Anthracnose drives assembly of phyllosphere epiphytic bacterial communities to increase disease resistance.

Plants can specifically assemble beneficial rhizosphere microbiota through the 'cry for help' mechanism triggered by non-pathogenic elicitors, thereby promoting plant health. However, it remains unknown whether non-pathogenic strains can be used to induce plants to form a rhizomicrobiome capable of resisting herbivores. Here, we investigated how tomatoes enhance their defense capacity via the 'cry for help' response triggered by the entomopathogenic fungus Beauveria bassiana. Our findings show that B. bassiana induces the formation of beneficial soil legacy in tomatoes, which significantly impacts the performance of whitefly (Bemisia tabaci) on tomatoes. Amplicon sequencing revealed a specific enrichment of Pseudomonas in the soil legacy. Supplementing soils with Pseudomonas isolates reduced whitefly performance on tomatoes and increased the whitefly-induced levels of salicylic acid (SA) and jasmonic acid (JA) in the plants. Moreover, metabolomic and in vitro experiments demonstrated that the increased abundance of rhizosphere Pseudomonas, induced by enhanced root exudation of o-anisic acid, is responsible for the pest-suppressive effect of the soil legacy. This research uncovers a 'cry for help' mechanism whereby tomatoes, through interactions with a non-pathogenic strain, reshape their rhizosphere microbiome to bolster defense. It also deepens our understanding of microbiota-mediated plant defense and offers insights for biological control of herbivores.

The contribution of host tissue location and sex to epiphytic bacterial community assembly of Sargassum thunbergii

Large amounts of epiphytic bacteria live on the leaf surfaces of submerged macrophytes in freshwater lakes. Despite their important roles in affecting host plant's health and biogeochemical cycling, knowledge about epiphytic bacteria assembly is not sufficient. We studied epiphytic bacteria on two cohabiting plant species in Taihu Lake, China. In comparison with plant identity and geographic distance, the plant-growing season played a prominent role in driving alpha and beta diversity (compositional variations) of epiphytic bacterial communities. Phylogeny-based null model analysis revealed that the growing season also drove the relative importance of deterministic versus stochastic processes underlying bacterial community assembly. In May when both plants start growth, the deterministic processes were most prominent, while in months later than June, the stochastic processes' effects increased substantially. In addition, we found a significant positive relationship between alpha diversity and compositional stochasticity, implying that stochastic processes may have great effects on the maintenance of diversity and functioning of epiphytic bacteria in aquatic ecosystems. In summary, the growing season overwhelmed plant identity and spatial site in shaping epiphytic bacterial communities in Taihu Lake, which may suggest new clues in understanding the dynamics of epiphytic communities and their roles in large shallow lacustrine ecosystems.

ABSTRACTPlants recruit beneficial microbes to enhance their ability to fight pathogens. However, the current understanding of microbial recruitment is largely limited to belowground systems (root exudates and the rhizosphere). It remains unclear whether the changes in leaf metabolites induced by infectious pathogens can actively recruit beneficial microbes to mitigate the growth of foliar pathogens. In this study, we integrated microbiome and metabolomic analyses to systematically explore the dynamics of phyllosphere fungal and bacterial communities and key leaf metabolites in two crabapple species (Malus sp. “Flame” and Malus sp. “Kelsey”) at six stages following infection with Gymnosporangium yamadae. Our results showed that the phyllosphere microbiome changed during lesion expansion, as highlighted by a reduction in bacterial alpha-diversity and an increase in fungal alpha-diversity; a decreasing and then an increasing complexity of the microbial co-occurrence network was observed in Kelsey and a decreasing complexity occurred in Flame. In addition, nucleotide sugars, diarylheptanoids, and carboxylic acids with aromatic rings were more abundant in early stages of collection, which positively regulated the abundance of bacterial orders Pseudomonadales (in Kelsey), Acidimicrobiales, Bacillales, and Flavobacteriales (in Flame). In addition, metabolites such as flavonoids, lignin precursors, terpenoids, coumarins, and quaternary ammonium salts enriched with the expansion of lesions had a positive regulatory effect on fungal families Rhynchogastremataceae and Golubeviaceae (in Flame) and the bacterial order Actinomycetales (in Kelsey). Our findings highlight that plants may also influence phyllosphere microorganisms by adjusting leaf metabolites in response to biotic stress.IMPORTANCE Our findings demonstrate the response patterns of bacterial and fungal communities in the Malus phyllosphere to rust fungus G. yamadae infection, and they also reveal how the phyllosphere microbiome changes with the expansion of lesions. We identified several metabolites whose relative abundance varied significantly with lesion expansion. Using a framework for assessing the role of leaf metabolites in shaping the phyllosphere microbiome of the two Malus species, we identified several specific metabolites that have profoundly selective effects on the microbial community. In conclusion, our study provides new evidence of the ecological niche of the phyllosphere in supporting the “cry for help” strategy for plants.

Epiphytic bacteria on the surfaces of submerged macrophytes play an important role in lake biodiversity and ecological processes. However, compared with planktonic bacteria, there is poor understanding of the community structure and function of epiphytic bacteria. Here, we used 16S rRNA gene high-throughput sequencing and functional prediction analysis to explore the structural and functional diversity of epiphytic bacteria and planktonic bacteria of a typical submerged macrophyte (Potamogeton lucens) in Caohai Lake. The results showed that the species composition of epiphytic and planktonic bacteria was highly similar as 88.89% phyla, 77.21% genera and 65.78% OTUs were shared by the two kinds of samples. Proteobacteria and Bacteroidetes were dominant phyla shared by the two kinds of communities. However, there are also some special taxa. Furthermore, the epiphytic bacterial communities exhibited significantly different structures from those in water, and the abundant OTUs had opposite constituents. The explained proportion of the planktonic bacterial community by aquatic environmental parameters is significantly higher than that of epiphytic bacteria, implying that the habitat microenvironment of epiphytic biofilms may be a strong driving force of the epiphytic bacterial community. Functional predictive analysis (Functional Annotation of Prokaryotic Taxa, FAPROTAX) found that epiphytic bacteria and planktonic bacteria are dominated by heterotrophic functions, but epiphytic bacteria have more prominent fermentation and denitrification functions (nitrate reduction, nitrate respiration, and nitrite respiration) than planktonic bacteria. This study has increased our understanding of the communities and functions of epiphytic bacteria on submerged macrophyte leaves, and their role in lake denitrification cannot be ignored.

沉水植物叶表附着大量细菌,与沉水植物构成了复杂的共生体系.叶片附着细菌是水生态的重要组成部分,能影响沉水植物自身生长和水体物质循环过程.目前,对于沉水植物多样性对植物叶片附着细菌群落的影响知之甚少.本研究比较了不同沉水植物物种多样性对浮游细菌和叶片附着细菌群落的影响,同时探究不同植物——苦草(Vallisneria natans)、穗状狐尾藻(Myriophyllum spicatum)、微齿眼子菜(Potamogeton maackianus)和黑藻(Hydrilla verticillata)叶片附着细菌的群落结构和多样性特征.结果表明,浮游细菌和叶片附着细菌的群落α多样性和β多样性具有显著差异.与单一植物物种体系相比,高植物物种多样性体系中植物叶片附着细菌群落α多样性较高.在高植物物种多样性体系中,黑藻叶片附着细菌群落的α多样性显著较高而β多样性显著较低,苦草叶片附着细菌群落的α多样性较低.沉水植物叶片附着细菌群落优势菌群属于变形菌门(Proteobacteria)和拟杆菌门(Bacteroidetes).高植物物种多样性体系中苦草的物种共现网络最具模块性.嗜甲基菌(g_Methylophilus)、红杆菌(f_Rhodobacter)、黄杆菌(g_Flavobacterium)是物种共现网络的关键物种.本文研究植物物种多样性对淡水湖泊细菌群落结构的影响,并强调宿主植物对附着细菌群落的重要选择作用,加深对细菌群落在水生植物叶片定殖机制的理解.;Epiphytic bacteria, adhering to the leaf surface of aquatic submerged macrophytes, develop a complex symbiotic relationship with submerged macrophytes. Epiphytic bacteria are an important component of the aquatic ecosystem, which can affect not only the growth of submerged macrophytes but also the nutrient cycling in aquatic ecosystems. Currently, the effect of submerged macrophyte diversity on the epiphytic bacteria communities is far from well understood. This study compared the effects of submerged macrophyte on bacterioplankton and epiphytic bacterial communities, meanwhile explored the community structure and diversity of epiphytic bacterial communities on different macrophytes-Vallisneria natans,Myriophyllum spicatum, Potamogeton maackianus andHydrilla verticillata. The results showed that the α diversity and structure of planktonic bacterial communities were significantly different from those of the epiphytic bacterial communities. With the increase of submerged macrophyte diversity, the α diversity of epiphytic bacterial communities increased slightly. In the systems with high submerged macrophyte diversity, significantly higher α diversity and lower β diversity were found for the epiphytic bacterial community on H. verticillata. Bacteroidetes and Proteobacteria were dominant phyla on the submerged macrophyte leaves. Co-occurrence network analysis revealed that the modularity value of V. natans epiphytic bacterial network was relatively high. Methylophilus, Rhodobacter andFlavobacterium were core species in the co-occurrence networks. This study demonstrated the effect of submerged macrophytes on bacterial community structure in freshwater lakes, emphasizing the importance of host-specific selection for epiphytic bacterial communities, and deepening our understanding of the mechanism of bacterial colonization on submerged macrophytes.

In shallow macrophytic lakes, epiphytic biofilms are formed on the surface of submerged plant stems and leaves because of algae and bacterial accumulation. Epiphytic biofilms significantly impact the health of the host vegetation and the biogeochemical cycling of lake elements. However, community diversity, species interactions, and community assembly mechanisms in epiphytic bacterial communities (EBCs) of plants during different growth periods are not well understood. We investigated the successional dynamics, co-occurrence patterns, and community assembly processes of epiphytic biofilm bacterial communities of submerged plants, Najas marina and Potamogeton lucens, from July to November 2020. The results showed a significant seasonal variation in EBC diversity and richness. Community diversity and richness increased from July to November, and the temperature was the most important driving factor for predicting seasonal changes in EBC community structure. Co-occurrence network analysis revealed that the average degree and graph density of the network increased from July to November, indicating that the complexity of the EBC network increased. The bacterial community co-occurrence network was limited by temperature, pH, and transparency. The phylogeny-based null model analysis showed that deterministic processes dominated the microbial community assembly in different periods, increasing their contribution. In addition, we found that as the dominance of deterministic processes increased, the microbial co-occurrence links increased, and the potential interrelationships between species became stronger. Thus, the findings provide insights into the seasonal variability of EBC assemblage and co-occurrence patterns in lacustrine ecosystems.

Planktonic and epiphytic bacterial communities play an important role in wetland nitrogen pollutant removal and water purification, yet their community dynamics are far from understood compared with those of the wetland soil bacterial community. Taking the planktonic bacterial community in the Yuguqiao constructed wetland and the epiphytic bacterial community on the leaf surface of the common submerged plant Vallisneria natans as the research objects, the composition, structure, and functional diversity of planktonic and epiphytic bacterial communities were analyzed using high-throughput sequencing. The results showed that the compositions of the planktonic and epiphytic bacterial communities were significantly different, with more heterotrophic and denitrifying bacteria present in the epiphytic bacterial community than in the planktonic bacterial community. The α diversity of the planktonic bacterial community was significantly different among the three sampling sites but not in the epiphytic bacterial community. In general, the OTU index and Shannon index of the epiphytic bacterial community were significantly higher than those of the planktonic bacterial community, and they had obvious spatial heterogeneity. RDA analysis showed that DO, IC, TP, NH+4, and TOC had important effects on the structural changes of both planktonic and epiphytic bacterial communities but had a greater impact on planktonic bacterial communities. Co-occurrence network analysis showed that the epiphytic bacterial community had more niche differentiation, a more stable network, and stronger resistance to external disturbance. The results of FAPROTAX functional prediction analysis showed that the nitrogen cycling, especially denitrification of the epiphytic bacterial community, was significantly greater than that of the planktonic bacterial community. The results of this study revealed the driving mechanism for maintaining the diversity of planktonic and epiphytic bacterial communities, which can provide a scientific basis for excavating and utilizing planktonic and epiphytic bacterial community resources in the construction of constructed wetlands to improve the efficiency of water purification.

Leaves harbor distinct microbial communities that can have an important impact on plant health and microbial ecosystems worldwide. Nevertheless, the ecological processes that shape the composition of leaf microbial communities remain unclear, with previous studies reporting contradictory results regarding the importance of bacterial dispersal versus host selection. This discrepancy could be driven in part because leaf microbiome studies typically consider the upper and lower leaf surfaces as a single entity despite these habitats possessing considerable anatomical differences. We characterized the composition of bacterial phyllosphere communities from the upper and lower leaf surfaces across 24 plant species. Leaf surface pH and stomatal density were found to shape phyllosphere community composition, and the underside of leaves had lower richness and higher abundances of core community members than upper leaf surfaces. We found fewer endemic bacteria on the upper leaf surfaces, suggesting that dispersal is more important in shaping these communities, with host selection being a more important force in microbiome assembly on lower leaf surfaces. Our study illustrates how changing the scale in which we observe microbial communities can impact our ability to resolve and predict microbial community assembly patterns on leaf surfaces. IMPORTANCE Leaves can harbor hundreds of different bacterial species that form unique communities for every plant species. Bacterial communities on leaves are really important because they can, for example, protect their host against plant diseases. Usually, bacteria from the whole leaf are considered when trying to understand these communities; however, this study shows that the upper and lower sides of a leaf have a very different impact on how these communities are shaped. It seems that the bacteria on the lower leaf side are more closely associated with the plant host, and communities on the upper leaf side are more impacted by immigrating bacteria. This can be really important when we want to treat, for example, crops in the field with beneficial bacteria or when trying to understand host-microbe interactions on the leaves.

The rhizosphere and the phyllosphere represent two different epiphytic compartments of host plant, which are closely related to plant growth, health, and productivity. However, the understanding of the diversity, composition, and assembly of the bacterial communities in different epiphytic microenvironments of large emerged macrophytes has remained elusive, especially the abundant and rare taxa across rhizosphere and phyllosphere communities. In this study, we collected samples of two different epiphytic compartments (rhizosphere and phyllosphere) of Phragmites australis. Both 16S rRNA gene-based high-throughput sequencing and null-model analysis were employed to determine the difference in the composition and assembly of above-mentioned epiphytic bacterial communities. Our results indicated that bacterial communities of rhizosphere exhibited higher diversity and richness than those of phyllosphere. Deterministic processes dominated the assembly of bacterial community in both compartments, and stochastic processes contributed a certain proportion (30.30%) in the assembly of phyllosphere bacterial community. We also found that rare taxa contributed more significantly to the alpha- and beta-diversity of bacterial community than those of abundant taxa. The obtained data are useful for better understanding the bacterial community of different epiphytic compartments of P. australis.

The short-term effects of ocean acidification on the epiphytic bacterial community of Sargassum thunbergii via high-throughput sequencing.

Root microbiota have a significant effect on plant health. However, the role of root microbiota in the resistance of Rhododendron against root rot is not known. In this study, we employed amplicon 16S and ITS sequencing to investigate the bacterial and fungal communities associated with four distinct niches (bulk soil, rhizosphere, rhizoplane, and endosphere) of both healthy and diseased Rhododendron plants in the Baili Rhododendron nature reserve in China. The amplicon data analysis identified 182 bacterial genera and 141 fungal genera that were impacted by root rot across all niches. Specifically, the rhizoplane appeared to exert a selective gating effect, resulting in a reduction in the complexity of bacterial communities, but not fungal communities, in wild Rhododendron delavayi Franch roots. Nevertheless, the stress induced by root rot led to alterations in the root microbiota and compromised the gating function of the rhizoplane, thereby significantly increasing the complexity of the bacterial community within the plant root. In the root tissue following root rot outbreak, the relative abundance of the pathogenic species Pezicula brunnea and Diaporthe helianthi was enriched by as much as 6.13% and 1.71%, respectively. These findings provide novel insights into the contribution of enrichment of root-associated microbiota to wild plant hosts under the disease stress of root rot. The root rot-causing pathogenic fungi may interact with beneficial bacteria and induce plants to send out “cry for help” signals, which may encourage the specific assembly of microbiota. In the Rhododendron delavayi Franch root microbiota, we found 23 potentially beneficial microbes. Notably, certain beneficial bacteria, such as Sporolactobacillus and Stenotrophomonas, were found to accumulate in the rhizoplane and endosphere under root rot disease stress. Overall, our results lend support to our hypothesis that Rhododendron recruits protective microbes as a strategy to suppress root rot outbreaks. Future endeavors in isolating beneficial microbes capable of mitigating root rot have the potential to enhance plant resilience against root diseases.

Background Plants are exposed to diverse abiotic and biotic stressors during their lifecycle, including flooding and insect herbivory. To mitigate stressors, plants utilize several “cry for help” strategies, including producing volatile organic compounds (VOCs) aboveground and modifying microbial communities belowground. Although we have built strong understanding of plants “cry for help” strategies to individually occurring stressors, our knowledge about how these strategies are impacted by simultaneously-occurring stressors remains limited. Aims We examined the effects of flooding, insect herbivory, and their combination on aboveground VOC emissions and belowground rhizosphere bacterial and fungal communities and assessed how soil source influences these “cry for help” plant strategies. Methods In a greenhouse experiment, tomato plants grown in four soils sourced from different locations were subjected to treatments representing a full factorial combination of ± flooding and ± herbivory by Manduca sexta. VOCs were collected using the solid phase micro-extraction (SPME) technique, and plant growth parameters were recorded. Soil physicochemical characteristics were examined. Bacterial and fungal rhizosphere community changes were assessed using 16S rRNA amplicon sequencing and sequencing of the fungal ITS2 region respectively. Results Flooding was the primary driver of VOC emissions. The stress combination of flooding and insect herbivory significantly increased total VOCs. Soil characteristics, particularly iron, manganese, and ammonium nitrogen shaped VOCs profiles. Belowground, soil source was the dominant factor shaping bacterial and fungal communities. Conclusion Interactions between soil source, flooding, and insect herbivory shape above and belowground tomato plant “cry for help” strategies.

Rhizomicrobiome plays important roles in plant growth and health, contributing to the sustainable development of agriculture. Plants recruit and assemble the rhizomicrobiome to satisfy their functional requirements, which is widely recognized as the 'cry for help' theory, but the intrinsic mechanisms are still limited. In this study, we revealed a novel mechanism by which plants reprogram the functional expression of inhabited rhizobacteria, in addition to the de novo recruitment of soil microbes, to satisfy different functional requirements as plants grow. This might be an efficient and low-cost strategy and a substantial extension to the rhizomicrobiome recruitment theory. We found that the plant regulated the sequential expression of genes related to biocontrol and plant growth promotion in two well-studied rhizobacteria Bacillus velezensis SQR9 and Pseudomonas protegens CHA0 through root exudate succession across the plant developmental stages. Sixteen key chemicals in root exudates were identified to significantly regulate the rhizobacterial functional gene expression by high-throughput qPCR. This study not only deepens our understanding of the interaction between the plant-rhizosphere microbiome, but also provides a novel strategy to regulate and balance the different functional expression of the rhizomicrobiome to improve plant health and growth.

Soil microbial communities are crucial in ecosystem-level decomposition and nutrient cycling processes and are sensitive to climate change in peatlands. However, the response of the vertical distribution of microbial communities to warming remains unclear in the alpine peatland. In this study, we examined the effects of warming on the vertical pattern and assembly of soil bacterial and fungal communities across three soil layers (0–10, 10–20, and 20–30 cm) in the Zoige alpine peatland under a warming treatment. Our results showed that short-term warming had no significant effects on the alpha diversity of either the bacterial or the fungal community. Although the bacterial community in the lower layers became more similar as soil temperature increased, the difference in the vertical structure of the bacterial community among different treatments was not significant. In contrast, the vertical structure of the fungal community was significantly affected by warming. The main ecological process driving the vertical assembly of the bacterial community was the niche-based process in all treatments, while soil carbon and nutrients were the main driving factors. The vertical structure of the fungal community was driven by a dispersal-based process in control plots, while the niche and dispersal processes jointly regulated the fungal communities in the warming plots. Plant biomass was significantly related to the vertical structure of the fungal community under the warming treatments. The variation in pH was significantly correlated with the assembly of the bacterial community, while soil water content, microbial biomass carbon/microbial biomass phosphorous (MBC/MBP), and microbial biomass nitrogen/ microbial biomass phosphorous (MBN/MBP) were significantly correlated with the assembly of the fungal community. These results indicate that the vertical structure and assembly of the soil bacterial and fungal communities responded differently to warming and could provide a potential mechanism of microbial community assembly in the alpine peatland in response to warming.