Endophytic Bacterial Diversity Research Articles

Plant growth promoting activities of endophytic bacteria from Melia azedarach (Meliaceae) and their influence on plant growth under gnotobiotic conditions

Bacteria that live asymptomatically within plant tissues are known as endophytes. Because of the close relation with the plant host, they have been a matter of interest for application as plant growth promoters. Melia azedarach is a widely distributed medicinal tree with proven insecticidal, antimicrobial, and antiviral activity. The aim of this study was to isolate and characterize endophytic bacteria from M. azedarach and analyze their plant growth promoting activities for the potential application as biological products. Bacteria were isolated from roots and leaves of trees growing in two locations of Northeastern Argentina. The isolates were characterized by repetitive extragenic palindromic sequence PCR and 16S rDNA sequence analysis. The plant growth-promoting activities were assayed in vitro, improvement of plant growth of selected isolates was tested on M. azedarach plantlets, and the effect of selected ACC deaminase producing isolates was tested on tomato seedlings under salt-stress conditions. The highest endophytic bacterial abundance and diversity were obtained from the roots. All isolates had at least one of the assayed plant growth-promoting activities and 80 % of them had antagonistic activity. The most efficient bacteria were Pseudomonas monteilii, Pseudomonas farsensis, Burkholderia sp. and Cupriavidus sp. for phosphate solubilization (2064 μg P ml−1), IAA production (94.7 μg ml−1), siderophore production index (5.5) and ACC deaminase activity (1294 nmol α-ketobutyrate mg−1 h−1). M. azedarach inoculation assays revealed the bacterial growth promotion potential, with Pseudomonas monteilii, Pseudomonas farsensis and Cupriavidus sp. standing out for their effect on leaf area, leaf dry weight, specific leaf area, and total Chl, Mg and N content, with increases of up to 149 %, 58 %, 65 %, 178 %, 76 % and 97.7 %, respectively, compared to NI plants. Efficient ACC deaminase-producing isolates increased stress tolerance of tomato plants under saline condition. Overall, these findings indicate the potential of the endophytic isolates as biostimulant and biocontrol agents.

Root endophytic bacterial communities are shaped by the specific microbiota associated to mycorrhizal symbionts

Abstract Background and aims Arbuscular mycorrhizal fungi (AMF) are beneficial soil microorganisms establishing mutualistic symbioses with most crop plants and promoting plant growth and health. AMF beneficial activities are complemented by their associated microbiota, leading to synergistic interactions positively affecting plant performance. In this work we assessed whether AMF may act as drivers of root bacterial endophytes, facilitating root colonization of host plants by their associated bacteria. Methods Two AMF isolates were used, Funneliformis mosseae from Indiana (USA) and Septoglomus sp. from Tuscany (Italy) in an original experimental microcosm system, utilizing micropropagated plants of Prunus persica x Prunus amygdalus inoculated with either intact or mechanically crushed AMF spores, the former able and the latter unable to establish the symbiosis. Spore and root endophytic bacterial communities diversity were analysed by Illumina Miseq sequencing. Results This study revealed that AMF with their associated bacteria can shape the root endophytic bacterial communities, inducing differential recruitment depending on the composition of spore-associated microbiota. Such data were consistent between two AMF isolates, associated with diverse bacterial communities, as shown by PERMANOVA, Bray Curtis dissimilarity, hierarchical clustering and indicator species analyses. Moreover, specific bacterial taxa were found exclusively in mycorrhizal roots. Our findings suggested also a differential recruitment depending on the ability of AMF to establish mycorrhizal symbioses. Conclusion This work revealed that AMF represent drivers of the endophytic bacterial communities diversity and composition, facilitating root colonization of host plants by their associated bacteria, that become an integral part of the root microbiome as endophytes.

Leaf Health Status Regulates Endophytic Microbial Community Structure, Network Complexity, and Assembly Processes in the Leaves of the Rare and Endangered Plant Species Abies fanjingshanensis.

The rare and endangered plant species Abies fanjingshanensis, which has a limited habitat, a limited distribution area, and a small population, is under severe threat, particularly due to poor leaf health. The plant endophytic microbiome is an integral part of the host, and increasing evidence indicates that the interplay between plants and endophytic microbes is a key determinant for sustaining plant fitness. However, little attention has been given to the differences in the endophytic microbial community structure, network complexity, and assembly processes in leaves with different leaf health statuses. Here, we investigated the endophytic bacterial and fungal communities in healthy leaves (HLs) and non-healthy leaves (NLs) of A. fanjingshanensis using 16S rRNA gene and internal transcribed spacer sequencing and evaluated how leaf health status affects the co-occurrence patterns and assembly processes of leaf endophytic microbial communities based on the co-occurrence networks, the niche breadth index, a neutral community model, and C-score metrics. HLs had significantly greater endophytic bacterial and fungal abundance and diversity than NLs, and there were significant differences in the endophytic microbial communities between HLs and NLs. Leaf-health-sensitive endophytic microbes were taxonomically diverse and were mainly grouped into four ecological clusters according to leaf health status. Poor leaf health reduced the complexity of the endophytic bacterial and fungal community networks, as reflected by a decrease in network nodes and edges and an increase in degrees of betweenness and assortativity. The stochastic processes of endophytic bacterial and fungal community assembly were weakened, and the deterministic processes became more important with declining leaf health. These results have important implications for understanding the ecological patterns and interactions of endophytic microbial communities in response to changing leaf health status and provide opportunities for further studies on exploiting plant endophytic microbes to conserve this endangered Abies species.

Exploring endophytic bacteria communities of Vanilla planifolia

BackgroundRhizosphere bacterial community and endophytes are now known to influence plant health and response to environmental stress. Very few studies have reported the diversity of endophytic bacterial communities of Vanilla planifolia and their potential roles in promoting plant growth or contributing to aromatic quality.ResultsIn this study, the composition and diversity of the Vanilla rhizosphere bacterial community were explored by analyzing rhizosphere soil and root tissue samples as well as green pods of three accessions of Vanilla planifolia grown on different types of substrates (compost and leaf litter). In addition, the endophytic bacterial diversity of roots and green pods as well as the evolution of endophytic bacteria after the curing process of vanilla green pods were analyzed based on a metabarcoding approach. The results showed that bacterial species richness and diversity were higher in the compost. The analysis of the soil bacterial composition displayed that Halomonas, Pseudoalteromonas, Enterobacter and Bradyrhizobium were the most abundant genera. Moreover, the results indicated that the soil bacterial community structure was linked to the host plant genotype. Regarding the roots endophytic bacteria composition, the genera Halomonas, Pseudoalteromonas, Bacillus and Carboxydocella genera were present in all samples, independently from the substrate nature. Several genera including Bacillus, Bradyrhizobium, Burkholderia and Halomonas were transmitted internally from the roots to the green pods. The curing process reduced the bacterial richness and bacterial diversity associated with the green pods. Halomonas, Pseudoalteromonas, Bacillus, and Carboxydocella are the dominant genera in the pods after the curing process.ConclusionsThis study provides an overview of changes of the bacterial communities dynamics especially endophytic in the roots and the green pods. It highlighted bacterial genera (Halomonas, Pseudoalteromonas, Bacillus, and Carboxydocella) potentially implicated in the formation of aroma compounds of vanilla beans.

Soil Organic Matter and Total Nitrogen Reshaped Root-Associated Bacteria Community and Synergistic Change the Stress Resistance of Codonopsis pilosula.

The stress resistance of medicinal plants is essential to the accumulation of pharmacological active ingredients, but the regulation mechanism of biological factors and abiotic factors on medicinal plants is still unclear. To investigate the mechanism of soil nutrient and microecology on the stress resistance of C. pilosula, rhizosphere soil and roots were collected across the four seasons in Minxian, Gansu, and their physicochemical properties, as well as root-associated microorganisms, were examined. The results showed that the bacterial α-diversity indexes increased in the endosphere and rhizosphere from summer to autumn. At the same time, the community composition and function changed considerably. The stability of the endophytic bacterial community was higher than that rhizospheric bacteria, and the complexity of the endophytic bacterial community was lower than rhizospheric bacteria. Soil organic matter (OM), water content (WC), total potassium (TK), and total nitrogen (TN) have been identified as the key factors affecting bacterial community diversity and stress resistance of C. pilosula. WC, TN, and OM showed significant differences from summer to autumn (P < 0.5). Four key soil physiochemical factors changed significantly between seasons (P < 0.01). TN and OM change the stress resistance of C. pilosula mainly by changing the activity of antioxidant enzymes. Changes of OM and endophytic bacterial diversity affect the accumulation of soluble sugars to alter stress resistance. These four key soil physicochemical factors significantly influenced the diversity of endophytic bacteria. WC and OM were identified as the most important factors for endophytic and rhizospheric bacteria, respectively. This study provided the research basis for the scientific planting of C. pilosula.

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

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

Selection of the Dominant Endophytes Based on Illumina Sequencing Analysis for Controlling Bacterial Wilt of Patchouli Caused by Ralstonia solanacearum.

Bacterial wilt caused by Ralstonia solanacearum (RS) is one of the most devastating diseases in patchouli (Pogostemon cablin [Blanco] Benth.), which results in low yield and quality of patchouli. However, no stable and effective control methods have been developed yet. To evaluate the potential of dominant bacterial endophytes in biocontrol, the endophytic bacterial diversity of patchouli was investigated based on Illumina sequencing analysis, and the ability of isolates belonging to the dominant bacterial genera to control RS wilt of patchouli was explored in pot experiments. A total of 245 bacterial genera were detected in patchouli plants, with the highest relative abundance of operational taxonomic units belonging to the genus Pseudomonas detected in roots, leaves, and stems. The Pseudomonas isolates S02, S09, and S26 showed antagonistic activity against RS in vitro and displayed many plant growth-promoting characteristics, including production of indole-3-acetic acid, siderophores, and 1-aminocyclopropane-1-carboxylic acid deaminase and phosphate- and potassium-solubilizing capability. Inoculation of patchouli plants with the isolates S02, S09, and S26 significantly improved shoot growth and decreased the incidence of bacterial wilt caused by RS. The results suggest that screening of dominant bacterial endophytes for effective biocontrol agents based on Illumina sequencing analysis is more efficient than random isolation and screening procedures.

Unraveling the functional characteristics of endophytic bacterial diversity for plant growth promotion and enhanced secondary metabolite production in Pelargonium graveolens

The rich diversity of microbial endophytic communities associated with plants, often referred to as the second genome, serves as a compelling illustration of efficient co-evolution. This noteworthy partnership plays a pivotal role in sustaining plant well-being and enhancing plant adaptability across diverse habitats. Therefore, examining the diversity of endophytic microbes associated with their particular host plant is valuable for gaining insights into the vast spectrum of plant-microbe interactions. The present experiments aimed at investigating the bacterial endophytic diversity in both root and shoot tissues of Pelargonium graveolens, employing culture dependent and culture independent high-throughput metagenomics approach. A total of 614 and 620 operational taxonomic units (OTUs), encompassing 291 and 229 genera, were identified in the shoot and root tissues of P. graveolens, respectively. Furthermore, the subsequent classification of OTUs revealed 15 highly abundant phyla, with Proteobacteria dominating both root and shoot tissues. Notably, an exceptionally high abundance of Firmicutes phyla was observed in the shoot compared to the root. Additionally, 30 bacterial endophytes from the root, stem, petiole, and leaves were isolated and molecularly characterized, unveiling a consistent pattern of diversity distribution between the root and shoot of P. graveolens. Upon screening all isolates for plant growth promoting traits, Pseudomonas oryzihabitans was found to be positive for major biochemical test like nitrogen fixation, phosphate solubilization etc. and on inoculation resulted in about two-fold increase in content of essential oil accompanied by a significant rise in the geraniol and citronellol content. Diving deep into the genetic constitution of P. oryzihabitans unveiled a substantial number of genes directly and indirectly contributing to the endophyte’s capability in colonizing host plants effectively. In summary, data obtained from metagenomics and culture dependent approaches including glass house trials suggest potential bacterial endophytes suitable for field applications for yield enhancement and in planta secondary metabolite enhancement investigations.

Structure and Functions of Endophytic Bacterial Communities Associated with Sphagnum Mosses and Their Drivers in Two Different Nutrient Types of Peatlands

Sphagnum mosses are keystone plant species in the peatland ecosystems that play a crucial role in the formation of peat, which shelters a broad diversity of endophytic bacteria with important ecological functions. In particular, methanotrophic and nitrogen-fixing endophytic bacteria benefit Sphagnum moss hosts by providing both carbon and nitrogen. However, the composition and abundance of endophytic bacteria from different species of Sphagnum moss in peatlands of different nutrient statuses and their drivers remain unclear. This study used 16S rRNA gene amplicon sequencing to examine endophytic bacterial communities in Sphagnum mosses and measured the activity of methanotrophic microbial by the 13C-CH4 oxidation rate. According to the results, the endophytic bacterial community structure varied among Sphagnum moss species and Sphagnum capillifolium had the highest endophytic bacterial alpha diversity. Moreover, chlorophyll, phenol oxidase, carbon contents, and water retention capacity strongly shaped the communities of endophytic bacteria. Finally, Sphagnum palustre in Hani (SP) had a higher methane oxidation rate than S. palustre in Taishanmiao. This result is associated with the higher average relative abundance of Methyloferula an obligate methanotroph in SP. In summary, this work highlights the effects of Sphagnum moss characteristics on the endophytic bacteriome. The endophytic bacteriome is important for Sphagnum moss productivity, as well as for carbon and nitrogen cycles in Sphagnum moss peatlands.

Elucidating the endophytic bacterial and fungal community composition and diversity in the tree fern Alsophila spinulosa through meta-amplicon sequencing.

Plant tissues harbor abundant endophytes, which are crucial for plant growth. Endophytes present in Alsophila spinulosa, which is enriched with medicinal components, have not been isolated and characterized yet. Here we employed meta-amplicon sequencing to identify endophytic species and examined their diversity in the leaves, petioles, roots and stems of A. spinulosa. Our findings revealed 1,247 operational taxonomic units (OTUs) for endophytic bacteria across 210 species and 476 OTUs for endophytic fungi across 222 species. Alpha diversity analysis showed the highest endophytic bacterial diversity in A. spinulosa roots, whereas fungal diversity was similar across the leaf, petiole and root tissues. Fungal diversity in the leaves and petioles was markedly higher than that in the stems. Furthermore, beta diversity analysis revealed similarities in the endophytic bacterial and fungal compositions between the leaves and petioles, whereas the compositions in roots and stems considerably differed from those in the leaves and petioles. At the genus level, the predominant endophytic bacteria were Methylobacterium-Methylorubrum and Pseudomonas, whereas the predominant endophytic fungi were Cutaneotrichosporon and Pseudofabraea. Linear discriminant analysis effect size revealed characteristic endophytic bacterial genera specific to each tissue type and characteristic endophytic fungal genera specifically in the leaves, petioles and roots. The co-occurrence network analysis indicated that the complexity of endophyte networks was the highest in the leaves and the lowest in the stems of A. spinulosa. Overall, this study elucidates the distribution patterns of endophytes in A. spinulosa across various tissues, offering valuable microbial resources for the development of natural products for medicinal application.

Endophytic bacterial community structure and diversity of the medicinal plant Mirabilis himalaica from different locations

Endophytic bacteria play important roles in medicinal plant growth, abiotic stress, and metabolism. Mirabilis himalaica (Edgew.) Heimerl is known for its medicinal value as Tibetan traditional plant; however, little is known about the endophytic bacteria associated with this plant in different geographic conditions and vegetal tissues. To compare the endophytic bacterial community associated with this plant in different geographic conditions and vegetal tissues, we collected the leaves, stems, and roots of M. himalaica from five locations, Nongmu college (NM), Gongbujiangda (GB), Zhanang County (ZL), Lang County (LX), and Sangri County (SR), and sequenced the 16S rRNA V5-V7 region with the Illumina sequencing method. A total of 522,450 high-quality sequences and 4970 operational taxonomic units (OTUs) were obtained. The different tissues from different locations harbored unique bacterial assemblages. Proteobacteria and Actinobacteria were the dominant phyla in all the samples, while the dominant genera changed based on the different tissues. The endophytic bacterial structures in the leaf and stem tissues were different compared to root tissues. Redundancy analysis (RDA) showed that the endophytic bacterial community was significantly correlated with pH, available phosphorus (AP), total phosphorus (TP), total nitrogen (TN), and soil organic matter (SOM). These findings suggested that the geographic conditions, climate type, ecosystem type, and tissues determined the endophytic bacterial composition and relative abundances. This conclusion could facilitate an understanding of the relationship and ecological function of the endophytic bacteria associated with M. himalaica and provide valuable information for artificial planting of M. himalaica and identifying and applying functional endophytic bacteria.

Proteobacterial dominance in endophytic bacterial diversity in switchgrass growing under nitrogen range and effect on plant growth

Switchgrass (Panicum virgatum L.) is native to North America and cultivated as a forage and bioenergy crop. Inorganic fertilizers enhance biomass production, increase production costs, and pollute the environment. Switchgrass cultivation using an eco-friendly approach might be achieved by inoculation with beneficial microbes. Therefore, the diversity of cultivable endophytic bacteria from roots and shoots of switchgrass growing under a nitrogen regime was studied. The potential of bacteria for plant growth promotion (PGP) was tested under in vitro conditions. A total of 216 bacterial isolates obtained belonged to four phyla and 33 genera, and most isolates were obtained from plants growing under no (0 kg/ha) or low nitrogen (90 kg/ha) input, rather than higher N (180 kg/ha). Higher numbers of isolates belonged to the phylum Proteobacteria, and genus-wise representation showed the dominance of Pseudomonas, Enterobacter, and rhizobia. Bacterial isolates were tested for PGP properties, e.g. phosphate solubilization, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, Indole Acetic Acid (IAA) production, and nitrogen fixation. Many isolates were positive for one or more PGP properties. In in vitro analysis, selected bacterial isolates were inoculated in two commercial switchgrass cultivars and a showed cultivar-specific response. PGP isolates can be used for pot or field trials and eventually for the sustainable cultivation of switchgrass.

Endophytic bacterial community diversity in genetically related hybrid rice seeds.

The Food and Agriculture Organization of the United Nations (FAO) has identified hybrid rice as ideal for addressing food scarcity in poor nations. A comprehensive investigation of the endophytic bacteria in hybrid rice seeds is essential from a microecological perspective to illuminate the mechanisms underlying its high yield, high quality, and multi-resistance. The endophytic bacterial diversity and community structures of 11 genetically correlated hybrid rice seeds with different rice blast resistance levels were studied using high-throughput sequencing (HTS) on the Illumina MiSeq platform to reveal their "core microbiota" and explore the effect of genotypes, genetic relationships, and resistance. Proteobacteria (78.15-99.15%) represented the most abundant group in the 11 hybrid rice cultivars, while Pantoea, Pseudomonas, and Microbacterium comprised the "core microbiota." Hybrid rice seeds with different genotypes, genetic correlations, and rice blast resistance displayed endophytic bacterial community structure and diversity variation. In addition, the network relationships between the rice seed endophytic bacteria of "the same female parent but different male parents" were more complex than those from "the same male parent but different female parents." Matrilineal inheritance may be the primary method of passing on endophytic bacteria in rice from generation to generation. The endophytic bacterial interaction network in rice blast-resistant hybrid rice seed varieties was more complicated than in susceptible varieties. In summary, this study demonstrated that the genotype, genetic relationship, and rice blast resistance were important factors affecting the community structures and diversity of endophytic bacteria in hybrid rice seeds, which was vital for revealing the interaction between endophytic bacteria and the host. KEY POINTS: • Pantoea, Pseudomonas, and Microbacterium represent the main endophytic bacteria in hybrid rice seeds. • Genotype is the primary factor affecting endophytic bacterial diversity in hybrid rice seeds. • The diversity of the endophytic bacterial community in hybrid rice seeds is related to their genotypes, genetic relationships, and rice blast resistance.

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.

Isolation and Characterization of Bacterial Endophytes from Maize Genotypes Varying in Resistance against Macrophomina phaseolina

The present work aims to isolate and characterize the bacterial endophytes associated with different maize genotypes varying in resistance to disease reaction against Macrophomina phaseolina. A total of 50 endophytic bacteria were isolated from root and stem of healthy maize plants at 30 DAS, 60 DAS by using two different media like TSA, NA medium and maximum number of endophytic bacterial population were recovered from root followed by stem in all the genotypes and TSA medium was found to be the most suitable medium for deciphering maximum endophytic bacterial diversity. The isolated bacterial endophytes were characterized on the basis of morphological parameters viz., size, shape, colour, margin and texture, elevation, gram staining reaction and it was observed that Gram positive bacteria (68.0 %) formed the dominant group. The colony characterization revealed that circular forms (38.0 %) were dominated. Among the colony features the colonies with entire margins (66.0 %) and convex elevation (44.0 %) were found to be dominating.

Cadmium alters the rhizosphere bacterial community structure in blueberry roots and increases the content of lipids in the soil

Vaccinium spp. Is a small berry that grows in acidic environments. Relying on the exchange of nutrients and defense against adverse environments through the root system microbiota, bacteria play an important role. As a widely distributed pollutant, the mobility and bioavailability of Cd are enhanced in acidic environments, which can affect the community composition of blueberry root microbiota and alter the composition of soil metabolites. Therefore, studying the changes in the bacterial microbiota of blueberry roots and soil metabolomics under Cd stress can provide a foundation for the development of blueberry microbial fertilizers and the management of soil Cd pollution. In this study, 16 S rDNA sequencing and untargeted metabolomics were used to analyze the rhizosphere, root surface and root endophytic bacterial diversity as well as soil metabolites of Vaccinium spp. Under cadmium (Cd) contamination. The results indicate that the addition of cadmium (Cd) significantly reduces the α-diversity of the rhizosphere, rhizoplane, and endophytic bacteria in blueberries and has a significant impact on the dominant bacterial species. With the application of Cd, the relative abundance of the dominant taxa such as Diplorickettsiaceae_unclassified, Legionella, Streptomyces and Rhodanobacter decreased significantly at the genus level and turned into general or rare bacterial taxa. Meanwhile, the relative abundance of LWQ8_unclassified, WPS-2_unclassified, Acetobacteraceae_unclassified, Acidibacter, Acidiphilium and Granulicella with extreme tolerances increased significantly and gradually became the dominant taxa. Of the 364 metabolites in the soil, 31 varied significantly as the structure of the rhizosphere bacterial community changed. Among them, the lipids and lipid-like molecules clade showed the greatest variation in species and a significant increase in content. It was also associated with changes in bacterial taxa such as Tundrisphaera, Spirochaetaceae_unclassified, Dyella and CHAB_XI_27_unclassified.

Analysis of Endophytic Bacterial Diversity in Rice Seeds with Regional Characteristics in Yunnan Province, China, Based on High-Throughput Sequencing Technology.

Examining the endophytic bacteria in rice seeds from Yunnan Province displaying regional characteristics is vital for exploring strain resources, improving rice production, and conducting subsequent research. This study investigated nine characteristic rice varieties from Yunnan Province using high-throughput sequencing technology based on the Illumina Novaseq platform to reveal their dominant bacterial communities and discussed their endophytic bacterial community differences. A total of 829 shared OTUs, and 233 unique OTUs were identified in the nine samples, while the bacteria included Proteobacteria, Actinobacteriota, and Firmicutes, of which Proteobacteria was the most dominant. Pantoea and Methylorubrum were the most abundant at the genus level, with Curtobacterium, Brevundimonas, and Luteibacter representing the specific genera in the rice seed samples. This study revealed the endophytic structure and diversity in the seeds of nine rice varieties displaying regional characteristics and provided a foundation for further research into rice containing endophytic bacteria.

Endophytic bacterial taxonomic and functional diversity in the seeds of wheat genotypes from different agroecologies

ABSTRACT Plant genotype and agroecology influence the composition and functionality of seed endophytic bacterial communities. Taxonomic analysis of 123 wheat seeds endophytic bacteria classified these into 23 genera predominantly under Firmicutes followed by Actinobacteria and Proteobacteria. Genus Bacillus was most abundant (30.7%) followed by Streptomyces (18.4%) with other representative genera such as Stenotrophomonas, Paenibacillus, Mixta, Enterobacter, Micrococcus, Pantoea, Alkalihalobacillus, Cortiobacterium, and more. Across agroecologies, the core microbiota of seeds consists of Bacillus, Streptomyces, Paenibacillus, and Stenotrophomonas, with maximum diversity and abundance observed in seeds of the North Western Plain Zone of India. Seed endophytic bacteria had PGP traits; nitrogen fixation (n = 101), production of IAA (n = 65), siderophores (n = 43), ammonia (n = 82) and solubilization of phosphate (n = 47), potassium (n = 37), and zinc (n = 8). The isolates produced HCN and hydrolytic enzymes and displayed antagonism against fungal pathogens. Overall, the information generated on wheat seeds’ endophytic bacterial taxonomy and beneficial traits may pave the path for the development of novel bioinoculants. Key message Wheat seeds from various agro-ecologies of India harbor diverse endophytic bacteria. Firmicutes were dominant followed by Actinobacteria and Proteobacteria. Genus Bacillus, Stenotrophomonas, Streptomyces, and Paenibacillus were core endophytic bacteria in different agro-ecologies. The endophytic bacterial strains were displaying diverse functional traits.

A reduced but stable core microbiome found in seeds of hyperaccumulators

The seed microbiota is currently of great interest in the scientific community since seed germination is a critical stage in plant life cycle. Some seed endophytic bacteria could be commonly found in seeds of hyperaccumulating plants and may confer them an evolutionary advantage over non-hyperaccumulating plants when confronted to biotic or abiotic stress. This study focuses on the endophytic bacterial diversity of a wide diversity of metal hyperaccumulating and non-hyperaccumulating plants (93 seed samples from Mediterranean regions, Oceania, South-East Asia) to reveal the core endophyte communities specific of hyperaccumulating plants. The rather low richness of the seed bacterial communities found in all seeds suggest that a sub-population of specialized endophytic strains is able to colonize seeds and survive. The factor that shapes the diversity of those bacterial communities was first the botanical family and secondly the hyperaccumulation trait of the host plants. Based on the taxonomic affiliation, we revealed that the Brassicales had 1349 OTUs that were specific to them and the Asterales 204 OTUs, independently of their metal accumulation strategy. Nonetheless, a set of 12 OTUs were shared by the seeds of all the hyperaccumulators independently of the taxonomic order of the plants (among Asterales and Brassicales) and could be considered as a ‘stable’ core microbiome. Those OTUs identified as Luteibacter, Alphaproteobacteria unclassified, Sphingopyxis, Alishewanella, bacteria unclassified, Heliimonas, Aeromicrobium, Proteobacteria unclassified, Xanthomonadales unclassified and Micromonosporaceae unclassified may constitute an endophytic bacterial core with PGP traits. Further studies are needed to extend our knowledge of the possible role played by those bacteria.

Different assembly mechanisms of leaf epiphytic and endophytic bacterial communities underlie their higher diversity in more diverse forests

Abstract Plant microbiomes are known to influence host fitness and ecosystem functioning, but mechanisms regulating their structure are poorly understood. Here, we explored the assembly mechanisms of leaf epiphytic and endophytic bacterial communities using a subtropical forest biodiversity experiment. Both epiphytic and endophytic bacterial diversity increased as host tree diversity increased. However, the increased epiphytic diversity in more diverse forests was driven by greater epiphytic diversity (i.e. greater α‐diversity) on individual trees, whereas the increased endophytic diversity in more diverse forests was driven by greater dissimilarity in endophytic composition (i.e. greater β‐diversity) among trees. Mechanistically, responses of epiphytes to changes in host diversity were consistent with mass effects, whereas responses of endophytes were consistent with species sorting. Synthesis. These results provided novel experimental evidence that biodiversity declines of plant species will lead to biodiversity declines of plant‐associated microbiomes, but the underlying mechanism may differ between habitats on the plant host.