A review on the impact of domestication of the rhizosphere of grain crops and a perspective on the potential role of the rhizosphere microbial community for sustainable rice crop production

Chang, Jingjing; Veen, Johannes A. van; Tian, Chunjie; Kuramae, E.E.

doi:10.1016/j.scitotenv.2022.156706

Cited by 11 publications

(7 citation statements)

References 72 publications

(82 reference statements)

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“…The results reported in this work are also in alignment with agricultural studies pertaining to the root bed in plants showing heavy presence of certain microbes “seed to rhizo-micro-biomes”( Neemisha et al, 2022 ; Orozco-Mosqueda et al, 2022 ) which dominate plant growth ( Chang et al, 2022 ; Zhang et al, 2020 ), rigor, fitness, and crop yield ( Abdullaeva et al, 2021 ) Koprivova and Kopriva, 2022 ; Li et al, 2022 ). Microbial communities residing in roots are diverse, some including non – pathogenic B. cereus group, and spp of Enterobacter, Pseudomonas, Cronobacter , with those close to water having the greatest diversity ( Sun et al, 2019 ).…”

Section: Rootssupporting

confidence: 83%

Functional immune boosters; the herb or its dead microbiome? Antigenic TLR4 agonist MAMPs found in 65 medicinal roots and algae’s

Mazzio,

Barnes,

Badisa

et al. 2023

Journal of Functional Foods

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Section: Rootssupporting

confidence: 83%

Functional immune boosters; the herb or its dead microbiome? Antigenic TLR4 agonist MAMPs found in 65 medicinal roots and algae’s

Mazzio,

Barnes,

Badisa

et al. 2023

Journal of Functional Foods

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“…The root-associated microbiome and its functioning are considered signi cant factors affecting crop growth, yield, and resistance against biotic and abiotic stresses under sustainable agriculture (Nerva et al 2022). The landraces recruit their rhizo-microbiome depending on the soil and environmental factors, while the high-yielding cultivars fail to form a potential host-microbiome interaction, hence unsuccessful in performing when unexpected drought, pest, and diseases occur (Chang et al 2022). Therefore, understanding the mechanisms of microbiome interaction by landraces will help to develop interventions for the growth and tness of high-yielding cultivars to ensure sustainability.…”

Section: Discussionmentioning

confidence: 99%

“…Under that circumstances, the crop heavily depends on synthetic chemical fertilizers for readily available nutrients. Further, the plant cannot withstand the biotic and abiotic stresses due to the less-functional rhizosphere (Abdullaeva et al 2021;Chang et al 2022;Nerva et al 2022;Ray et al 2020;Sun et al 2021b). In the present work, we showed that the drought-tolerant landrace Norungan and high-yielding cultivar Co51 performed more or less similar rhizosphere functioning under normal conditions.…”

Section: Discussionmentioning

confidence: 99%

Rhizosphere functioning and rhizo-microbiome of two contrasting genotypes of rice under drought-induced conditions

Nunna¹,

Balachandar

2022

Preprint

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Background and aim Rhizosphere function is the key determinant of crop growth and fitness under moisture-stress conditions. Human-centered breeding adversely affects microbiome recruitment of crops. Hence, during drought, wild types and landraces adapt to stress, while modern cultivars and hybrids fail to do so and are susceptible to drought. Understanding the rhizosphere difference between landraces and cultivars will help to improve microbiome-mediated drought mitigation. Methods We compared rhizospheres of rice landrace, Norungan, and high-yielding cultivar, Co51, grown under normal moisture and drought-induced conditions using soil biochemical and 16S rRNA gene sequencing approach. Results Soil carbon pools, enzymes, and respiration were adversely affected due to drought in both genotypes' rhizospheres. However, Norungan rhizosphere accounted for less harm to the soil attributes than Co51. Reduction in soil organic carbon (3.94%), microbial biomass carbon (14.26%), labile carbon (1.94%), dehydrogenase (10.1%), urease (21.27%), phosphatase (9.61%), and respiration rate (15.02%) was accounted in Co51 than Norungan, during drought. Alpha diversity of bacterial communities in rice's rhizosphere was significantly lower than in bulk soil, and drought further reduced the diversity in both genotypes. Moisture-stress reduced the abundance of Firmicutes (180%) and Bacteroidetes (57%) in Norungan's rhizosphere, while, Acidobacteria (51%), Actinobacteria (54%), Chlolorflexi (41%), and Proteobacteria (34%) got increased. On the other hand, Co51 rhizosphere acquired an enhanced abundance of Firmicutes (79%) and Bacteriodetes (170%) and lessened abundance of Acidobacteria (15%) and Proteobacteria (31%) due to drought. Conclusion These results suggest that landrace Norungan under moisture-stress conditions recruits less-diversified, specific groups of microorganisms to augment rhizosphere functioning.

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“…With increasing emphasis on understanding the ecosystems of agricultural production [13], arti cial remodeling of microbiome engineering is a promising tool to improve the ecological adaptability of crops for sustainable development [14,15]. Wild rice, the origin of cultivated rice (Oryza sativa L.), possesses various potent and distinct characteristics, such as disease resistance and drought tolerance [16][17][18]. According to reports, wild rice has a peculiar microbial community mechanism, particularly its rhizosphere microbial community, with tremendous domestication potential [20].…”

Section: Introductionmentioning

confidence: 99%

Endophytic Acrocalymma vagum drives the microbiome variations for rice health

Zeng

Wang

et al. 2023

Preprint

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Background: Endophytic fungi are essential members of the plant microbial community, which play a vital role in promoting plant growth and development, and inducing disease resistance. However, little is known about the ecological mechanisms of endophytic fungi impacting the root microbiota community to improve crop health. Results: An endophytic fungus Acrocalymma vagum (Code A21) isolated from wild rice enhanced rice yield by 5.73% and induced resistance against rice blast with 83.24% control efficiency in the field. The root microbiota community variations were discovered through 16S and ITS metabarcoding methods. A. vagum simplified the complexity of the rice microbiome community, reducing the proportion of the dominant pathogens Burkholderia and Ralstonia, and driving rice to recruit beneficial bacteria (Aquabacterium, Flavobacterium, and Lactobacillus) and fungi (Rhizophagus, Sarocladium, and Nigrospora). The recruited microbes were enriched in nutrient synthesis and stress resistance, especially biosynthesis of lactate, vitamin B12, and thiazole. We further isolated and identified 279 bacteria and 82 fungi from the A. vagum-fertilized rice roots to confirm the probiotic's functions. Among them, 5 Lactobacillus strains and 2 Nigrospora strains possessed significantly inhibitive activity on rice blast pathogen Magnaporthe oryzae. Additionally, 3 fungal strains in Sarocladium and Nigrospora genera promoted rice growth. Mutualistic mechanisms of A. vagum-rice were uncovered by the LC-MS/MS-based label-free quantitative assay. 13 secretory proteins of A. vagum cooperated to evade the host immune response and stimulate the symbiont resistance, such as alkaline phosphatases (ALP) as specific marker enzymes to symbiosis with the host and glycoside hydrolases (GHs) as effectors to colonize the host. Correspondingly, 206 rice proteins were induced to up-regulate, especially families of peroxidase (OsPRX), copper transporter (OsCOPT), and glutathione S-transferase (OsGSTU) related to growth and stress resistance. Conclusion: Our study verified that endophytic fungi isolated from wild rice had great practical value on cultivated rice. A. vagum reshaped the microbiota community of cultivated rice by enhancing host traits, as the first report of simplification and optimization effect of endophytic fungi on plant recruiting microbes, which offers novel perspectives on using endophytic fungi to increase agricultural productivity.

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A review on the impact of domestication of the rhizosphere of grain crops and a perspective on the potential role of the rhizosphere microbial community for sustainable rice crop production

Cited by 11 publications

References 72 publications

Functional immune boosters; the herb or its dead microbiome? Antigenic TLR4 agonist MAMPs found in 65 medicinal roots and algae’s

Functional immune boosters; the herb or its dead microbiome? Antigenic TLR4 agonist MAMPs found in 65 medicinal roots and algae’s

Rhizosphere functioning and rhizo-microbiome of two contrasting genotypes of rice under drought-induced conditions

Endophytic Acrocalymma vagum drives the microbiome variations for rice health

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