Enrichment of beneficial cucumber rhizosphere microbes mediated by organic acid secretion

Resistant cultivars have played important roles in controlling Fusarium wilt disease,but the roles of rhizosphere interactions among different levels of resistant cultivars are still unknown.Here,two phenotypes of cucumber,one resistant and one with increased susceptibility to Fusarium oxysporum f.sp.cucumerinum(Foc),were grown in the soil and hydroponically,and then 16S rRNA gene sequencing and nontargeted metabolomics techniques were used to investigate rhizosphere microflora and root exudate profiles.Relatively high microbial community evenness for the Foc-susceptible cultivar was detected,and the relative abundances of Comamonadaceae and Xanthomonadaceae were higher for the Foc-susceptible cultivar than for the other cultivar.FishTaco analysis revealed that specific functional traits,such as protein synthesis and secretion,bacterial chemotaxis,and small organic acid metabolism pathways,were significantly upregulated in the rhizobacterial community of the Foc-susceptible cultivar.A machinelearning approach in conjunction with FishTaco plus metabolic pathway analysis revealed that four organic acids(citric acid,pyruvate acid,succinic acid,and fumarate)were released at higher abundance by the Foc-susceptible cultivar compared with the resistant cultivar,which may be responsible for the recruitment of Comamonadaceae,a potential beneficial microbial group.Further validation demonstrated that Comamonadaceae can be“cultured”by these organic acids.Together,compared with the resistant cultivar,the susceptible cucumber tends to assemble beneficial microbes by secreting more organic acids.

Functions of silicon in plant drought stress responses

Silicon(Si),the second most abundant element in Earth’s crust,exerts beneficial effects on the growth and productivity of a variety of plant species under various environmental conditions.However,the benefits of Si and its importance to plants are controversial due to differences among the species,genotypes,and the environmental conditions.Although Si has been widely reported to alleviate plant drought stress in both the Si-accumulating and nonaccumulating plants,the underlying mechanisms through which Si improves plant water status and maintains water balance remain unclear.The aim of this review is to summarize the morphoanatomical,physiological,biochemical,and molecular processes that are involved in plant water status that are regulated by Si in response to drought stress,especially the integrated modulation of Si-triggered drought stress responses in Si accumulators and intermediate-and excluder-type plants.The key mechanisms influencing the ability of Si to mitigate the effects of drought stress include enhancing water uptake and transport,regulating stomatal behavior and transpirational water loss,accumulating solutes and osmoregulatory substances,and inducing plant defense-associated with signaling events,consequently maintaining whole-plant water balance.This study evaluates the ability of Si to maintain water balance under drought stress conditions and suggests future research that is needed to implement the use of Si in agriculture.Considering the complex relationships between Si and different plant species,genotypes,and the environment,detailed studies are needed to understand the interactions between Si and plant responses under stress conditions.

Inaugural editorial:Soil Science and Environment

Soils are the key foundation of Earth's sustainability that drives biogeochemical cycling of nutrients,provides ecosystem functions and services including carbon sequestration,water retention and purification,toxic metal/organic pollutants immobilization and biodiversity conservation as well as landscape stabilization(Lehmann et al,2020).Soils protect physical habitats and provide biodiversity of underground biota also conditioning the physical environment for beautification of the landscape.Thus,the health of soil and environment is closely linked to One Health of global lives(Banerjee&van der Heijden,2022).Over the last decades,global soils have been at risk due to extensive soil degradation,along with climate change,biodiversity loss and environmental pollution(IPBES,2019).

Emerging contaminants:A One Health perspective

Environmental pollution is escalating due to rapid global development that often prioritizes human needs over planetary health.Despite global efforts to mitigate legacy pollutants,the continuous introduction of new substances remains a major threat to both people and the planet.In response,global initiatives are focusing on risk assessment and regulation of emerging contaminants,as demonstrated by the ongoing efforts to establish the UN’s Intergovernmental Science-Policy Panel on Chemicals,Waste,and Pollution Prevention.This review identifies the sources and impacts of emerging contaminants on planetary health,emphasizing the importance of adopting a One Health approach.Strategies for monitoring and addressing these pollutants are discussed,underscoring the need for robust and socially equitable environmental policies at both regional and international levels.Urgent actions are needed to transition toward sustainable pollution management practices to safeguard our planet for future generations.

Decreased nitrous oxide emissions associated with functional microbial genes under bio-organic fertilizer application in vegetable fields

Bio-organic fertilizers enriched with plant growth-promoting microbes(PGPMs)have been widely used in crop fields to promote plant growth and maintain soil microbiome functions.However,their potential effects on N_(2)O emissions are of increasing concern.In this study,an in situ measurement experiment was conducted to investigate the effect of organic fertilizer containing Trichoderma guizhouense(a plant growth-promoting fungus)on soil N_(2)O emissions from a greenhouse vegetable field.The following four treatments were used:no fertilizer(control),chemical fertilizer(NPK),organic fertilizer derived from cattle manure(O),and organic fertilizer containing T.guizhouense(O+T,referring to bio-organic fertilizer).The abundances of soil N cycling-related functional genes(amoA)from ammonium-oxidizing bacteria(AOB)and archaea(AOA),as well as nirS,nirK,and nosZ,were simultaneously determined using quantitative PCR(qPCR).Compared to the NPK plot,seasonal total N_(2)O emissions decreased by 11.7%and 18.7%in the O and O+T plots,respectively,which was attributed to lower NH_(4)^(+)-N content and AOB amoA abundance in the O and O+T plots.The nosZ abundance was significantly greater in the O+T plot,whilst the AOB amoA abundance was significantly lower in the O+T plot than in the O plot.Relative to the organic fertilizer,bio-organic fertilizer application tended to decrease N_(2)O emissions by 7.9%and enhanced vegetable yield,resulting in a significant decrease in yield-scaled N_(2)O emissions.Overall,the results of this study suggested that,compared to organic and chemical fertilizers,bio-organic fertilizers containing PGPMs could benefit crop yield and mitigate N_(2)O emissions in vegetable fields.

Effects of Local Nitrogen Supply on Water Uptake of Bean Plants in a Split Root System

To study the effects of local nitrogen supply on water and nutrient absorption, French bean （Phaseolus vulgaris L.） plants were grown in a split root system. Five treatments supplied with different nitrogen forms were compared： homogeneous nitrate （NN） and homogenous ammonium （AA） supply, spatially separated supply of nitrate and ammonium （NA）, half of the root system supplied with N-free nutrient solution, the other half with either nitrate （NO） or ammonium （AO）. The results showed that 10 d after onset of treatments, root dry matter （DM） in the nitratesupplied vessels treated with NA was more than two times higher than that in the ammonium-supplied vessels. Water uptake from the nitrate-supplied vessels treated with NA was 281% higher than under ammonium supply. In treatments NO and AO, the local supply of N resulted in clearly higher root DM, and water uptake from the nitratesupplied vessels was 82% higher than in the -N vessels. However, in AO plants, water uptake from the -N nutrient solution was 129% higher than from the ammonium-supplied vessels. This indicates a compensatory effect, which resulted in almost identical rates of total water uptake of treatments AA and AO, which had comparable shoot DM and leaf area. Ammonium supply reduced potassium and magnesium absorption. Water uptake was positively correlated with N, Mg and K uptake.

Rhizosphere immunity: targeting the underground for sustainable plant health management

Managing plant health is a great challenge formodern food production and is further complicated by thelack of common ground between the many disciplinesinvolved in disease control. Here we present the concept ofrhizosphere immunity, in which plant health is consideredas an ecosystem level property emerging from networks ofinteractions between plants, microbiota and the surround-ing soil matrix. These interactions can potentially extendthe innate plant immune system to a point where therhizosphere immunity can fulfil all four core functions ofafull immune system: pathogen prevention, recognition,response and homeostasis. We suggest that consideringplant health from a meta-organism perspective will help indeveloping multidisciplinary pathogen management stra-tegies that focus on steering the whole plant-microbe-soilnetworks instead of individual components. This might beachieved by bringing together the latest discoveries inphytopathology, microbiome research, soil science andagronomy to pave the way toward more sustainable andproductive agriculture.

Root exudates mediate plant defense against foliar pathogens by recruiting beneficial microbes

Plants are capable of releasing specific root exudates to recruit beneficial rhizosphere microbes upon foliar pathogen invasion attack,including long-chain fatty acids,amino acids,short-chain organic acids and sugars.Although long-chain fatty acids and amino acids application have been linked to soil legacy effects that improve future plant performance in the presence of the pathogen,the precise mechanisms involved are to a large extent still unknown.Here,we conditioned soils with long-chain fatty acids and amino acids application(L+A)or short-chain organic acids and sugars(S+S)to examine the direct role of such exudates on soil microbiome structure and function.The L+A treatment recruited higher abundances of Proteobacteria which were further identified as members of the genera Sphingomonas,Pseudomonas,Roseiflexus,and Flavitalea.We then isolated the enriched bacterial strains from these groups,identifying ten Pseudomonas strains that were able to help host plant to resist foliar pathogen infection.Further investigation showed that the L+A treatment resulted in growth promotion of these Pseudomonas strains.Collectively,our data suggest that long-chain fatty acids and amino acids stimulated by foliar pathogen infection can recruit specific Pseudomonas populations that can help protect the host plant or future plant generations.

The best practice for microbiome analysis using R

With the gradual maturity of sequencing technology,many microbiome studies have published,driving the emergence and advance of related analysis tools.R language is the widely used platform for microbiome data analysis for powerful functions.However,tens of thousands of R packages and numerous similar analysis tools have brought major challenges for many researchers to explore microbiome data.How to choose suitable,efficient,convenient,and easy-to-learn tools from the numerous R packages has become a problem for many microbiome researchers.We have organized 324 common R packages for microbiome analysis and classified them according to application categories(diversity,difference,biomarker,correlation and network,functional prediction,and others),which could help researchers quickly find relevant R packages for microbiome analysis.Furthermore,we systematically sorted the integrated R packages(phyloseq,microbiome,MicrobiomeAnalystR,Animalcules,microeco,and amplicon)for microbiome analysis,and summarized the advantages and limitations,which will help researchers choose the appropriate tools.Finally,we thoroughly reviewed the R packages for microbiome analysis,summarized most of the common analysis content in the microbiome,and formed the most suitable pipeline for microbiome analysis.This paper is accompanied by hundreds of examples with 10,000 lines codes in GitHub,which can help beginners to learn,also help analysts compare and test different tools.This paper systematically sorts the application of R in microbiome,providing an important theoretical basis and practical reference for the development of better microbiome tools in the future.All the code is available at GitHub github.com/taowenmicro/EasyMicrobiomeR.

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.

植物促生芽孢杆菌中新型脂肪酸通过两组分调控系统OmpS/R和毒素转运蛋白介导的“嗜食同类”机制促进生物被膜的形成

当单细胞繁殖进入多细胞水平时,为了应对环境压力,细菌必须进化出维持其群体稳定的作用机制.“嗜食同类”是芽孢杆菌应对环境营养缺乏的一种策略,维持了芽孢杆菌的生存.作为芽孢杆菌的模式种群,枯草芽孢杆菌的“嗜食同类”行为已被广泛研究,但其他芽孢杆菌的“嗜食同类”机制仍然未知.生物被膜是一种被胞外基质包裹的多细胞群体,维持细菌在自然环境中的生存.本研究报道了由贝莱斯芽孢杆菌SQR9合成的新型次级代谢物杆菌酸(bacillunoic acids,BAs)介导的“嗜食同类”行为及机制,以及它对菌株SQR9生物被膜形成的促进作用.菌株SQR9细胞群体分化为两个亚群,一个亚群合成BAs并通过两组分调控系统OmpS-OmpR激活相应免疫基因bnaAB的表达,而不能合成BAs的亚群对该物质敏感.因而,群体中合成BAs的亚群通过该物质裂解部分不合成BAs的同类,由此释放的胞外DNA促进了生物被膜的形成.该研究结果阐明了菌株SQR9群体中的一些细胞如何牺牲自己,从而使群体中其它细胞有更好的机会在环境中存活下来.因此,菌株SQR9群体受益于“嗜食同类”系统.

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.

Growth substrates alter aboveground plant microbial and metabolic properties thereby influencing insect herbivore performance

The gut microbiome of plant-eaters is affected by the food they eat,but it is currently unclear how the plant metabolome and microbiome are influenced by the substrate the plant grows in and how this subsequently impacts the feeding behavior and gut microbiomes of insect herbivores.Here,we use Plutella xylostella caterpillars and show that the larvae prefer leaves of cabbage plants growing in a vermiculite substrate to those from plants growing in conventional soil systems.From a plant metabolomics analysis,we identified 20 plant metabolites that were related to caterpillar feeding performance.In a bioassay,the effects of these plant metabolites on insects'feeding were tested.Nitrate and compounds enriched with leaves of soilless cultivation promoted the feeding of insects,while compounds enriched with leaves of plants growing in natural soil decreased feeding.Several microbial groups(e.g.,Sporolactobacillus,Haliangium)detected inside the plant correlated with caterpillar feeding performance and other microbial groups,such as Ramlibacter and Methylophilus,correlated with the gut microbiome.Our results highlight the role of growth substrates on the food metabolome and microbiome and on the feeding performance and the gut microbiome of plant feeders.It illustrates how belowground factors can influence the aboveground properties of plant-animal systems,which has important implications for plant growth and pest control.

The bZIP transcription factor ATF1 regulates blue light and oxidative stress responses in Trichoderma guizhouense

In several filamentous fungi,incident light and environmental stress signaling share the mitogen-activated protein kinase(MAPK)HOG(SAK)pathway.It has been revealed that short-term illumination with blue light triggers the activation of the HOG pathway in Trichoderma spp.In this study,we demonstrate the crucial role of the basic leucine zipper transcription factor ATF1 in blue light responses and signaling downstream of the MAPK HOG1 in Trichoderma guizhouense.The lack of ATF1 severely impaired photoconidiation and delayed vegetative growth and conidial germination.Upon blue light or H2O2 stimuli,HOG1 interacted with ATF1 in the nucleus.Genome-wide transcriptome analyses revealed that 61.8%(509 out of 824)and 85.2%(702 out of 824)of blue light-regulated genes depended on ATF1 and HOG1,respectively,of which 58.4%(481 out of 824)were regulated by both of them.Our results also show that blue light promoted conidial germination and HOG1 and ATF1 played opposite roles in controlling conidial germination in the dark.Additionally,the lack of ATF1 led to reduced oxidative stress resistance,probably because of the downregulation of catalase-encoding genes.Overall,our results demonstrate that ATF1 is the downstream component of HOG1 and is responsible for blue light responses,conidial germination,vegetative growth,and oxidative stress resistance in T.guizhouense.

The relative importance of soil moisture in predicting bacterial wilt disease occurrence

Soil-borne plant diseases cause major economic losses globally.This is partly because their epidemiology is difficult to predict in agricultural fields,where multiple environmental factors could determine disease outcomes.Here we used a combination of field sampling and direct experimentation to identify key abiotic and biotic soil properties that can predict the occurrence of bacterial wilt caused by pathogenic Ralstonia solanacearum.By analyzing 139 tomato rhizosphere soils samples isolated from six provinces in China,we first show a clear link between soil properties,pathogen density and plant health.Specifically,disease outcomes were positively associated with soil moisture,bacterial abundance and bacterial community composition.Based on soil properties alone,random forest machine learning algorithm could predict disease outcomes correctly in 75%of cases with soil moisture being the most significant predictor.The importance of soil moisture was validated causally in a controlled greenhouse experiment,where the highest disease incidence was observed at 60%of maximum water holding capacity.Together,our results show that local soil properties can predict disease occurrence across a wider agricultural landscape,and that management of soil moisture could potentially offer a straightforward method for reducing crop losses to R.solanacearum.

Compositional variations of active autotrophic bacteria in paddy soils with elevated CO_(2) and temperature

Global warming is an increasingly serious ecological problem,we examined how the active autotrophic microbes in paddy soils respond to the elevated CO_(2) and temperature.Here we employed stable isotope probing(SIP)to label the active bacteria using the soil samples from a fully factorial Simulated Climate Change(SCC)field experiment where soils were exposed to ambient CO_(2) and temperature,elevated temperature,elevated CO_(2),and both elevated CO_(2) and temperature.Around 28.9% of active OTUs belonged to ammonia-oxidizing bacteria(AOB)and nitrite-oxidizing bacteria(NOB).Nitrosospira taxa was dominant in all soils and 80.4% of carbon-fixing bacteria under elevated temperature were classified as Nitrosomonas nitrosa.While no labeled NOBs were detected when temperature or CO_(2) were elevated independently,diverse NOBs were detected in the ambient conditions.We found that elevated CO_(2) and temperature had contrasting effects on microbial community composition,while relatively small changes were observed when CO_(2) and temperature were elevated simultaneously.Summarily these results suggest that carbon-fixing bacteria can respond positively to elevated CO_(2) concentrations,but when it’s accompanied with increase in the temperature this positive response could be weakened.Multiple abiotic factors thus need to be considered when predicting how microbial communities will respond to multiple climatic factors.

Effect of bacterial intra-species community interactions on the production and activity of volatile organic compounds

Microorganisms experience intra-and inter-species interactions in the soil,and how these interactions affect the production of microbial volatile organic compounds(VOCs)is still not well-known.Here we evaluated the production and activity of microbial VOCs as driven by bacterial intra-species community interactions.We set up bacterial communities of increasing biodiversity out of 1–4 strains each of the Gram-positive Bacillus and Gram-negative Pseudomonas genera.We evaluated the ability of each community to provide two VOCmediated services,pathogen suppression and plant-growth promotion and then correlated these services to the production of VOCs by each community.The results showed that an increase in community richness from 1 to 4 strains of both genera increased VOC-mediated pathogen suppression and plant-growth promotion on agar medium and in the soil,which was positively correlated with the production of pathogen suppressing and plant growth-promoting VOCs.Pseudomonas strains maintained while Bacillus strains reduced community productivity with an increase in community richness and produced eight novel VOCs compared with the monocultures.These results revealed that intra-species interactions may vary between Gram-negative and Gram-positive species but improved VOC-mediated functioning with respect to pathogen suppression and plant-growth promotion by affecting the amount and diversity of produced VOCs potentially affecting plant disease outcomes.

Healthy soils for sustainable food production and environmental quality

Soil is the foundation for sustainable foodproduction and environmental protection. Created byunsustainable land management practices and a range ofsocial, economic and environmental drivers, soil degrada-tion and pollution have been an ongoing threat tointernational food security and environmental quality.Soil degradation and pollution assessments are, however,often focused on the soil itself with little scope to devisenew soil management approaches that match foodproduction systems and/or environmentalprotection.This study draws lessons from an Australia-China JointResearch Center Program, Healthy Soils for SustainableFood Production and Environmental Quality: a researchplatform that has brought together multi-disciplinaryapproaches fromworld-renowned universitiesandresearch organizations in Australia and China. To thisend, a framework is presented for future soil managementin a new way that combines excellence in research,industry and policymakers in a partnership that will ensurenot only the right focus of the research but also that high-quality outputs will be transferable to industry and end-users.

Changes in bulk soil affect the disease-suppressive rhizosphere microbiome against Fusarium wilt disease

Harnessing disease suppressive microbiomes constitutes a promising strategy for optimizing plant growth.However,relatively lttle information is available about the relationship between bulk and rhizosphere soil microbiomes.Here,the assembly of banana bulk soil and rhizosphere microbiomes was investigated in a mono-culture system consisting of bio-organic(BIO)and organic management practices.Applying BIO practice in newly reclaimed fields resulted in a high-efficiency biocontrol rate,thus providing a promising strategy for pre-control of Fusarium wilt disease.The soil microbiota was further characterized by MiSeq sequencing and quantitative PCR.The results indicate that disease suppression was mediated by the structure of a suppressive rhizosphere microbiome with respect to distinct community composition,diversity and abundance.Overall microbiome suppressiveness was primarily related to a particular set of enriched bacterial taxa affiliated with Pseudomonas,Terrimonas,Cupriavi-dus,Gp6,Ohtaekwangia and Duganella.Finally,struc-tural equation modeling was used to show that the changes in bulk soil bacterial community determined its induced rhizosphere bacterial community,which serves as an important and direct factor in restraining the pathogen.Collectively,this study provides an integrative approach to disentangle the biological basis of disease-suppressive microbiomes in the context of agricultural practice and soil management.

Microbial diversity assembled from series-diluted suspensions of disease-suppressive soil determines pathogen invasion resistance

Dear Editor,Soil microbial biodiversity loss caused by agricultural intensification, climate change, and the application of chemical fertilizer has become a serious problem that threatens humans (Wall et al., 2015). One phenomenon responsible for economic and food security issues is soil-borne diseases(Fisher et al., 2012), which were reported to be associated with microbial diversity loss (Shen et al., 2013;Fu et al.,2017).