Microbial dynamics and interactions in the spermosphere

Soil Bacterial Diversity and Community Structure of Cotton Rhizosphere under Mulched Drip-Irrigation in Arid and Semi-arid Regions of Northwest China

Xinjiang is situated in an arid and semi-arid region, where abundant heat and sunlight create highly favorable conditions for cotton cultivation. Xinjiang's cotton output accounts for nearly one-quarter of global production. Moreover, the implementation of advanced planting techniques, such as 'dwarfing, high-density, early-maturing' strategies combined with mulched drip irrigation, ensures stable and high yields in this region. Despite these advancements, limited research has focused on the microbial mechanisms in cotton fields employing these advanced planting methods. In this study, high-throughput sequencing technology was utilized to investigate the diversity and composition of bacterial and phoD (Alkaline phosphatases encoding gene) communities in the rhizosphere of cotton grown under different yield levels in Xinjiang Province, China. The Mantel test, redundancy analysis (RDA) and partial least squares path modeling (PLS-PM) were employed to explore the interactions between soil bacterial and phoD communities, their network structures, and environmental factors. The bacterial and phoD communities in the cotton rhizosphere were predominantly composed of nine bacterial phyla (i.e., Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, Chloroflexi, Bacteroidetes, Rokubacteria, Firmicutes, and Nitrospirae) and five phoD phyla (i.e., Proteobacteria, Actinobacteria, Planctomycetes, Acidobacteria, and Firmicutes), respectively. Alpha diversity analysis indicated that the medium yield cotton field (MYF) exhibited higher bacterial richness and diversity indices compared to low yield (LYF) and high yield (HYF) fields. The symbiotic network analysis of LYF revealed greater values of average degree, number of edges, and modularity, suggesting a more complex network structure in both bacterial and phoD communities. The Mantel test, RDA, and PLS-PM model identified soil pH, electrical conductivity (EC), organic phosphorus (OP), available phosphorus (AP), total nitrogen (TN), microbial biomass carbon (MBC), and clay content as the main driving factors influencing changes in the rhizosphere bacterial community diversity and network structure. These findings provide a theoretical basis for future research aimed at improving soil quality and cotton yield.

Decoding endosperm endophytes in Pinus armandi: a crucial indicator for host response to climate change

BACKGROUND

Plant-associated microorganisms significantly contribute to plant survival in diverse environments. However, limited information is available regarding the involvement of endophytes in responding to climate change and their potential to enhance host plants' adaptation to future environmental shifts. Pinus armandi, endemic to China and widely distributed in climate-sensitive regions, serves as an ideal subject for investigating microbiome interactions that assist host plants in climate change response. Despite this, a comprehensive understanding of the diversity, community composition, and factors influencing endosperm endophytes in P. armandi, as well as the response of these endophytes to climate change, remains elusive.

RESULTS

In this study, transcriptome data from 55 P. armandi samples from 13 populations were analyzed to evaluate the composition and diversity of active endosperm endophytes and predict their response to future climate change. The results revealed variations in community composition, phylogenetic diversity, and interaction network between the northern and southern groups. Temperature and precipitation correlated with endosperm endophytic species richness and diversity. Under projected future climate conditions, the northern group exhibits greater genomic vulnerability and anticipates increased threats, reflecting a corresponding trend in endosperm endophytes, particularly within the Ascomycota community.

CONCLUSION

The consistent threat trend from climate change impacting both hosts and endophytes emphasizes the potential importance of host-related fungi as crucial indicators for predicting future climate impacts. Meanwhile, this study establishes an initial framework for exploring host-microbial interactions within the context of climate warming and provides valuable insights for studies related to plant protection.

Metagenomics and plant-microbe symbioses: Microbial community dynamics, functional roles in carbon sequestration, nitrogen transformation, sulfur and phosphorus mobilization for sustainable soil health

Biogeochemical cycles are fundamental processes that regulate the flow of essential elements such as carbon, nitrogen, and phosphorus, sustaining ecosystem productivity and global biogeochemical equilibrium. These cycles are intricately influenced by plant-microbe symbioses, which facilitate nutrient acquisition, organic matter decomposition, and the transformation of soil nutrients. Through mutualistic interactions, plants and microbes co-regulate nutrient availability and promote ecosystem resilience, especially under environmental stress. Metagenomics has emerged as a transformative tool for deciphering the complex microbial communities and functional genes driving these cycles. By enabling the high-throughput sequencing and annotation of microbial genomes, metagenomics provides unparalleled insights into the taxonomic diversity, metabolic potential, and functional pathways underlying microbial contributions to biogeochemical processes. Unlike previous reviews, this work integrates recent advancements in metagenomics with complementary omics approaches to provide a comprehensive perspective on how plant-microbe interactions modulate biogeochemical cycles at molecular, genetic, and ecosystem levels. By highlighting novel microbial processes and potential biotechnological applications, this review aims to guide future research in leveraging plant-microbe symbioses for sustainable agriculture, ecosystem restoration, and climate change mitigation.

Physicochemical properties and microbial community structure of the rhizosphere soil of Cymbidium tracyanum

To investigate the compositional characteristics of microbial communities in the rhizosphere soil of Cymbidium tracyanum (C. tracyanum) across different production regions in Tibet, as well as the correlation between these microorganisms and soil physicochemical factors, we analyzed soil microbial community composition in Bayi District, Chayu County, and Mêdog County in Linzhi City, Tibet, using Illumina MiSeq high-throughput sequencing technology. The results indicate that 7,467 bacterial operational taxonomic units (OTUs) and 2,866 fungal OTUs were identified in the rhizosphere soil of C. tracyanum. Significant differences were observed in the structural composition of bacterial and fungal communities across the different regions. The dominant bacterial phyla in the rhizosphere soil included Proteobacteria, Acidobacteria, Planctomycetota, and Firmicutes, while Ascomycota and Basidiomycota were the predominant fungal phyla. Additionally, variations in the physicochemical properties of the rhizosphere soil were observed among the different regions. Core microbiota analysis identified 214 core bacterial genera and 79 core fungal genera in the rhizosphere soil of C. tracyanum in Tibet. Correlation analysis revealed that changes in the core microbial community were associated with soil physicochemical factors to varying degrees, with total phosphorus and available phosphorus emerging as key factors influencing microbial diversity in the rhizosphere soil. In summary, the composition and diversity of bacterial and fungal communities in the rhizosphere soil of C. tracyanum varied across different production regions, and shifts in microbial community structure were closely linked to soil physicochemical factors.

Seed endophytes of malting barley from different locations are shaped differently and are associated with malt quality traits

Maximizing microbial functions for improving crop performance requires better understanding of the important drivers of plant-associated microbiomes. However, it remains unclear the forces that shapes microbial structure and assembly, and how plant seed-microbiome interactions impact grain quality. In this work, we characterized the seed endophytic microbial communities of malting barley from different geographical locations and investigated associations between microbial (bacterial and fungal) species diversity and malt quality traits. Host genotype, location, and interactions (genotype x location) significantly impacted the seed endophytic microbial communities. Taxonomic composition analysis identified the most abundant genera for bacterial and fungal communities to be Bacillus (belonging to phylum Firmicutes) and Blumeria (belonging to phylum Ascomycota), respectively. We observed that a greater proportion of bacterial amplicon sequence variants (bacterial ASVs) were shared across genotypes and across locations while the greater proportion of the fungal ASVs were unique to each genotype and location. Association analysis showed a significant negative correlation between bacterial alpha diversity indices (Faith PD and Shannon indices) and malt quality traits for barley protein (BP), free amino nitrogen (FAN), diastatic power (DP) and alpha amylase (AA), while fungal alpha diversity (Shannon and Simpson) showed significant negative relationship with β-D-glucan content. In addition, some bacterial and fungal genera were significantly associated with malt extract (ME) -a key trait for maltsters and brewers. We conclude that barley genotype, location, and their interactions shape the seed endophytic microbiome and is key to microbiome manipulation and management during barley production and/or malting.

Sowing success: ecological insights into seedling microbial colonisation for robust plant microbiota engineering

Manipulating the seedling microbiota through seed or soil inoculations has the potential to improve plant health. Mixed in-field results have been attributed to a lack of consideration for ecological processes taking place during seedling microbiota assembly. In this opinion article, we (i) assess the contribution of ecological processes at play during seedling microbiota assembly (e.g., propagule pressure and priority effects); (ii) investigate how life history theory can help us identify microbial traits involved in successful seedling colonisation; and (iii) suggest how different plant microbiota engineering methods could benefit from a greater understanding of seedling microbiota assembly processes. Finally, we propose several research hypotheses and identify outstanding questions for the plant microbiota engineering community.

Tetracycline but not sulfamethazine inhibits early root growth of wild grassland species, while seed germination is hardly affected by either antibiotic

Seed germination and early growth of grassland species might be influenced by veterinary antibiotics that are extensively released into agricultural habitats. Therefore, we tested impacts of the commonly used antibiotics tetracycline and sulfamethazine, single and in mixture, on seed germination and seedling root growth of six typical species of temperate European grasslands (Carum carvi, Centaurea jacea, Galium mollugo, Plantago lanceolata, Silene latifolia, Dactylis glomerata). In standardised germination experiments, we assessed three germination variables (germination percentage, mean germination time, synchrony of germination) and one post-germination variable (seedling root length) under different environmentally realistic antibiotic concentrations (0.1, 1, 10 mg l-1 and a water control). While the germination variables were only irregularly and weakly affected by both antibiotics, seedling root length was strongly reduced by tetracycline, but not by sulfamethazine. Among the test species, D. glomerata was most sensitive to tetracycline with the average root length reduced up to 81 % in the 10 mg l-1 treatment. Its germination behaviour, however, was almost insensitive to the two antibiotics. Mixture effects were only shown in relation to the germination of single species, where the binary mixture produced effects but not the two single antibiotics or, conversely, effects of single antibiotics were lost in the mixture. These findings highlight the potential threat of plant regeneration from seed by veterinary antibiotics, particularly affecting early root growth and potentially influencing plant population growth in natural habitats.

The contribution of beneficial wheat seed fungal communities beyond disease-causing fungi: Advancing heritable mycobiome-based plant breeding

Wheat (Triticum sp.) is a staple cereal crop, providing nearly a fifth of the world's protein and available calories. While fungi associated with wheat plants have been known for centuries, attention to fungi associated with wheat seeds has increased over the last hundred years. Initially, research focused on fungal taxa that cause seed-borne diseases. Seeds act as a physical link between generations and host specialized fungal communities that affect seed dormancy, germination, quality, and disease susceptibility. Interest in beneficial, non-disease-causing fungal taxa associated with seeds has grown since the discovery of Epichloë in fescue, leading to a search for beneficial fungal endophytes in cereal grains. Recent studies of the wheat seed mycobiome have shown that disease, seed development, and temporal variation significantly influence the composition and structure of these fungal communities. This research, primarily descriptive, aims to better understand the wheat seed mycobiome's function in relation to the plant host. A deeper understanding of the wheat seed mycobiome's functionality may offer potential for microbiome-assisted breeding.

Conservation and Dynamics of Maize Seed Endophytic Bacteria Across Progeny Transmission

Maize (Zea mays L.) is an important cereal crop species for food, feedstock and industrial material. Maize seeds host a suitable ecosystem for endophytic bacteria, facilitating seed germination and seedling growth. However, the inheritance, diversity and potential function of seed endophytic bacteria in maize remain largely unexplored. In this study, the endophytic bacteria in the seeds of maize inbred line WU109 collected during three consecutive seasons were identified using 16S rDNA sequencing. Core community composition was essentially consistent across three seed generations and two planting locations. In total, 212 operational taxonomic units (OTUs) belonging to 11 phyla were identified, among which proteobacteria was the dominant phylum. Fifty-six OTUs were conserved across three seed generations. Within them, 16 OTUs were core components and the dominant OTUs were Ralstonia solanacearum, Delftia tsuruhatensis, Bacillu svelezensis and Shigella boydii, accounting for 60% of the total abundance of OTUs. COG and KEGG analyses showed that the function of seed endophytic bacteria was mainly enriched in metabolic processes, especially in amino acid, carbohydrate and energy metabolism. Taken together, the results suggested that the community of maize seed endophytic bacteria was likely co-shaped by both genetic determination and the environment, while the core constitutes of seed endophytes were largely conserved due to transgenerational transmission. Establishing the mutualistic link between the maize seed and its endophytic bacteria enables the exploitation of the potential of endophytes for enhancing crop production. This finding provides a reference to better understand the inheritance and composition of seed core endophytic bacteria in maize.

Impact of thermal seed treatment on spermosphere microbiome, metabolome and viability of winter wheat

Thermal seed treatment can be used as an alternative method to prevent infection by seed-borne diseases, but exposure duration and temperature during thermal treatment are important to maintain high seed viability and emergence whilst decreasing infection rate. A method for predicting suitable treatment parameters to maintain viability and eliminate seed-borne pathogens is therefore needed. Seeds of winter wheat were subjected to thermal treatment at four levels of intensity and pre-treatments with or without imbibition. Treatment impact was measured by metabolome analysis using LC-MS and GC-MS, analysis of spermosphere bacterial and fungal metagenomes using Illumina MiSeq, and detection of presence of Fusarium spp. and Microdochium spp. using ddPCR. The results showed that moderate treatment intensity reduced signs of infection and increased seedling emergence. In imbibed samples, myo-inositol concentration and myo-inositol: glucose ratio were positively correlated with treatment intensity, whereas concentrations of glucose and citric acid were negatively correlated. No correlations were found for non-imbibed samples. Imbibition had a large significant impact on microbial community composition of the wheat spermosphere. Imbibition of wheat seeds prior to thermal treatment altered wheat spermosphere microbiota. The concentration of myo-inositol, potentially in combination with glucose, could be a candidate predictor for suitable thermal treatment intensity of wheat seeds.

Heterosis of endophytic microbiomes in hybrid rice varieties improves seed germination

Seed endophytic microbiomes are shaped by host and environmental factors and play a crucial role in their host growth and health. Studies have demonstrated that host genotype, including hybridization, affects seed microbiomes. Heterosis features are also observed in root-associated microbiomes. It remains unclear, however, whether heterosis exists in seed endophytic microbiomes and whether hybrid microbiota provide noticeable advantages to host plant growth, especially to seed germination. Here, we investigated the structure of seed endophytic bacterial and fungal communities from three hybrid rice varieties and their respective parents using amplicon sequencing targeting 16S rRNA and ITS2 genes. Heterosis was found in diversity and composition of seed endophytic microbiomes in hybrids, which hosted more diverse communities and significantly higher abundances of plant growth-promoting taxa, such as Pseudomonas and Rhizobium genera compared with their parental lines. Co-occurrence network analysis revealed that there are potentially tighter microbial interactions in the hybrid seeds compared with their parent seeds. Finally, inoculation of seed-cultivable endophytes, isolated from hybrids, resulted in a greater promotion of seed germination compared with those isolated from parent lines. These findings suggest that heterosis exists not only in plant traits but also in seed endophytic microbiota, the latter in turn promotes seed germination, which offers valuable guidance for microbiome-assisted rice breeding.IMPORTANCEGenetic and physiological changes associated with plant hybridization have been studied for many crop species. Still, little is known about the impact of hybridization on the seed microbiota. In this study, we indicate that hybridization has a significant impact on the endophytic bacterial and fungal communities in rice seeds. The seed endophytic microbiomes of hybrids displayed distinct characteristics from those of their parental lines and exhibited potential heterosis features. Furthermore, the inoculation of seed-cultivable endophytes isolated from hybrids exhibited a greater promotion effect on seed germination compared with those isolated from the parents. Our findings make a valuable contribution to the emerging field of microbiome-assisted plant breeding, highlighting the potential for a targeted approach that aims to achieve not only desired plant traits but also plant-beneficial microbial communities on the seeds.

Analysis of endophytic bacterial diversity in seeds of different genotypes of cotton and the suppression of Verticillium wilt pathogen infection by a synthetic microbial community

BACKGROUND

In agricultural production, fungal diseases significantly impact the yield and quality of cotton (Gossypium spp.) with Verticillium wilt posing a particularly severe threat.

RESULTS

This study is focused on investigating the effectiveness of endophytic microbial communities present in the seeds of disease-resistant cotton genotypes in the control of cotton Verticillium wilt. The technique of 16S ribosomal RNA (16S rRNA) amplicon sequencing identified a significant enrichment of the Bacillus genus in the resistant genotype Xinluzao 78, which differed from the endophytic bacterial community structure in the susceptible genotype Xinluzao 63. Specific enriched strains were isolated and screened from the seeds of Xinluzao 78 to further explore the biological functions of seed endophytes. A synthetic microbial community (SynCom) was constructed using the broken-rod model, and seeds of the susceptible genotype Xinluzao 63 in this community that had been soaked with the SynCom were found to significantly control the occurrence of Verticillium wilt and regulate the growth of cotton plants. Antibiotic screening techniques were used to preliminarily identify the colonization of strains in the community. These techniques revealed that the strains can colonize plant tissues and occupy ecological niches in cotton tissues through a priority effect, which prevents infection by pathogens.

CONCLUSION

This study highlights the key role of seed endophytes in driving plant disease defense and provides a theoretical basis for the future application of SynComs in agriculture.

Wild mushrooms as potential reservoirs of plant pathogenic bacteria: a case study on Burkholderia gladioli

Fruit bodies (sporocarps) of wild mushrooms growing in natural environments play a substantial role in the preservation of microbial communities, for example, clinical and food-poisoning bacteria. However, the role of wild mushrooms as natural reservoirs of plant pathogenic bacteria remains almost entirely unknown. Furthermore, bacterial transmission from a mushroom species to agricultural plants has rarely been recorded in the literature. In September 2021, a creamy-white Gram-negative bacterial strain was isolated from the sporocarp of Suillus luteus (slippery jack) growing in Bermuda grass (Cynodon dactylon) lawn in Southern Iran. A similar strain was isolated from the same fungus in the same area in September 2022. Both strains were identified as Burkholderia gladioli based on phenotypic features as well as phylogeny of 16S rRNA and three housekeeping genes. The strains were not only pathogenic on white button mushrooms (Agaricus bisporus) but also induced hypersensitive reaction (HR) on tobacco and common bean leaves and caused soft rot on a set of diverse plant species, that is, chili pepper, common bean pod, cucumber, eggplant, garlic, gladiolus, narcissus, onion, potato, spring onion, okra, kohlrabi, mango, and watermelon. Isolation of plant pathogenic B. gladioli strains from sporocarp of S. luteus in two consecutive years in the same area could be indicative of the role of this fungus in the preservation of the bacterium in the natural environment. B. gladioli associated with naturally growing S. luteus could potentially invade neighboring agricultural crops, for example, vegetables and ornamentals. The potential role of wild mushrooms as natural reservoirs of phytopathogenic bacteria is further discussed.IMPORTANCEThe bacterial genus Burkholderia contains biologically heterogeneous strains that can be isolated from diverse habitats, that is, soil, water, diseased plant material, and clinical specimens. In this study, two Gram-negative pectinolytic bacterial strains were isolated from the sporocarps of Suillus luteus in September 2021 and 2022. Molecular phylogenetic analyses revealed that both strains belonged to the complex species Burkholderia gladioli, while the pathovar status of the strains remained undetermined. Biological investigations accomplished with pathogenicity and host range assays showed that B. gladioli strains isolated from S. luteus in two consecutive years were pathogenic on a set of diverse plant species ranging from ornamentals to both monocotyledonous and dicotyledonous vegetables. Thus, B. gladioli could be considered an infectious pathogen capable of being transmitted from wild mushrooms to annual crops. Our results raise a hypothesis that wild mushrooms could be considered as potential reservoirs for phytopathogenic B. gladioli.

Seed-borne bacterial synthetic community resists seed pathogenic fungi and promotes plant growth

AIMS

In this study, the control effects of synthetic microbial communities composed of peanut seed bacteria against seed aflatoxin contamination caused by Aspergillus flavus and root rot by Fusarium oxysporum were evaluated.

METHODS AND RESULTS

Potentially conserved microbial synthetic communities (C), growth-promoting synthetic communities (S), and combined synthetic communities (CS) of peanut seeds were constructed after 16S rRNA Illumina sequencing, strain isolation, and measurement of plant growth promotion indicators. Three synthetic communities showed resistance to root rot and CS had the best effect after inoculating into peanut seedlings. This was achieved by increased defense enzyme activity and activated salicylic acid (SA)-related, systematically induced resistance in peanuts. In addition, CS also inhibited the reproduction of A. flavus on peanut seeds and the production of aflatoxin. These effects are related to bacterial degradation of toxins and destruction of mycelia.

CONCLUSIONS

Inoculation with a synthetic community composed of seed bacteria can help host peanuts resist the invasion of seeds by A. flavus and seedlings by F. oxysporum and promote the growth of peanut seedlings.

Seed-Borne Bacterial Diversity of Fescue (Festuca ovina L.) and Properties Study

Rich endophytic bacterial communities exist in fescue (Festuca ovina L.) and play an important role in fescue growth, cold tolerance, drought tolerance and antibiotic tolerance. To screen for probiotics carried by fescue seeds, seven varieties were collected from three different regions of China for isolation by the milled seed method and analyzed for diversity and motility, biofilm and antibiotic resistance. A total of 91 bacterial isolates were obtained, and based on morphological characteristics, 36 representative dominant strains were selected for 16S rDNA sequencing analysis. The results showed that the 36 bacterial strains belonged to four phyla and nine genera. The Firmicutes was the dominant phylum, and Bacillus, Paenibacillus and Pseudomonas were the dominant genera. Most of the strains had motility (80%) and were biofilm-forming (91.7%). In this study, 15 strains were capable of Indole-3-acetic acid (IAA) production, 24 strains were capable of nitrogen fixation, and some strains possessed amylase and protease activities, suggesting their potential for growth promotion. Determination of the minimum inhibitory concentration (MIC) against the bacteria showed that the strains were not resistant to tetracycline and oxytetracycline. Pantoea (QY6, LH4, MS2) and Curtobacterium (YY4) showed resistance to five antibiotics (ampicillin, kanamycin, erythromycin, sulfadiazine and rifampicin). Using Pearson correlation analysis, a significant correlation was found between motility and biofilm, and between biofilm and sulfadiazine. In this study, we screened two strains of Pantoea (QY6, LH4) with excellent growth-promoting ability as well as broad-spectrum antibiotic resistance. which provided new perspectives for subsequent studies on the strong ecological adaptations of fescue, and mycorrhizal resources for endophytic bacteria and plant interactions.

Revealing the seed microbiome: Navigating sequencing tools, microbial assembly, and functions to amplify plant fitness

Microbial communities within seeds play a vital role in transmitting themselves to the next generation of plants. These microorganisms significantly impact seed vigor and early seedling growth, for successful crop establishment. Previous studies reported on seed-associated microbial communities and their influence on processes like dormancy release, germination, and disease protection. Modern sequencing and conventional methods reveal microbial community structures and environmental impacts, these information helps in microbial selection and manipulation. These studies form the foundation for using seed microbiomes to enhance crop resilience and productivity. While existing research has primarily focused on characterizing microbiota in dried mature seeds, a significant gap exists in understanding how these microbial communities assemble during seed development. The review also discusses applying seed-associated microorganisms to improve crops in the context of climate change. However, limited knowledge is available about the microbial assembly pattern on seeds, and their impact on plant growth. The review provides insight into microbial composition, functions, and significance for plant health, particularly regarding growth promotion and pest control.

Vertical transfer and functional characterization of cotton seed core microbiome

Introduction

Microbiome within plant tissues is pivotal for co-evolution with host plants. This microbiome can colonize the plant, with potential transmission via seeds between parents and offspring, affecting seedling growth and host plant adaptability to the environment.

Methods

We employed 16S rRNA gene amplicon analysis to investigate the vertical distribution of core microbiome in cotton seeds across ecological niches [rhizosphere, root, stem, leaf, seed and seed-P (parental seed)] of the three cotton genotypes.

Results

The findings demonstrated a significant decrease in microbiome diversity and network complexity from roots, stems, and leaves to seeds. The microenvironment exerted a more substantial influence on the microbiome structure of cotton than the genotypes. The core endophytic microorganisms in cotton seeds comprised 29 amplicon sequence variants (ASVs) affiliated with Acidimicrobiia, Alphaproteobacteria, Bacilli, Bacteroidia, Clostridia, Gammaproteobacteria, and unclassified_Proteobacteria. These vertically transmitted taxa are widely distributed in cotton plants. Through 16S rRNA gene-based function prediction analysis of the cotton microbiome, we preliminarily understood that there are potential differences in metabolic capabilities and phenotypic traits among microbiomes in different microhabitats.

Discussion

In conclusion, this study demonstrated the crucial role of the microenvironment in influencing the cotton microbiome and offered insights into the structures and functions of the cotton seed microbiome, facilitating future crop yield enhancement through core seed microbiome regulation.

Effect of Infection Timing by Four Pythium spp. on Soybean Damping-Off Symptoms with and Without Cold Stress

Pythium spp. cause damping-off of soybean, especially when soil conditions at or shortly after planting are cool and wet. Soybean planting dates continue to shift to earlier dates, so germinating seed and seedlings are exposed to periods of cold stress at a time which favors infection by Pythium, and seedling disease occurs. The objective of this study was to assess infection timing and cold stress on soybean seedling disease severity caused by four Pythium spp. prevalent in Iowa, namely P. lutarium, P. oopapillum, P. sylvaticum, and P. torulosum. Each species was used individually to inoculate soybean cultivar 'Sloan' using a rolled towel assay. Two temperature treatments (continuous 18°C [C18]; a 48-h cold stress period at 10°C [CS]) were applied. Soybean seedling age was divided into five growth stages (GS1 to GS5). Root rot severity and root length were assessed at 2, 4, 7, and 10 days after inoculation (DAI). At C18, root rot was greatest when soybean was inoculated with P. lutarium or P. sylvaticum at GS1 (seed imbibes water) and with P. oopapillum or P. torulosum at GS1, GS2 (radicle elongation), and GS3 (hypocotyl emergence). After CS, soybean susceptibility to P. lutarium and P. sylvaticum was reduced compared to C18 for inoculation at all GSs except GS5 (unifoliate leaf emergence). Conversely, root rot by P. oopapillum and P. torulosum was greater after CS compared to C18. Data from this study demonstrate that greater root rot, and consequently more damping-off, is likely if infection occurs at early germination stages before seedling emergence.

Botrytis cinerea hypovirulent strain △BcSpd1 induced Panax ginseng defense

Background

Gray mold, caused by Botrytis cinerea, is one of the major fungal diseases in agriculture. Biological methods are preferred over chemical fungicides to control gray mold since they are less toxic to the environment and could induce the resistance to pathogens in plants. In this work, we try to understand if ginseng defense to B. cinerea could be induced by fungal hypovirulent strain △BcSpd1. BcSpd1 encodes Zn(II)2Cys6 transcription factor which regulates fungal pathogenicity and we recently reported △BcSpd1 mutants reduced fungal virulence.

Methods

We performed transcriptomic analysis of the host to investigate the induced defense response of ginseng treated by B. cinerea △BcSpd1. The metabolites in ginseng flavonoids pathway were determined by UPLC-ESI-MS/MS and the antifungal activates were then performed.

Results

We found that △BcSpd1 enhanced the ginseng defense response when applied to healthy ginseng leaves and further changed the metabolism of flavonoids. Compared with untreated plants, the application of △BcSpd1 on ginseng leaves significantly increased the accumulation of p-coumaric acid and myricetin, which could inhibit the fungal growth.

Conclusion

B. cinerea △BcSpd1 could effectively induce the medicinal plant defense and is referred to as the biological control agent in ginseng disease management.

Isolation and Identification of Endophytic Bacteria Bacillus sp. ME9 That Exhibits Biocontrol Activity against Xanthomonas phaseoli pv. manihotis

In recent years, the bacterial blight of cassava has caused substantial economic losses to the Chinese cassava industry. Chemical control methods have become the primary approach to control this disease; however, their widespread usage and harmful residues have raised concerns about environmental pollution. In order to avoid this, it is urgent to seek a green ecological method to prevent and control it. Biological control through the utilization of microorganisms not only effectively inhibits the disease, but also gives consideration to environmental friendliness. Therefore, investigating an endophytic biological control method for cassava bacterial blight is of great importance. In this study, cassava leaf tissues were used as test specimens in order to isolate endophytic bacteria by using dilution and separation methods. Bacillus ME9, derived from cassava endophytic bacteria, exhibits good antagonism against a diverse range of pathogens, including Xpm11. Its genome consists of a series of genes encoding antibacterial lipopeptides, which may be directly related to its antibacterial capabilities. Furthermore, inoculation resulted in a substantial change in the diversity of the endophytic bacterial community, characterized by improved diversity, and displayed an obvious inhibition of pathogenic bacterial growth, demonstrating successful colonization within plants. The results laid a foundation and provided theoretical support for the development and utilization of cassava endophytic bacterial diversity and endogenous disease control strategies.

Early inoculation of an endophyte alters the assembly of bacterial communities across rice plant growth stages

The core endophytes of plants are regarded as promising resources in future agroecosystems. How they affect the assembly of rice-related bacterial communities after early inoculation remains unclear. Here, we examined bacterial communities across 148 samples, including bulk and rhizosphere soils, sterilized roots, stems, and seeds at the seedling, tillering, booting, and maturity stages. Tissue cultured rice seedlings were inoculated with Xathomonas sacchari JR3-14, a core endophytic bacterium of rice seeds, before transplanting. The results revealed that α-diversity indices were significantly enhanced in the root and stem endosphere at the seedling stage. β-diversity was altered at most plant developmental stages, except for the root and stem at the booting stage. Network complexity consequently increased in the root and stem across rice growth stages, other than the stem endosphere at the booting stage. Four abundant beneficial bacterial taxa, Bacillus, Azospira, Azospirillum, and Arthrobacter, were co-enriched during the early growth stage. Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model analysis revealed a higher relative contribution of drift and other eco-evolutionary processes mainly in root compartments across all growth stages, but the opposite pattern was observed in stem compartments. IMPORTANCE Endophytic bacteria are regarded as promising environmentally friendly resources to promote plant growth and plant health. Some of microbes from the seed are able to be carried over to next generation, and contribute to the plant's ability to adapt to new environments. However, the effects of early inoculation with core microbes on the assembly of the plant microbiome are still unclear. In our study, we demonstrate that early inoculation of the rice seed core endophytic bacterium Xanthomonas sacchari could alter community diversity, enhance complexity degree of network structure at most the growth stages, and enrich beneficial bacteria at the seedling stage of rice. We further analyzed the evolutionary processes caused by the early inoculation. Our results highlight the new possibilities for research and application of sustainable agriculture by considering the contribution of seed endophytes in crop production and breeding.

Soybean and Cotton Spermosphere Soil Microbiome Shows Dominance of Soilborne Copiotrophs

The spermosphere is the transient, immediate zone of soil around imbibing and germinating seeds. It represents a habitat where there is contact between seed-associated microbes and soil microbes, but it is studied less than other plant habitats. Previous studies on spermosphere microbiology were primarily culture based or did not sample the spermosphere soil as initially defined in space and time. Thus, the objectives of this study were to develop an efficient strategy to collect spermosphere soils around imbibing soybean and cotton in nonsterile soil and investigate changes in microbial communities. The method employed sufficiently collected spermosphere soil as initially defined in space by constraining the soil sampled with a cork borer and confining the soil to a 12-well microtiter plate. Spermosphere prokaryote composition changed over time and depended on the crop within 6 h after seeds were sown. By 12 to 18 h, crops had unique microbial communities in spermosphere soils. Prokaryote evenness dropped following seed imbibition, with the proliferation of copiotrophic soil bacteria. Due to their long history of plant growth promotion, prokaryote operational taxonomic units (OTUs) in Bacillus, Paenibacillus, Burkholderia, Massilia, Azospirillum, and Pseudomonas were notable organisms enriched. Fungi and prokaryotes were hub taxa in cotton and soybean spermosphere networks. Additionally, the enriched taxa were not hubs in networks, suggesting that other taxa besides those enriched may be important for spermosphere communities. Overall, this study advances knowledge in the assembly of the plant microbiome early in a plant's life, which may have plant health implications in more mature plant growth stages. IMPORTANCE The central hypothesis of this research was that plant species and seed exudate release would alter the assembly of microbes in the spermosphere soil. Our research investigated the response of microbes to the initial burst of nutrients into the spermosphere soil, filling knowledge gaps from previous studies that pregerminated seeds under sterile conditions. We identified several copiotrophic bacterial lineages with a long history of plant growth promotion proliferating in response to the initial exudate release. With a comparative network approach, we show that these copiotrophic bacteria are not central to networks, demonstrating that other microbes (including fungi) may be important for community structure. This study improves knowledge on microbial dynamics in the understudied spermosphere and helps inform solutions for biologically or ecologically motivated solutions to spermosphere pathogens.

Exploring the Phytobeneficial and Biocontrol Capacities of Endophytic Bacteria Isolated from Hybrid Vanilla Pods

In this study, 58 endophytic bacterial strains were isolated from pods of two hybrid vanilla plants from Madagascar, Manitra ampotony and Tsy taitra. They were genetically characterized and divided into four distinct phylotypes. Three were associated to genus Bacillus species, and the fourth to the genus Curtobacterium. A selection of twelve strains corresponding to the identified genetic diversity were tested in vitro for four phytobeneficial capacities: phosphate solubilisation, free nitrogen fixation, and phytohormone and siderophore production. They were also evaluated in vitro for their ability to biocontrol the growth of the vanilla pathogenic fungi, Fusarium oxysporum f. sp. radicis vanillae and Cholletotrichum orchidophilum. Three bacteria of phylotype 4, m62a, m64 and m65, showed a high nitrogen fixation capacity in vitro, similar to the Pseudomonas florescens F113 bacterium used as a control (phospate solubilizing efficiency respectively 0.50 ± 0.07, 0.43 ± 0.07 and 0.40 ± 0.06 against 0.48 ± 0.03). Strain t2 related to B. subtilis showed a higher siderophore production than F113 (respectively 1.40 ± 0.1 AU and 1.2 ± 0.1 AU). The strain m72, associated with phylotype 2, showed the highest rate of production of Indole-3-acetic acid (IAA) in vitro. Bacteria belonging to the pylotype 4 showed the best capacity to inhibit fungal growth, especially the strains m62b m64 and t24, which also induced a significant zone of inhibition, suggesting that they may be good candidates for controlling fungal diseases of vanilla. This competence was highlighted with spectral imaging showing the production of lipopeptides (Iturin A2 and A3, C₁₆ and C₁₅-Fengycin A and C₁₄ and C₁₅-Surfactin) by the bacterial strains m65 confronted with the pathogenic fungi of vanilla.

Endophytes in Agriculture: Potential to Improve Yields and Tolerances of Agricultural Crops

Endophytic fungi and bacteria live asymptomatically within plant tissues. In recent decades, research on endophytes has revealed that their significant role in promoting plants as endophytes has been shown to enhance nutrient uptake, stress tolerance, and disease resistance in the host plants, resulting in improved crop yields. Evidence shows that endophytes can provide improved tolerances to salinity, moisture, and drought conditions, highlighting the capacity to farm them in marginal land with the use of endophyte-based strategies. Furthermore, endophytes offer a sustainable alternative to traditional agricultural practices, reducing the need for synthetic fertilizers and pesticides, and in turn reducing the risks associated with chemical treatments. In this review, we summarise the current knowledge on endophytes in agriculture, highlighting their potential as a sustainable solution for improving crop productivity and general plant health. This review outlines key nutrient, environmental, and biotic stressors, providing examples of endophytes mitigating the effects of stress. We also discuss the challenges associated with the use of endophytes in agriculture and the need for further research to fully realise their potential.

Recruitment of the rhizo-microbiome army: assembly determinants and engineering of the rhizosphere microbiome as a key to unlocking plant potential

The viable community of microorganisms in the rhizosphere significantly impacts the physiological development and vitality of plants. The assembly and functional capacity of the rhizosphere microbiome are greatly influenced by various factors within the rhizosphere. The primary factors are the host plant genotype, developmental stage and status, soil properties, and resident microbiota. These factors drive the composition, dynamics, and activity of the rhizosphere microbiome. This review addresses the intricate interplay between these factors and how it facilitates the recruitment of specific microbes by the host plant to support plant growth and resilience under stress. This review also explores current methods for engineering and manipulating the rhizosphere microbiome, including host plant-mediated manipulation, soil-related methods, and microbe-mediated methods. Advanced techniques to harness the plant's ability to recruit useful microbes and the promising use of rhizo-microbiome transplantation are highlighted. The goal of this review is to provide valuable insights into the current knowledge, which will facilitate the development of cutting-edge strategies for manipulating the rhizosphere microbiome for enhanced plant growth and stress tolerance. The article also indicates promising avenues for future research in this field.

From seed to seed: the role of microbial inheritance in the assembly of the plant microbiome

Despite evidence that the microbiome extends host genetic and phenotypic traits, information on how the microbiome is transmitted and maintained across generations remains fragmented. For seed-bearing plants, seeds harbor a distinct microbiome and play a unique role by linking one generation to the next. Studies on microbial inheritance, a process we suggest including both vertical transmission and the subsequent migration of seed microorganisms to the new plant, thus become essential for our understanding of host evolutionary potential and host-microbiome coevolution. We propose dividing the inheritance process into three stages: (i) plant to seed, (ii) seed dormancy, and (iii) seed to seedling. We discuss the factors affecting the assembly of the microbiome during the three stages, highlight future research directions, and emphasize the implications of microbial inheritance for fundamental science and society.

Single Seed Microbiota: Assembly and Transmission from Parent Plant to Seedling

The seed acts as the primary inoculum source for the plant microbiota. Understanding the processes involved in its assembly and dynamics during germination and seedling emergence has the potential to allow for the improvement of crop establishment. Changes in the bacterial community structure were tracked in 1,000 individual seeds that were collected throughout seed developments of beans and radishes. Seeds were associated with a dominant bacterial taxon that represented more than 75% of all reads. The identity of this taxon was highly variable between the plants and within the seeds of the same plant. We identified selection as the main ecological process governing the succession of dominant taxa during seed filling and maturation. In a second step, we evaluated the seedling transmission of seed-borne taxa in 160 individual plants. While the initial bacterial abundance on seeds was not a good predictor of seedling transmission, the identities of the seed-borne taxa modified the phenotypes of seedlings. Overall, this work revealed that individual seeds are colonized by a few bacterial taxa of highly variable identity, which appears to be important for the early stages of plant development. IMPORTANCE Seeds are key components of plant fitness and are central to the sustainability of the agri-food system. Both the seed quality for food consumption and the seed vigor in agricultural settings can be influenced by the seed microbiota. Understanding the ecological processes involved in seed microbiota assembly will inform future practices for promoting the presence of important seed microorganisms for plant health and productivity. Our results highlighted that seeds were associated with one dominant bacterial taxon of variable taxonomic identity. This variety of dominant taxa was due to (i) spatial heterogeneity between and within plants and (ii) primary succession during seed development. According to neutral models, selection was the main driver of microbial community assembly for both plant species.

Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes

BACKGROUND

Plants and their associated microbiota constitute an assemblage of species known as holobionts. The plant seed microbiome plays an important role in nutrient uptake and stress attenuation. However, the core vertically transmitted endophytes remain largely unexplored.

RESULTS

To gain valuable insights into the vertical transmission of rice seed core endophytes, we conducted a large-scale analysis of the microbiomes of two generations of six different rice varieties from five microhabitats (bulk soil, rhizosphere, root, stem, and seed) from four geographic locations. We showed that the microhabitat rather than the geographic location and rice variety was the primary driver of the rice microbiome assemblage. The diversity and network complexity of the rice-associated microbiome decreased steadily from far to near the roots, rice exterior to interior, and from belowground to aboveground niches. Remarkably, the microbiomes of the roots, stems, and seeds of the rice interior compartments were not greatly influenced by the external environment. The core bacterial endophytes of rice were primarily comprised of 14 amplicon sequence variants (ASVs), 10 of which, especially ASV_2 (Pantoea) and ASV_48 (Xanthomonas), were identified as potentially vertically transmitted taxa because they existed across generations, were rarely present in exterior rice microhabitats, and were frequently isolated from rice seeds. The genome sequences of Pantoea and Xanthomonas isolated from the parental and offspring seeds showed a high degree of average nucleotide and core protein identity, indicating vertical transmission of seed endophytes across generations. In silico prediction indicated that the seed endophytes Pantoea and Xanthomonas possessed streamlined genomes with short lengths, low-complexity metabolism, and various plant growth-promoting traits. We also found that all strains of Pantoea and Xanthomonas exhibited cellulase activity and produced indole-3-acetic acid. However, most strains exhibited insignificant antagonism to the major pathogens of rice, such as Magnaporthe oryzae and X. oryzae pv. oryzae.

CONCLUSION

Overall, our study revealed that microhabitats, rather than site-specific environmental factors or host varieties, shape the rice microbiome. We discovered the vertically transmitted profiles and keystone taxa of the rice microbiome, which led to the isolation of culturable seed endophytes and investigation of their potential roles in plant-microbiome interactions. Our results provide insights on vertically transmitted microbiota and suggest new avenues for improving plant fitness via the manipulation of seed-associated microbiomes.  Video Abstract.

Plant species-dependent transmission of Escherichia coli O157:H7 from the spermosphere to cotyledons and first leaves

The colonization of six edible plant species: alfalfa, broccoli, coriander, lettuce, parsley and rocket, by the human pathogen Shigatoxigenic Escherichia coli was investigated following two modes of artificial inoculation of seeds, by soaking or watering. The frequency and extent of colonization of cotyledons depended on the mode of inoculation, with three, rapidly germinating species being successfully colonized after overnight soaking, but slower germinating species requiring prolonged exposure to bacteria by watering of the surrounding growth media. Separate analysis of the cotyledons and leaves from individual plants highlighted that successful colonization of the true leaves was also species dependent. For three species, failure of transfer, or lack of nutrients or suitable microhabitat on the leaf surface resulted in infrequent bacterial colonization. Colonization of leaves was lower and generally in proportion to that in cotyledons, if present. The potential risks associated with consumption of leafy produce are discussed.

The culturable seed mycobiome of two Banksia species is dominated by latent saprotrophic and multi-trophic fungi

Seed fungal endophytes play an important beneficial role in the formation of the seedling mycobiome and contribute to plant establishment, but can also occur as latent pathogens and saprotrophs. Current knowledge on the function and diversity of seed fungal endophytes has been gained through studies in agricultural systems whilst knowledge from natural systems is relatively less. We used two co-occurring species from the genus Banksia from four sites in Australia's Sydney Basin Bioregion to investigate the abundance and diversity of seed fungal endophyte communities present in natural ecosystem hosts. Based on results from culturing and DNA sequence analysis of multiple loci, we found that Banksia seeds house a diverse range of fungal endophyte species, that when assigned to functional guilds belonged to multiple trophic modes. Thirty-one of the fungal taxa identified had not been previously reported as endophytes. Amongst the 58 Operational Taxonomic Units identified, Leotiomycetes and Sordariomycetes were the dominant classes and Banksiamyces (Leotiomycetes) and Penicillium (Sordariomycetes) the dominant genera, with many of the species isolated recorded in the literature as having a limited distribution. The two Banksias shared few fungal endophyte species, which were not always present across all study sites. We revealed a 'hidden diversity' within seeds of Banksia from natural ecosystems and provided insights into the influence host species can have on the seed mycobiome.

Culture dependent and independent characterization of endophytic bacteria in the seeds of highland barley

Endophytes in the seeds of plants have shown plant growth promoting (PGP) properties. Highland barley is an economically important crop and a major part of the local diet in the Tibetan Plateau, China, with potential health benefits. We applied culture-dependent and culture-independent methods to study endophytic bacteria in the seeds of eight Highland barley varieties. Based on the seed properties, the variety Ali was clearly separated from the other varieties except the variety CM. Most of the 86 isolates were assigned into genus Bacillus. Approximately half of the isolates showed PGP properties in vitro. Compared to the not-inoculated plants, inoculation with the isolate Bacillus tequilensis LZ-9 resulted in greater length and number of roots, and in bigger aboveground and root weights. Based on the 16S rRNA gene sequencing, the seed microbiome was majorly affiliated with the phylum Proteobacteria and the family Enterobacteriaceae. Overall, the bacterial community compositions in the different varieties were different from each other, yet the between variety differences in community composition seemed relatively small. The differences in community compositions were associated with differences in the total and reducing sugar contents and viscosity of the seeds, thus possibly connected to differences in the osmotic pressure tolerance of the endophytes. The results suggested that the seed endophytes are likely to promote the growth of Highland barley since germination.

Antifungal Activity and Biochemical Profiling of Exudates from Germinating Maize Nostrano di Storo Local Variety

Plant pathogens are responsible for important damages to valuable crops causing important economic losses. Agrobiodiversity protection is crucial for the valorization of local varieties that could possess higher resistance to biotic and abiotic stress. At the beginning of germination, seeds are susceptible to pathogens attacks, thus they can release endogenous antimicrobial compounds of different natures in the spermosphere, to contrast proliferation of microorganisms. The work aimed at characterizing the maize of local variety Nostrano di Storo seed exudates secreted during the first phases of germination, to identify compounds active in the defense towards pathogens. Storo seed exudates were proven to inhibit F. verticilloides germination. In order to investigate the cause of the described effect, compositional profiling of the exudates was performed through NMR, lipidomic, and proteomic analyses. This study suggests an important role of microbial endophytic communities in the protection of the seed during the early phases of the germination process and their interplay with fatty acids released by the seeds, rather than a specific antifungal compound. The valorization of agronomically acceptable maize lines with pre-harvest enhanced resistances to pathogens contamination could lead, in the near future, to commercially available varieties potentially requiring more limited chemical protective treatments.

Comparison of the Endophytic Bacterial Microbiota of Asymptomatic and Symptomatic Ginger Rhizomes During the Activation of Adventitious Bud Development

Bacterial infections are the cause of rhizome rot in ginger (Zingiber officinale). Key members of the endophytic microbial community in ginger rhizomes have not been identified, and their impact on the decay of rhizomes during the activation of adventitious bud development has not been investigated. High-throughput, 16S rRNA amplicon sequencing and inoculation experiments were used to analyze the microbial diversity, community structure and composition, and pathogenicity of isolated bacteria. Our results indicated that the composition of the endophytic microbiota underwent a shift during the progression of rhizome rot disease. Enterobacteriaceae, Lachnospiraceae, and the bacterial genera Clostridium, Bacteroides, Acrobacter, Dysgonomonas, Anaerosinus, Pectobacterium, and Lactococcus were relatively abundant in the bacterial community of rhizomes exhibiting bacterial decay symptoms but were also present in asymptomatic rhizomes. The presence of Enterobacteriaceae and Pseudomonadaceae were positively correlated (ρ = 0.83) at the beginning of the sampling period in the symptomatic group, while a positive correlation (ρ = 0.89) was only observed after 20 days in the asymptomatic group. These data indicate that the co-occurrence of Enterobacteriaceae and Pseudomonadaceae may be associated with the development of ginger rot. Bacterial taxa isolated from ginger rhizomes, such as Enterobacter cloacae, E. hormaechei, and Pseudomonas putida, induced obvious rot symptoms when they were inoculated on ginger rhizomes. Notably, antibiotic-producing bacterial taxa in the Streptococcaceae and Flavobacteriaceae were also relatively abundant in rhizomes with rot and appeared to be linked to the onset of rhizome rot disease. Our results provide important information on the establishment and management of disease in ginger rhizomes.

From Soil Amendments to Controlling Autophagy: Supporting Plant Metabolism under Conditions of Water Shortage and Salinity

Crop resistance to environmental stress is a major issue. The globally increasing land degradation and desertification enhance the demand on management practices to balance both food and environmental objectives, including strategies that tighten nutrient cycles and maintain yields. Agriculture needs to provide, among other things, future additional ecosystem services, such as water quantity and quality, runoff control, soil fertility maintenance, carbon storage, climate regulation, and biodiversity. Numerous research projects have focused on the food–soil–climate nexus, and results were summarized in several reviews during the last decades. Based on this impressive piece of information, we have selected only a few aspects with the intention of studying plant–soil interactions and methods for optimization. In the short term, the use of soil amendments is currently attracting great interest to cover the current demand in agriculture. We will discuss the impact of biochar at water shortage, and plant growth promoting bacteria (PGPB) at improving nutrient supply to plants. In this review, our focus is on the interplay of both soil amendments on primary reactions of photosynthesis, plant growth conditions, and signaling during adaptation to environmental stress. Moreover, we aim at providing a general overview of how dehydration and salinity affect signaling in cells. With the use of the example of abscisic acid (ABA) and ethylene, we discuss the effects that can be observed when biochar and PGPB are used in the presence of stress. The stress response of plants is a multifactorial trait. Nevertheless, we will show that plants follow a general concept to adapt to unfavorable environmental conditions in the short and long term. However, plant species differ in the upper and lower regulatory limits of gene expression. Therefore, the presented data may help in the identification of traits for future breeding of stress-resistant crops. One target for breeding could be the removal and efficient recycling of damaged as well as needless compounds and structures. Furthermore, in this context, we will show that autophagy can be a useful goal of breeding measures, since the recycling of building blocks helps the cells to overcome a period of imbalanced substrate supply during stress adjustment.

Community Assembly and Stability in the Root Microbiota During Early Plant Development

Little is known about how community composition in the plant microbiome is affected by events in the life of a plant. For example, when the plant is exposed to soil, microbial communities may be an important factor in root community assembly. We conducted two experiments asking whether the composition of the root microbiota in mature plants could be determined by either the timing of root exposure to microbial communities or priority effects by early colonizing microbes. Timing of microbial exposure was manipulated through an inoculation experiment, where plants of different ages were exposed to a common soil inoculum. Priority effects were manipulated by challenging roots with established microbiota with an exogenous microbial community. Results show that even plants with existing microbial root communities were able to acquire new microbial associates, but that timing of soil exposure affected root microbiota composition for both bacterial and fungal communities in mature plants. Plants already colonized were only receptive to colonizers at 1 week post-germination. Our study shows that the timing of soil exposure in the early life stages of a plant is important for the development of the root microbiota in mature plants.

The Role of Soil Microbial Diversity in the Conservation of Native Seed Bacterial Microbiomes

Research into understanding the structure, composition and vertical transmission of crop seed microbiomes has intensified, although there is much less research into the seed microbiomes of crop wild relatives. Our previous study showed that the standard seed storage procedures (e.g., seed drying and storage temperature) can influence the seed microbiome of domesticated Glycine max. In this study, we characterized the seed microbiota of Glycine clandestina, a perennial wild relative of soybean (G. max (L.) Merr.) to expand our understanding about the effect of other storage procedures such as the periodic regeneration of seed stocks to bulk up seed numbers and secure viability on the seed microbiome of said seed. The G. clandestina microbiota was analysed from Generation 1 (G1) and Generation 2 (G2) seed and from mature plant organs grown in two different soil treatments T (treatment [native soil + potting mix]) and C (control [potting mix only]). Our dataset showed that soil microbiota had a strong influence on next generation seed microbiota, with an increased contribution of root microbiota by 90% and seed transmissibility by 36.3% in G2 (T) seed. Interestingly, the G2 seed microbiota primarily consisted of an initially low abundance of taxa present in G1 seed. Overall, our results indicate that seed regeneration can affect the seed microbiome composition and using native soil from the location of the source plant can enhance the conservation of the native seed microbiota.

Wheat Microbiome: Structure, Dynamics, and Role in Improving Performance Under Stress Environments

Wheat is an important cereal crop species consumed globally. The growing global population demands a rapid and sustainable growth of agricultural systems. The development of genetically efficient wheat varieties has solved the global demand for wheat to a greater extent. The use of chemical substances for pathogen control and chemical fertilizers for enhanced agronomic traits also proved advantageous but at the cost of environmental health. An efficient alternative environment-friendly strategy would be the use of beneficial microorganisms growing on plants, which have the potential of controlling plant pathogens as well as enhancing the host plant's water and mineral availability and absorption along with conferring tolerance to different stresses. Therefore, a thorough understanding of plant-microbe interaction, identification of beneficial microbes and their roles, and finally harnessing their beneficial functions to enhance sustainable agriculture without altering the environmental quality is appealing. The wheat microbiome shows prominent variations with the developmental stage, tissue type, environmental conditions, genotype, and age of the plant. A diverse array of bacterial and fungal classes, genera, and species was found to be associated with stems, leaves, roots, seeds, spikes, and rhizospheres, etc., which play a beneficial role in wheat. Harnessing the beneficial aspect of these microbes is a promising method for enhancing the performance of wheat under different environmental stresses. This review focuses on the microbiomes associated with wheat, their spatio-temporal dynamics, and their involvement in mitigating biotic and abiotic stresses.

OUP accepted manuscript

During germination, the seed releases nutrient-rich exudates into the spermosphere, thereby fostering competition between resident microorganisms. However, insight into the composition and temporal dynamics of seed-associated bacterial communities under field conditions is currently lacking. This field study determined the temporal changes from 11 to 31 days after sowing in the composition of seed-associated bacterial communities of winter wheat as affected by long-term soil fertilization history, and by introduction of the plant growth-promoting microbial inoculants Penicillium bilaiae and Bacillus simplex. The temporal dynamics were the most important factor affecting the composition of the seed-associated communities. An increase in the relative abundance of genes involved in organic nitrogen metabolism (ureC and gdhA), and in ammonium oxidation (amoA), suggested increased mineralization of plant-derived nitrogen compounds over time. Dynamics of the phosphorus cycling genes ppt, ppx and cphy indicated inorganic phosphorus and polyphosphate cycling, as well as phytate hydrolysis by the seed-associated bacteria early after germination. Later, an increase in genes for utilization of organic phosphorus sources (phoD, phoX and phnK) indicated phosphorus limitation. The results indicate that community temporal dynamics are partly driven by changed availability of major nutrients, and reveal no functional consequences of the added inoculants during seed germination.

Seed-Transmitted Bacteria and Fungi Dominate Juvenile Plant Microbiomes

Plant microbiomes play an important role in agricultural productivity, but there is still much to learn about their provenance, diversity, and organization. In order to study the role of vertical transmission in establishing the bacterial and fungal populations of juvenile plants, we used high-throughput sequencing to survey the microbiomes of seeds, spermospheres, rhizospheres, roots, and shoots of the monocot crops maize (B73), rice (Nipponbare), switchgrass (Alamo), Brachiaria decumbens, wheat, sugarcane, barley, and sorghum; the dicot crops tomato (Heinz 1706), coffee (Geisha), common bean (G19833), cassava, soybean, pea, and sunflower; and the model plants Arabidopsis thaliana (Columbia-0) and Brachypodium distachyon (Bd21). Unsterilized seeds were planted in either sterile sand or farm soil inside hermetically sealed jars, and after as much as 60 days of growth, DNA was extracted to allow for amplicon sequence-based profiling of the bacterial and fungal populations that developed. Seeds of most plants were dominated by Proteobacteria and Ascomycetes, with all containing operational taxonomic units (OTUs) belonging to Pantoea and Enterobacter. All spermospheres also contained DNA belonging to Pseudomonas, Bacillus, and Fusarium. Despite having only seeds as a source of inoculum, all plants grown on sterile sand in sealed jars nevertheless developed rhizospheres, endospheres, and phyllospheres dominated by shared Proteobacteria and diverse fungi. Compared to sterile sand-grown seedlings, growth on soil added new microbial diversity to the plant, especially to rhizospheres; however, all 63 seed-transmitted bacterial OTUs were still present, and the most abundant bacteria (Pantoea, Enterobacter, Pseudomonas, Klebsiella, and Massilia) were the same dominant seed-transmitted microbes observed in sterile sand-grown plants. While most plant mycobiome diversity was observed to come from soil, judging by read abundance, the dominant fungi (Fusarium and Alternaria) were also vertically transmitted. Seed-transmitted fungi and bacteria appear to make up the majority of juvenile crop plant microbial populations by abundance, and based on occupancy, there seems to be a pan-angiosperm seed-transmitted core bacterial microbiome. Further study of these seed-transmitted microbes will be important to understand their role in plant growth and health, as well as their fate during the plant life cycle and may lead to innovations for agricultural inoculant development.

McpT, a Broad-Range Carboxylate Chemoreceptor in Sinorhizobium meliloti

Chemoreceptors enable the legume symbiont Sinorhizobium meliloti to detect and respond to specific chemicals released from their host plant alfalfa, which allows the establishment of a nitrogen-fixing symbiosis. The periplasmic region (PR) of transmembrane chemoreceptors act as the sensory input module for chemotaxis systems via binding of specific ligands, either directly or indirectly. S. meliloti has six transmembrane and two cytosolic chemoreceptors. However, the function of only three of the transmembrane receptors have been characterized so far, with McpU, McpV, and McpX serving as general amino acid, short-chain carboxylate, and quaternary ammonium compound sensors, respectively. In the present study, we analyzed the S. meliloti chemoreceptor McpT. High-throughput differential scanning fluorimetry assays, using Biolog phenotype microarray plates, identified 15 potential ligands for McpT^PR, with the majority classified as mono-, di-, and tricarboxylates. S. meliloti exhibited positive chemotaxis toward seven selected carboxylates, namely, α-ketobutyrate, citrate, glyoxylate, malate, malonate, oxalate, and succinate. These carboxylates were detected in seed exudates of the alfalfa host. Deletion of mcpT resulted in a significant decrease of chemotaxis to all carboxylates except for citrate. Isothermal titration calorimetry revealed that McpT^PR bound preferentially to the monocarboxylate glyoxylate and with lower affinity to the dicarboxylates malate, malonate, and oxalate. However, no direct binding was detected for the remaining three carboxylates that elicited an McpT-dependent chemotaxis response. Taken together, these results demonstrate that McpT is a broad-range carboxylate chemoreceptor that mediates chemotactic response via direct ligand binding and an indirect mechanism that needs to be identified. IMPORTANCE Nitrate pollution is one of the most widespread and challenging environmental problems that is mainly caused by the agricultural overapplication of nitrogen fertilizers. Biological nitrogen fixation by the endosymbiont Sinorhizobium meliloti enhances the growth of its host Medicago sativa (alfalfa), which also efficiently supplies the soil with nitrogen. Establishment of the S. meliloti-alfalfa symbiosis relies on the early exchange and recognition of chemical signals. The present study contributes to the disclosure of this complex molecular dialogue by investigating the underlying mechanisms of carboxylate sensing in S. meliloti. Understanding individual steps that govern the S. meliloti-alfalfa molecular cross talk helps in the development of efficient, commercial bacterial inoculants that promote the growth of alfalfa, which is the most cultivated forage legume in the world, and improves soil fertility.

The effect of plant domestication on host control of the microbiota

Macroorganisms are colonized by microbial communities that exert important biological and ecological functions, the composition of which is subject to host control and has therefore been described as "an ecosystem on a leash". However, domesticated organisms such as crop plants are subject to both artificial selection and natural selection exerted by the agricultural ecosystem. Here, we propose a framework for understanding how host control of the microbiota is influenced by domestication, in which a double leash acts from domesticator to host and host to microbes. We discuss how this framework applies to a plant compartment that has demonstrated remarkable phenotypic changes during domestication: the seed.

Filtrates from cultures of endophytic fungi isolated from leaves of Copaifera oblongifolia (Fabaceae) affect germination and seedling development differently

Interactions between endophytic fungi (EFs) and their host plants range from positive to neutral to negative. The results of such interactions can vary depending on the organ of the infected host plant. EFs isolated from the leaves of some species of plants have potential for use as agents to inhibit seed germination and control invasive plants. The objectives of this study were to identify EFs present in the leaves of Copaifera oblongifolia and to evaluate the role of these fungi in seed germination and seedling development. A total of 11 species of EFs were isolated, which were identified using the internal transcribed spacers (ITS) sequence of the nuclear ribosomal DNA. The isolated species of EFs are generalists and probably are transmitted horizontally. Laboratory tests revealed that filtrates of these fungal isolates differently affect seed germination and seedling development of C. oblongifolia. The species Curvularia intermedia, Neofusicoccum parvum, Pseudofusicoccum stromaticum and Phomopsis sp. negatively affected seed germination, with N. parvum standing out for its negative effects, inhibiting seedling germination and survival in 89 and 222%, respectively. In addition, Cochliobolus intermedius negatively affected seedling development. Thus, the combined use of N. parvum and C. intermedius, or products from the metabolism of these microorganisms, in the control of invasive plants deserves attention from future studies.

Transmission of Seed and Soil Microbiota to Seedling

The seed microbial community constitutes an initial inoculum for plant microbiota assembly. Still, the persistence of seed microbiota when seeds encounter soil during plant emergence and early growth is barely documented. We characterized the encounter event of seed and soil microbiota and how it structured seedling bacterial and fungal communities by using amplicon sequencing. We performed eight contrasting encounter events to identify drivers influencing seedling microbiota assembly. To do so, four contrasting seed lots of two Brassica napus genotypes were sown in two soils whose microbial diversity levels were manipulated by serial dilution and recolonization. Seedling root and stem microbiota were influenced by soil but not by initial seed microbiota composition or by plant genotype. A strong selection on the seed and soil communities occurred during microbiota assembly, with only 8% to 32% of soil taxa and 0.8% to 1.4% of seed-borne taxa colonizing seedlings. The recruitment of seedling microbiota came mainly from soil (35% to 72% of diversity) and not from seeds (0.3% to 15%). Soil microbiota transmission success was higher for the bacterial community than for the fungal community. Interestingly, seedling microbiota was primarily composed of initially rare taxa (from seed, soil, or unknown origin) and intermediate-abundance soil taxa.

IMPORTANCE Seed microbiota can have a crucial role for crop installation by modulating dormancy, germination, seedling development, and recruitment of plant symbionts. Little knowledge is available on the fraction of the plant microbiota that is acquired through seeds. We characterize the encounter between seed and soil communities and how they colonize the seedling together. Transmission success and seedling community assemblage can be influenced by the variation of initial microbial pools, i.e., plant genotype and cropping year for seeds and diversity level for soils. Despite a supposed resident advantage of the seed microbiota, we show that transmission success is in favor of the soil microbiota. Our results also suggest that successful plant-microbiome engineering based on native seed or soil microbiota must include rare taxa.

Culturable Seed Microbiota of Populus trichocarpa

Plants harbor a diverse community of microbes, whose interactions with their host and each other can influence plant health and fitness. While microbiota in plant vegetative tissues has been extensively studied, less is known about members of the seed microbiota. We used culture-based surveys to identify bacteria and fungi found in the seeds of the model tree, Populus trichocarpa, collected from different sites. We found that individual P. trichocarpa seeds typically contained zero or one microbe, with common taxa including species of Cladosporium, Aureobasidium, Diaporthe, Alternaria, and Pseudomonas, a bacterium. Pseudomonas isolates were associated with seed mortality and were negatively associated with the occurrence of fungal isolates within Epicoccum, Alternaria, and Aureobasidium from the same seed. Next, we conducted an inoculation experiment with one of the isolated seed microbes, Pseudomonas syringae pv. syringae, and found that it reduced seed germination and increased seedling mortality for P. trichocarpa. Our findings highlight common fungi and bacteria in the seeds of P. trichocarpa, prompting further study of their functional consequences. Moreover, our study confirms that P. syringae pv. syringae is a seed pathogen of P. trichocarpa and is the first report that P. syringae pv. syringae is a lethal seedling pathogen of P. trichocarpa, allowing for future work on the pathogenicity of this bacterium in seedlings and potential antagonism with other seed microbes.

Rhizobial Chemoattractants, the Taste and Preferences of Legume Symbionts

The development of host-microbe interactions between legumes and their cognate rhizobia requires localization of the bacteria to productive sites of initiation on the plant roots. This end is achieved by the motility apparatus that propels the bacterium and the chemotaxis system that guides it. Motility and chemotaxis aid rhizobia in their competitiveness for space, resources, and nodulation opportunities. Here, we examine studies on chemotaxis of three major model rhizobia, namely Sinorhizobium meliloti, Rhizobium leguminosarum, and Bradyrhizobium japonicum, cataloging their range of attractant molecules and correlating this in the context of root and seed exudate compositions. Current research areas will be summarized, gaps in knowledge discussed, and future directions described.

Maternal effects shape the seed mycobiome in Quercus petraea

The tree seed mycobiome has received little attention despite its potential role in forest regeneration and health. The aim of the present study was to analyze the processes shaping the composition of seed fungal communities in natural forests as seeds transition from the mother plant to the ground for establishment. We used metabarcoding approaches and confocal microscopy to analyze the fungal communities of seeds collected in the canopy and on the ground in four natural populations of sessile oak (Quercus petraea). Ecological processes shaping the seed mycobiome were inferred using joint species distribution models. Fungi were present in seed internal tissues, including the embryo. The seed mycobiome differed among oak populations and trees within the same population. Its composition was largely influenced by the mother, with weak significant environmental influences. The models also revealed several probable interactions among fungal pathogens and mycoparasites. Our results demonstrate that maternal effects, environmental filtering and biotic interactions all shape the seed mycobiome of sessile oak. They provide a starting point for future research aimed at understanding how maternal genes and environments interact to control the vertical transmission of fungal species that could then influence seed dispersal and germination, and seedling recruitment.

Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health

Intense agricultural practices to meet rising food demands have caused ecosystem perturbations. For sustainable crop production, biological agents are gaining attention, but exploring their functional potential on a multi-layered complex ecosystem like the rhizosphere is challenging. This review explains the significance of genomics as a culture-independent molecular tool to understand the diversity and functional significance of the rhizosphere microbiome for sustainable agriculture. It discusses the recent significant studies in the rhizosphere environment carried out using evolving techniques like metagenomics, metatranscriptomics, and metaproteomics, their challenges, constraints infield application, and prospective solutions. The recent advances in techniques such as nanotechnology for the development of bioformulations and visualization techniques contemplating environmental safety were also discussed. The need for development of metagenomic data sets of regionally important crops, their plant microbial interactions and agricultural practices for narrowing down significant data from huge databases have been suggested. The role of taxonomical and functional diversity of soil microbiota in understanding soil suppression and part played by the microbial metabolites in the process have been analyzed and discussed in the context of 'omics' approach. 'Omics' studies have revealed important information about microbial diversity, their responses to various biotic and abiotic stimuli, and the physiology of disease suppression. This can be translated to crop sustainability and combinational approaches with advancing visualization and analysis methodologies fix the existing knowledge gap to a huge extend. With improved data processing and standardization of the methods, details of plant-microbe interactions can be successfully decoded to develop sustainable agricultural practices.