The Phragmites Root-Inhabiting Microbiome: A Critical Review on Its Composition and Environmental Application

As widespread wetland plants,Phragmites play a vital role in water purification and are widely utilized in constructed wetlands(accounting for 15.5%of applied wetland plants)as a natural alternative to wastewater treatment.However,despite such common applications,current understanding of the basic composition of the Phragmites root-inhabiting microbiome and the complex functions of each member of this microbiome remains incomplete,especially regarding pollution remediation.This review summa-rizes the advances that have been made in ecological and biochemical research on the Phragmites root microbiome,including bacteria,archaea,and fungi.Based on next-generation sequencing,microbial com-munity compositions have been profiled under various environmental conditions.Furthermore,culture-based methods have helped to clarify the functions of the microbiome,such as metal iron stabilization,organic matter degradation,and nutrient element transformation.The unique community structure and functions are highly impacted by Phragmites lineages and environmental factors such as salinity.Based on the current understanding of the Phragmites root microbiome,we propose that synthetic microbial com-munities and iron–manganese plaque could be applied and intensified in constructed wetlands to help promote their water purification performance.

Underground communication:Long non-coding RNA signaling in the plant rhizosphere

Long non-coding RNAs(lncRNAs)have emerged as integral gene-expression regulators underlying plant growth,development,and adaptation.To adapt to the heterogeneous and dynamic rhizosphere,plants use interconnected regulatory mechanisms to optimally fine-tune gene-expression-governing interactions with soil biota,as well as nutrient acquisition and heavy metal tolerance.Recently,high-throughput sequencing has enabled the identification of plant lncRNAs responsive to rhizosphere biotic and abiotic cues.Here,we examine lncRNA biogenesis,classification,and mode of action,highlighting the functions of lncRNAs in mediating plant adaptation to diverse rhizosphere factors.We then discuss studies that reveal the significance and target genes of lncRNAs during developmental plasticity and stress responses at the rhizobium interface.A comprehensive understanding of specific lncRNAs,their regulatory targets,and the intricacies of their functional interaction networks will provide crucial insights into how these transcriptomic switches fine-tune responses to shifting rhizosphere signals.Looking ahead,we foresee that single-cell dissection of cell-type-specific lncRNA regulatory dynamics will enhance our understanding of the precise developmental modulation mechanisms that enable plant rhizosphere adaptation.Overcoming future challenges through multi-omics and genetic approaches will more fully reveal the integral roles of lncRNAs in governing plant adaptation to the belowground environment.

Coupling of the chemical niche and microbiome in the rhizosphere:implications from watermelon grafting

Grafting is commonly used to overcome soilborne diseases. However, its effects on the rhizodeposits as well as the linkages between the rhizosphere chemical niche and microbiome remained unknown. In this paper,significant negative correlations between the bacterial alpha diversity and both the disease incidence(r = – 0.832,P = 0.005) and pathogen population(r = – 0.786, P = 0.012)were detected. Moreover, our results showed that the chemical diversity not only predicts bacterial alpha diversity but also can impact on overall microbial community structure(beta diversity) in the rhizosphere.Furthermore, some anti-fungal compounds including heptadecane and hexadecane were identified in the rhizosphere of grafted watermelon. We concluded that grafted watermelon can form a distinct rhizosphere chemical niche and thus recruit microbial communities with high diversity. Furthermore, the diverse bacteria and the antifungal compounds in the rhizosphere can potentially serve as biological and chemical barriers, respectively, to hinder pathogen invasion. These results not only lead us toward broadening the view of disease resistance mechanism of grafting, but also provide clues to control the microbial composition by manipulating the rhizosphere chemical niche.

RIN enhances plant disease resistance via root exudate-mediated assembly of diseasesuppressive rhizosphere microbiota

The RIPENING-INHIBITOR(RIN)transcriptional factor is a key regulator governing fruit ripening.While RIN also affects other physiological processes,its potential roles in triggering interactions with the rhizosphere microbiome and plant health are unknown.Here we show that RIN affects microbiome-mediated disease resistance via root exudation,leading to recruitment of microbiota that suppress the soil-borne,phytopathogenic Ralstonia solanacearum bacterium.Compared with the wild-type(WT)plant,RIN mutants had different root exudate profiles,which were associated with distinct changes in microbiome composition and diversity.Specifically,the relative abundances of antibiosis-associated genes and pathogensuppressing Actinobacteria(Streptomyces)were clearly lower in the rhizosphere of rin mutants.The composition,diversity,and suppressiveness of rin plant microbiomes could be restored by the application of 3-hydroxyflavone and riboflavin,which were exuded in much lower concentrations by the rin mutant.Interestingly,RIN-mediated effects on root exudates,Actinobacteria,and disease suppression were evident from the seedling stage,indicating that RIN plays a dual role in the early assembly of diseasesuppressive microbiota and late fruit development.Collectively,our work suggests that,while plant disease resistance is a complex trait driven by interactions between the plant,rhizosphere microbiome,and the pathogen,it can be indirectly manipulated using"prebiotic"compounds that promote the recruitment of disease-suppressive microbiota.

Insights into plant salt stress signaling and tolerance

Soil salinization is an essential environmental stressor,threatening agricultural yield and ecological security worldwide.Saline soils accumulate excessive soluble salts which are detrimental to most plants by limiting plant growth and productivity.It is of great necessity for plants to efficiently deal with the adverse effects caused by salt stress for survival and successful reproduction.Multiple determinants of salt tolerance have been identified in plants,and the cellular and physiological mechanisms of plant salt response and adaption have been intensely characterized.Plants respond to salt stress signals and rapidly initiate signaling pathways to re-establish cellular homeostasis with adjusted growth and cellular metabolism.This review summarizes the advances in salt stress perception,signaling,and response in plants.A better under-standing of plant salt resistance will contribute to improving crop performance under saline conditions using multiple engineering approaches.The rhizosphere microbiome-mediated plant salt tolerance as well as chemical priming for enhanced plant salt resistance are also discussed in this review.

Global-scale analysis reveals distinct patterns of non-ribosomal peptide and polyketide synthase encoding genes in root and soil bacterial communities

Secondary metabolites(SMs)produced by soil bacteria,for instance antimicrobials and siderophores,play a vital role in bacterial adaptation to soil and root ecosystems and can contribute to plant health.Many SMs are non-ribosomal peptides and polyketides,assembled by non-ribosomal peptides synthetase(NRPS)and polyketide synthase(PKS)and encoded by biosynthetic gene clusters(BGCs).Despite their ecological importance,little is known about the occurrence and diversity of NRPs and PKs in soil.We extracted NRPS-and PKS-encodiing BGCs from 20 publicly available soil and root-associated metagenomes and annotated them using antiSMASH-DB.We found that the overall abundance of NRPSs and PKSs is similar in both environments,however NRPSs and PKSs were significantly clustered between soil and root samples.Moreover,the majority of identified sequences were unique to either soil-or root-associated datasets and had low identity to known BGCs,suggesting their novelty.Overall,this study illuminates the huge untapped diversity of predicted SMs in soil and root microbiomes,and indicates presence of specific SMs,which may play a role in inter-and intra-bacteriial interactions in root ecosystems.

Potential of plant growth-promoting rhizobacteria-plant interactions in mitigating salt stress for sustainable agriculture:A review

Soil salinization affecting different crops is one of the serious threats to global food security.Soil salinity affects 20%and 33%of the total cultivated and irrigated agricultural lands,respectively,and has been reported to caused a global crop production loss of 27.3 billion USD.The conventional approaches,such as using salt-tolerant varieties,saline soil scrapping,flushing,leaching,and adding supplements (e.g.,gypsum and lime),often fail to alleviate stress.In this context,developing diverse arrays of microbes enhancing crop productivity under saline soil conditions without harming soil health is necessary.Various advanced omics approaches have enabled gaining new insights into the structure and metabolic functions of plant-associated beneficial microbes.Various genera of salt-tolerating rhizobacteria ameliorating biotic and abiotic stresses have been isolated from different legumes,cereals,vegetables,and oil seeds under extreme alkaline and saline soil conditions.Rapid progress in rhizosphere microbiome research has revived the belief that plants may be more benefited from their association with interacting diverse microbial communities as compared with individual members in a community.In the last decade,several salt-tolerating plant growth-promoting rhizobacteria (PGPR) that improve crop production under salt stress have been exploited for the reclamation of saline agrosystems.This review highlights that the interaction of salt-tolerating microbes with plants improves crop productivity under salinity stress along with potential salt tolerance mechanisms involved and will open new avenues for capitalizing on cultivable diverse microbial communities to strengthen plant salt tolerance and,thus,to refine agricultural practices and production under saline conditions.