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.

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.

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.

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.

Loss of two families of SPX domain-containing proteins required for vacuolar polyphosphate accumulation coincides with the transition to phosphate storage in green plants

Phosphorus is an essential nutrient for plants.It is stored as inorganic phosphate(Pi)in the vacuoles of land plants but as inorganic polyphosphate(polyP)in chlorophyte algae.Although it is recognized that the SPX-Major Facilitator Superfamily(MFS)and VPE proteins are responsible for Pi influx and efflux,respectively,across the tonoplast in land plants,the mechanisms that underlie polyP homeostasis and the transition of phosphorus storage forms during the evolution of green plants remain unclear.In this study,we showed that CrPTCI,encoding a protein with both SPX and SLC(permease solute carrier 13)domains for Pi transport,and CrVTC4,encoding a protein with both SPX and vacuolar transporter chaperone(VTC)domains for polyP synthesis,are required for vacuolar polyP accumulation in the chlorophyte Chlamydomonas rein-hardtii.Phylogenetic analysis showed that the SPX-SLC,SPX-VTC,and SPX-MFS proteins were present in the common ancestor of green plants(Viridiplantae).The SPX-SLC and SPX-VTC proteins are conserved among species that store phosphorus as vacuolar polyP and absent from genomes of plants that store phosphorus as vacuolar Pi.By contrast,SPX-MFS genes are present in the genomes of streptophytes that store phosphorus as Pi in the vacuoles.These results suggest that loss of SPX-SLC and SPX-VTC genes and functional conservation of SPX-MFS proteins during the evolution of streptophytes accompanied the change from ancestral polyP storage to Pi storage.

Interspecific plant interaction via root exudates structures the disease suppressiveness of rhizosphere microbiomes

Terrestrial plants can affect the growth and health of adjacent plants via interspecific interaction.Here,we studied the mechanism by which plant root exudates affect the recruitment of the rhizosphere microbiome in adjacent plants—with implications for plant protection—using a tomato(Solanum lycopersicum)–potatoonion(Allium cepa var.agrogatum)intercropping system.First,we showed that the intercropping system results in a disease-suppressive rhizosphere microbiome that protects tomato plants against Verticillium wilt disease caused by the soilborne pathogen Verticillium dahliae.Second,16S rRNA gene sequencing revealed that intercropping with potatoonion altered the composition of the tomato rhizosphere microbiome by promoting the colonization of specific Bacillus sp.This taxon was isolated and shown to inhibit V.dahliae growth and induce systemic resistance in tomato plants.Third,a belowground segregation experiment found that root exudates mediated the interspecific interaction between potatoonion and tomato.Moreover,experiments using split-root tomato plants found that root exudates from potatoonion,especially taxifolin—a flavonoid compound—stimulate tomato plants to recruit plant-beneficial bacteria,such as Bacillus sp.Lastly,ultra-high-pressure liquid chromatography–mass spectrometry analysis found that taxifolin alters tomato root exudate chemistry;thus,this compound acts indirectly in modulating root colonization by Bacillus sp.Our results revealed that this intercropping system can improve tomato plant fitness by changing rhizosphere microbiome recruitment via the use of signaling chemicals released by root exudates of potatoonion.This study revealed a novel mechanism by which interspecific plant interaction modulates the establishment of a disease-suppressive microbiome,thus opening up new avenues of research for precision plant microbiome manipulations.

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.

Humic-Like Substances from Different Compost Extracts Could Significantly Promote Cucumber Growth

The effects of direct extracts of compost (DEC), aerated fermentation extracts of compost (AFEC) and non-aerated fermentation extracts of compost (NAFEC) on cucumber growth and the action mechanisms were evaluated based on the structure and activity analysis of humic-like substances. AFEC increased cucumber growth most significantly, followed by DEC and NAFEC, which was insignificant compared to the control treatment. Humic-like substances from compost extracts played an important role in promoting cucumber growth. Application of humic-like substances stimulated auxin-like activity and increased chlorophyll content and nitrogen accumulation in plants. The positive auxin-like activity of humic-like substances could be attributed to the relative distribution of special carbon groups, such as those with a large amount of peptidic and carbohydratic groups or with a low content of phenolic groups. In conclusion, the best growth promotion by application of AFEC was mainly attributed to the humic-like substances in the AFEC.

Root exudate chemistry affects soil carbon mobilization via microbial community reassembly

Plant roots are one of the major mediators that allocate carbon captured from the atmosphere to soils as rhizodeposits,including root exudates.Although rhizodeposition regulates both microbial activity and the biogeochemical cycling of nutrients,the effects of particular exudate species on soil carbon fluxes and key rhizosphere microorganisms remain unclear.By combining high-throughput sequencing,q-PCR,and NanoSIMS analyses,we characterized the bacterial community structure,quantified total bacteria depending on root exudate chemistry,and analyzed the consequences on the mobility of mineral-protected carbon.Using well-controlled incubation experiments,we showed that the three most abundant groups of root exudates(amino acids,carboxylic acids,and sugars)have contrasting effects on the release of dissolved organic carbon(DOC)and bioavailable Fe in an Ultisol through the disruption of organo-mineral associations and the alteration of bacterial communities,thus priming organic matter decomposition in the rhizosphere.High resolution(down to 50 nm)NanoSIMS images of mineral particles indicated that iron and silicon colocalized significantly more organic carbon following amino acid inputs than treatments without exudates or with carboxylic acids.The application of sugar strongly reduced microbial diversity without impacting soil carbon mobilization.Carboxylic acids increased the prevalence of Actinobacteria and facilitated carbon mobilization,whereas amino acid addition increased the abundances of Proteobacteria that prevented DOC release.In summary,root exudate functions are defined by their chemical composition that regulates bacterial community composition and,consequently,the biogeochemical cycling of carbon in the rhizosphere.

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.

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.

构巢曲霉硫代谢关键转录调控因子MetR严格调控光敏色素依赖型红光响应过程

真菌可以利用光敏色素(phytochrome)感受红光,在构巢曲霉中,光敏色素Fph A感受红光后激活下游压力响应Hog A/Sak A信号通路,控制相关基因的表达,最终抑制菌体有性生殖过程,促进菌体无性分生孢子的产生.构巢曲霉中转录调控因子Met R是调控硫代谢的关键因子.本研究发现,met R基因突变株不能表达光敏色素编码基因fph A.同时,与次级代谢产物合成相关的多个基因簇在met R基因突变株中出现显著的上调或下调.进一步研究发现,转录调控因子Met R通过严格调控光敏色素Fph A编码基因的表达控制Hog A/Sak A信号通路,进而调控菌体红光响应过程.本研究证明,构巢曲霉中硫代谢关键调控因子Met R是一个全局性调控因子,除调控硫代谢外,还可以严格调控菌体光响应和次级代谢等过程.