Linking plant functional genes to rhizosphere microbes: a review

Liu, Qi; Ling, Cheng; Nian, Hai; Jin, Jian; Lian, Tengxiang

doi:10.1111/pbi.13950

Cited by 42 publications

(11 citation statements)

References 279 publications

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“…Transcriptomics analysis revealed that beneficial and anti-pathogenic microbes correlated positively with the root MEblue module, whereas potential pathogens correlated negatively with the root MEblue module. The results of several studies have shown similar findings with root-associated microbes [64,65]. Plant functions can be reg-ulated directly or indirectly by microbes [66,67].…”

Section: Discussionmentioning

confidence: 58%

The Responses of a Grapevine Rhizosphere System to Mulching Using Amplicon Sequencing and Transcriptomic Analysis

Wang

et al. 2023

Agronomy

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Although mulching is a widely used agronomic practice, its effects on the rhizosphere remain poorly understood. Here, we employed amplicon and transcriptomic sequencing to investigate variations in a grapevine rhizosphere system under mulch treatment (rice straw + felt + plastic film). Analyzing 16S and intergenic spacer (ITS) rRNA sequences indicated that the Shannon and Simpson indices of the bacterial and fungal communities increased markedly under mulch treatment. The bacterial and fungal compositions varied significantly between the control and mulch treatments. Mulching enriched for potentially beneficial microbes that confer disease resistance to plants or participate in nitrogen metabolism (Kaistobacter, Ammoniphilus, Lysobacter, Ammoniphilus, Alicyclobacillus, Aquicella, Nitrospira, Chaetomium, and Microascus), whereas more potentially pathogenic microbes (Fusarium and Gibberella) were detected in the control. Moreover, certain bacteria and fungi exhibited different correlations with the root transcriptome functions of the MEBlue module. The complexity of the bacterial and fungal co-occurrence networks increased with higher node numbers, positive and negative links after mulching. Following mulching, the rhizosphere showed elevated pH, organic matter, and catalase activities, and decreased sucrase and cellulase and β-glucosidase activities. Our results provide comprehensive data showing how a grapevine rhizosphere system responded to mulching treatment and shed important insight into mulching practices for fruit trees.

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Section: Discussionmentioning

confidence: 58%

The Responses of a Grapevine Rhizosphere System to Mulching Using Amplicon Sequencing and Transcriptomic Analysis

Wang

et al. 2023

Agronomy

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“…Finally, recent research has led to the discovery that plant functional genes, and in particular symbiotic signaling genes in legumes, are involved in modulating the structure of the root-associated microbiota and the interactions among these communities ( Zgadzaj et al., 2016 ; Thiergart et al., 2019 ; Liu et al., 2023 ). Legumes can establish mutualistic interactions with rhizobia and arbuscular mycorrizal fungi (AMF) that induce symbiotic signaling pathways involving specific components but also sharing some common components ( Oldroyd, 2013 ).…”

Section: The Rhizosphere Microbiome: a Hotspot For Microbial Interact...mentioning

confidence: 99%

The role of microbial interactions on rhizobial fitness

Granada Agudelo,

Ruiz,

Capela

et al. 2023

Front. Plant Sci.

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Rhizobia are soil bacteria that can establish a nitrogen-fixing symbiosis with legume plants. As horizontally transmitted symbionts, the life cycle of rhizobia includes a free-living phase in the soil and a plant-associated symbiotic phase. Throughout this life cycle, rhizobia are exposed to a myriad of other microorganisms that interact with them, modulating their fitness and symbiotic performance. In this review, we describe the diversity of interactions between rhizobia and other microorganisms that can occur in the rhizosphere, during the initiation of nodulation, and within nodules. Some of these rhizobia-microbe interactions are indirect, and occur when the presence of some microbes modifies plant physiology in a way that feeds back on rhizobial fitness. We further describe how these interactions can impose significant selective pressures on rhizobia and modify their evolutionary trajectories. More extensive investigations on the eco-evolutionary dynamics of rhizobia in complex biotic environments will likely reveal fascinating new aspects of this well-studied symbiotic interaction and provide critical knowledge for future agronomical applications.

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“…Some of the N-responsive genes help in the regulation of rhizomicrobiome and this molecular regulatory network of plant-microbe interactions could improve crop production [70]. Microbiomes have a great role in structuring plant phenotype by induction of more lateral roots for efficient absorption of nutrients and thus help in increasing NUE in crops [71].…”

Section: Role Of Microbes In Nitrogen Uptake and Trnsportmentioning

confidence: 99%

Molecular Frameworks of Nitrogen Response in Plants: A Review

Jose,

Soni K. B.,

Alex

et al. 2023

IJECC

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Nitrogen is a crucial element for all living organisms especially plants which rely on substantial nitrogen quantities to sustain their growth and productivity. Crop production is greatly influenced by nitrogen consumption efficiency and a significant amount of nitrogen fertilizers is used to increase yield. Approximately half of N fertilizers are not utilized by the crops and are lost to the environment by polluting water sources or by releasing pollutants into the atmosphere. From the rhizosphere, plants absorb nitrogen in the form of nitrate (NO3-), ammonium (NH4+), or organic nitrogen (amino acids and urea). Plants exhibit an array of sensing and adaptive mechanisms to respond to the diverse nitrogen nutrition conditions which include morphological and physiological responses. Two primary systems govern nitrogen uptake in plants: the High-affinity transport system (HATS) and the Low-affinity transport system (LATS). Nitrate transporters fall into two categories, Nitrate Transporter 1 (NRT1) and Nitrate Transporter 2 (NRT2) transporters, Chloride Channel Family (CLC) transporters and Slow Anion Associated Channel Homologs (SLAC/SLAHs). The ammonium transporter family includes Ammonium Transporter 1 (AMT1) and Ammonium Transporter 2 (AMT2) transporters. The uptake of organic nitrogen is facilitated through amino acid and urea uptake and transport systems. In fluctuating environmental conditions, plants employ nitrogen response mechanisms to fine-tune homeostasis. A comprehensive understanding of these regulatory mechanisms holds the potential to yield valuable insights for the development of crops with enhanced nitrogen use efficiency.

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Linking plant functional genes to rhizosphere microbes: a review

Cited by 42 publications

References 279 publications

The Responses of a Grapevine Rhizosphere System to Mulching Using Amplicon Sequencing and Transcriptomic Analysis

The Responses of a Grapevine Rhizosphere System to Mulching Using Amplicon Sequencing and Transcriptomic Analysis

The role of microbial interactions on rhizobial fitness

Molecular Frameworks of Nitrogen Response in Plants: A Review

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