Recent Developments in Systems Biology and Metabolic Engineering of Plant–Microbe Interactions

Kumar, Vishal; Baweja, Mehak; Singh, Puneet Kumar; Shukla, Pratyoosh

doi:10.3389/fpls.2016.01421

Cited by 74 publications

(35 citation statements)

References 116 publications

(110 reference statements)

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“…In addition to inoculation, mechanistic knowledge on links between plant traits and soil organismal networks could enable another promising approach for promoting soil organismal networks that deliver desirable functions (Kumar et al 2016). While there is accumulating evidence that plant traits, and in particular root traits, can predict soil faunal and microbial community structure and functioning (De Vries et al 2012b;Grigulis et al 2013;Legay et al 2016), there is only limited evidence that links plant traits to soil microbial networks.…”

Section: The Rhizosphere Interactions For Sustainable Agriculture Modelmentioning

confidence: 99%

Below‐ground connections underlying above‐ground food production: a framework for optimising ecological connections in the rhizosphere

2017

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Summary1. Healthy soils that contain an active microbiome and food web are critical to sustainably produce food for a growing global human population. Many studies have focussed on the role of microbial species diversity and the presence of key functional groups as important controls on the many functions that a sustainable food system relies on. 2. Here, we synthesise recent ecological empirical evidence and theory to propose that the interactions between organisms in the soil food web are the critical determinant of soil function. 3. We propose the Rhizosphere Interactions for Sustainable Agriculture Model, in which crop roots recruit small, modular, highly connected soil rhizosphere networks from large, static, relatively unconnected and diverse bulk soil networks. We argue that conventional agricultural management disrupts the connections between rhizosphere and bulk soil networks. 4. Synthesis. We identify future research directions for optimising ecological connections between roots and rhizosphere microbial and faunal networks, and between rhizosphere networks and bulk soil networks in agricultural production systems. Knowledge on these connections can be applied in agricultural systems to sustainability produce food for a growing global population.

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Section: The Rhizosphere Interactions For Sustainable Agriculture Modelmentioning

confidence: 99%

Below‐ground connections underlying above‐ground food production: a framework for optimising ecological connections in the rhizosphere

2017

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“…Belowground microorganisms and their interactions to plants connect the two communities of aboveground and belowground world and contribute to community structure and plant health (Hassani, Duran, & Hacquard, 2018), attracting both botanists and microbiologists. The plant microbiome can be subdivided into several important regions, such as rhizosphere, phyllosphere and endosphere, due to their unique conditions present on and in different areas of plants (Bulgarelli, Schlaeppi, Spaepen, van Themaat, & Schulze-Lefert, 2013;Kumar, Baweja, Singh, & Shukla, 2016). The microorganisms living in these different spheres play important roles in plant nutrition acquisition, mutualistic defence and co-evolution (Fitzpatrick et al, 2018;Kenrick & Strullu-Derrien, 2014;Martin, Uroz, & Barker, 2017).…”

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confidence: 99%

Interdomain ecological networks between plants and microbes

Feng

Zhang

et al. 2019

Molecular Ecology Resources

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While macroscopic interkingdom relationships have been intensively investigated in various ecosystems, the above–belowground ecology in natural ecosystems has been poorly understood, especially for the plant–microbe associations at a regional scale. In this study, we proposed a workflow to construct interdomain ecological networks (IDEN) between multiple plants and various microbes (bacteria and archaea in this study). Across 30 latitudinal forests in China, the regional IDEN showed particular topological features, including high connectance, nested structure, asymmetric specialization and modularity. Also, plant species exhibited strong preference to specific microbial groups, and the observed network was significantly different from randomly rewired networks. Network module analysis indicated that a majority of microbes associated with plants within modules rather than across modules, suggesting specialized associations between plants and microorganisms. Consistent plant–microbe associations were captured via IDENs constructed within individual forest locations, which reinforced the validity of IDEN analysis. In addition, the plant–forest link distribution showed the geographical distribution of plants had higher endemicity than that of microorganisms. With cautious experimental design and data processing, this study shows interdomain species associations between plants and microbes in natural forest ecosystems and provides new insights into our understanding of meta‐communities across different domain species.

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“…The interactions of probiotics with prebiotics have a beneficial role in improving the growth of normal microflora, resulting in immune system modulation of the host. A number of systems biology tools have been studied to comprehend the interactions between microorganisms and plant or human cell (Kumar et al, 2016). Furthermore, various genetic modifications which involve the introduction of desired genes may also have a constructive impact in the probiotic field (Gupta and Shukla, 2015).…”

Section: Introductionmentioning

confidence: 99%

Catalytic Interactions and Molecular Docking of Bile Salt Hydrolase (BSH) from L. plantarum RYPR1 and Its Prebiotic Utilization

Yadav¹,

Singh²,

Puniya³

et al. 2017

Front. Microbiol.

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Prebiotics are the non-digestible carbohydrate, which passes through the small intestine into unmetabolized form, reaches the large intestine and undergoes fermentation by the colonic bacteria thus; prebiotics stimulate the growth of probiotic bacteria. Further, bile salt hydrolase (BSH) is an enzyme that catalyses the deconjugation of bile salt, so it has enormous potential toward utilizing such capability of Lactobacillus plantarum RYPR1 toward detoxifying through BSH enzyme activity. In the present study, six isolates of Lactobacillus were evaluated for the co-aggregation assay and the isolate Lactobacillus plantarum RYPR1 was further selected for studies of prebiotic utilization, catalytic interactions and molecular docking. The prebiotic utilization ability was assessed by using commercially available prebiotics lactulose, inulin, xylitol, raffinose, and oligofructose P95. The results obtained revealed that RYPR1 is able to utilize these probiotics, maximum with lactulose by showing an increase in viable cell count (7.33 ± 0.02 to 8.18 ± 0.08). In addition, the molecular docking of BSH from Lactobacillus plantarum RYPR1 was performed which revealed the binding energy –4.42 and 7.03 KJ/mol. This proves a considerably good interactions among BSH and its substrates like Taurocholic acid (–4.42 KJ/mol) and Glycocholic acid (–7.03 KJ/mol). These results from this study establishes that Lactobacillus plantarum RYPR1 possesses good probiotic effects so it could be used for such applications. Further, molecular dynamics simulations were used to analyze the dynamic stability of the of modeled protein to stabilize it for further protein ligand docking and it was observed that residues Asn12, Ile8, and Leu6 were interacting among BSH and its substrates, i.e., Taurocholic acid and Lys88 and Asp126 were interacting with Glycocholic acid. These residues were interacting when the docking was carried out with stabilized BSH protein structure, thus, these residues may have a vital role in stabilizing the binding of the ligands with the protein.

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Recent Developments in Systems Biology and Metabolic Engineering of Plant–Microbe Interactions

Cited by 74 publications

References 116 publications

Below‐ground connections underlying above‐ground food production: a framework for optimising ecological connections in the rhizosphere

Below‐ground connections underlying above‐ground food production: a framework for optimising ecological connections in the rhizosphere

Interdomain ecological networks between plants and microbes

Catalytic Interactions and Molecular Docking of Bile Salt Hydrolase (BSH) from L. plantarum RYPR1 and Its Prebiotic Utilization

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