characterize bacterial (16S) and fungal (ITS2) communities, and we used targeted metabolite analysis across 5 stages of FOM host progression. ResultsWe found that microbiome and metabolome profiles were markedly altered in FOM-inoculated and non-inoculated samples of resistant Col-0 and susceptible Ler-0. Co-occurrence network analysis revealed robust microbial networks in the resistant Col-0 compared to the susceptible Ler-0, during FOM infection. Specific metabolites and microbial OTUs (including indicator and hub OTUs) correlated in both non-inoculated and inoculated Col-0 and Ler-0. The glucosinolates 4-hydroxyglucobrassicin, neoglucobrassicin and indole-3 carbinol, but also phenolic compounds were active in structuring the A. thaliana-microbiome. ConclusionsOur results highlight the interactive effects of host resistance and its associated microbiota on Fusarium infection and progression. These findings shed significant insights into plant inter-omics dynamics during pathogen invasion and could possibly facilitate the exploitation of microbiomes for plant disease control.

scholarly journals Identification of Root-Secreted Compounds Involved in the Communication Between Cucumber, the Beneficial Bacillus amyloliquefaciens, and the Soil-Borne Pathogen Fusarium oxysporum

2017 ◽  
Vol 30 (1) ◽  
pp. 53-62 ◽  
Author(s):  
Yunpeng Liu ◽  
Lin Chen ◽  
Gengwei Wu ◽  
Haichao Feng ◽  
Guishan Zhang ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Root System ◽  
Root Exudates ◽  
Bacillus Amyloliquefaciens ◽  
Root Colonization ◽  
Plant Root ◽  
Root Exudation ◽  
Soil Borne Pathogens ◽  
Split Root System ◽  
Cucumber Roots

Colonization of plant growth–promoting rhizobacteria (PGPR) is critical for exerting their beneficial effects on the plant. Root exudation is a major factor influencing the colonization of both PGPR and soil-borne pathogens within the root system. However, the tripartite interaction of PGPR, plant roots, and soil-borne pathogens is poorly understood. We screened root exudates for signals that mediate tripartite interactions in the rhizosphere. In a split-root system, we found that root colonization of PGPR strain Bacillus amyloliquefaciens SQR9 on cucumber root was significantly enhanced by preinoculation with SQR9 or the soil-borne pathogen Fusarium oxysporum f. sp. cucumerinum, whereas root colonization of F. oxysporum f. sp. cucumerinum was reduced upon preinoculation with SQR9 or F. oxysporum f. sp. cucumerinum. Root exudates from cucumbers preinoculated with SQR9 or F. oxysporum f. sp. cucumerinum were analyzed and 109 compounds were identified. Correlation analysis highlighted eight compounds that significantly correlated with root colonization of SQR9 or F. oxysporum f. sp. cucumerinum. After performing colonization experiments with these chemicals, raffinose and tryptophan were shown to positively affect the root colonization of F. oxysporum f. sp. cucumerinum and SQR9, respectively. These results indicate that cucumber roots colonized by F. oxysporum f. sp. cucumerinum or SQR9 increase root secretion of tryptophan to strengthen further colonization of SQR9. In contrast, these colonized cucumber roots reduce raffinose secretion to inhibit root colonization of F. oxysporum f. sp. cucumerinum.

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