Rhizosphere microbial community structure at different maize plant growth stages and root locations

Analysis of microbial community composition and diversity in the rhizosphere of Salvia miltiorrhiza at different growth stages

Salvia miltiorrhiza is a kind of medicinal plant with various pharmacological activities. Few studies on the composition and diversity of rhizosphere microbial communities at different growth stages have been conducted on Salvia miltiorrhiz; in particular, salviorrhiza grows in soil that has been continuously planted for 3 years. The purpose of this study was to understand the changes of soil physicochemical properties of Salvia miltiorrhiza at different growth stages, and to study the composition and diversity of rhizosphere microbial community at different growth stages. Illumina NovaSeq sequencing technology was used to analyze the bacterial 16S rRNA gene and the fungal ITS region in the rhizosphere soil of Salvia miltiorrhiza at different growth stages. The results showed that the dominant bacterial phyla in the Salvia miltiorrhiza rhizosphere were Proteobacteria, Bacteroidetes, Acidobacteria, Firmicutes, Actinobacteria, and Chloroflexi. The dominant fungal phyla were Ascomycota, Mortierellomycota, Basidiomycota, and Rozellomycota. During the growth of Salvia miltiorrhiza, the physical and chemical properties of soil changed. As the Salvia miltiorrhiza grew, the content of available phosphorus, available potassium, pH, nitrate nitrogen, and ammonium nitrogen significantly decreased. Ammonium nitrogen and nitrate nitrogen had a greater impact on the bacterial community structure in the rhizosphere than on the fungal community structure. The work was to reveal differences in the rhizosphere bacterial and fungal community structure during different growth stages of Salvia miltiorrhiza, further understand the changes of rhizosphere microbial ecological characteristics and soil physicochemical properties during the cultivation of Salvia miltiorrhiza.

Aflatoxins in maize and groundnuts on markets in Accra and consumers risk

This study presents the results of aflatoxin contamination of maize and groundnuts in major markets in Accra and assesses the population's exposure to aflatoxins. Raw maize and groundnuts from 6 major markets in Accra were sampled and analysed for their aflatoxin content. A total of 92 samples comprising 48 maize and 44 groundnuts were analysed using high-performance liquid chromatography, after extraction with methanol/water and cleanup on an immunoaffinity column. Total aflatoxins were quantified in 98% of the maize samples and 70% of the groundnut samples, with concentrations ranging from 0.60 to 1065 µg/kg and 0.20 to 627 µg/kg, respectively. Exposure assessment showed an estimated daily intake of 0.436 μg/kg bw/day and 0.0632 μg/kg bw/day for maize and groundnut consumption, respectively, suggesting significant health risks for consumers. The high prevalence and concentrations of aflatoxins call for an urgent need for measures to control exposure of the Ghanaian population.

Changes in bacterial communities induced by integrated production systems and the phenological stages of soybean

Plant development and productivity depend on interactions with soil microorganisms for nutrient availability, promotion of growth and protection against phytopathogens. Although the influence of the phenological stages of soybean crops and their environmental conditions on the soil bacterial communities have already been reported, no studies have focused on the influence of integrated agrosilvopastoral systems on bacterial consortia. In this study, we evaluated the influence of the phenological stages of soybean cultivated under conventional full sunlight (CFS) and integrated crop-livestock-forestry (ICLF) systems on bacterial communities in the rhizosphere and in bulk soil using high-throughput sequencing techniques. Proteobacteria, Actinobacteriota and Acidobacteriota were the most abundant phyla in both the rhizosphere and the bulk soil at all growth stages. The results support our hypotheses that the richness and diversity of soil bacterial communities are influenced by different cultivation systems, and that the structure of the bacterial communities in the rhizosphere and the bulk soil are modulated by the phenological stages of the soybean crop.

Genomic and Metabolic Characterization of Plant Growth-Promoting Rhizobacteria Isolated from Nodules of Clovers Grown in Non-Farmed Soil

The rhizosphere microbiota, which includes plant growth-promoting rhizobacteria (PGPR), is essential for nutrient acquisition, protection against pathogens, and abiotic stress tolerance in plants. However, agricultural practices affect the composition and functions of microbiota, reducing their beneficial effects on plant growth and health. Among PGPR, rhizobia form mutually beneficial symbiosis with legumes. In this study, we characterized 16 clover nodule isolates from non-farmed soil to explore their plant growth-promoting (PGP) potential, hypothesizing that these bacteria may possess unique, unaltered PGP traits, compared to those affected by common agricultural practices. Biolog profiling revealed their versatile metabolic capabilities, enabling them to utilize a wide range of carbon and energy sources. All isolates were effective phosphate solubilizers, and individual strains exhibited 1-aminocyclopropane-1-carboxylate deaminase and metal ion chelation activities. Metabolically active strains showed improved performance in symbiotic interactions with plants. Comparative genomics revealed that the genomes of five nodule isolates contained a significantly enriched fraction of unique genes associated with quorum sensing and aromatic compound degradation. As the potential of PGPR in agriculture grows, we emphasize the importance of the molecular and metabolic characterization of PGP traits as a fundamental step towards their subsequent application in the field as an alternative to chemical fertilizers and supplements.

Unveiling the novel role of ryegrass rhizospheric metabolites in benzo[a]pyrene biodegradation

Rhizoremediation is a promising remediation technology for the removal of soil persistent organic pollutants (POPs), especially benzo[a]pyrene (BaP). However, our understanding of the associations among rhizospheric soil metabolites, functional microorganisms, and POPs degradation in different plant growth stages is limited. We combined stable-isotope probing (SIP), high-throughput sequencing, and metabolomics to analyze changes in rhizospheric soil metabolites, functional microbes, and BaP biodegradation in the early growth stages (tillering, jointing) and later stage (booting) of ryegrass. Microbial community structures differed significantly among growth stages. Metabolisms such as benzenoids and carboxylic acids tended to be enriched in the early growth stage, while lipids and organic heterocyclic compounds dominated in the later stage. From SIP, eight BaP-degrading microbes were identified, and most of which such as Ilumatobacter and Singulisphaera were first linked with BaP biodegradation. Notably, the relationship between the differential metabolites and BaP degradation efficiency further suggested that BaP-degrading microbes might metabolize BaP directly to produce benzenoid metabolites (3-hydroxybenzo[a]pyrene), or utilize benzenoids (phyllodulcin) to stimulate the co-metabolism of BaP in early growth stage; some lipids and organic acids, e.g. 1-aminocyclopropane-1-carboxylic acid, might provide nutrients for the degraders to promote BaP metabolism in later stage. Accordingly, we determined that certain rhizospheric metabolites might regulate the rhizospheric microbial communities at different growth stages, and shift the composition and diversity of BaP-degrading bacteria, thereby enhancing in situ BaP degradation. Our study sheds light on POPs rhizoremediation mechanisms in petroleum-contaminated soils.

Urban biogeography of fungal endophytes across San Francisco

In natural and agricultural systems, the plant microbiome-the microbial organisms associated with plant tissues and rhizosphere soils-has been shown to have important effects on host physiology and ecology, yet we know little about how these plant-microbe relationships play out in urban environments. Here we characterize the composition of fungal communities associated with living leaves of one of the most common sidewalk trees in the city of San Francisco, California. We focus our efforts on endophytic fungi (asymptomatic microfungi that live inside healthy leaves), which have been shown in other systems to have large ecological effects on the health of their plant hosts. Specifically, we characterized the foliar fungal microbiome of Metrosideros excelsa (Myrtaceae) trees growing in a variety of urban environmental conditions. We used high-throughput culturing, PCR, and Sanger sequencing of the internal transcribed spacer nuclear ribosomal DNA (ITS nrDNA) region to quantify the composition and structure of fungal communities growing within healthy leaves of 30 M. excelsa trees from six distinct sites, which were selected to capture the range of environmental conditions found within city limits. Sequencing resulted in 854 high-quality ITS sequences. These sequences clustered into 85 Operational Taxonomic Units (97% OTUs). We found that these communities encompass relatively high alpha (within) and beta (between-site) diversity. Because the communities are all from the same host tree species, and located in relatively close geographical proximity to one another, these analyses suggest that urban environmental factors such as heat islands or differences in vegetation or traffic density (and associated air quality) may potentially be influencing the composition of these fungal communities. These biogeographic patterns provide evidence that plant microbiomes in urban environments can be as dynamic and complex as their natural counterparts. As human populations continue to transition out of rural areas and into cities, understanding the factors that shape environmental microbial communities in urban ecosystems stands to become increasingly important.

Cover Crop Amendments and Lettuce Plant Growth Stages Alter Rhizobacterial Properties and Roles in Plant Performance

Lettuce plants respond differently to cover crop amendments by altering their biomass and nitrogen uptake (Nup) at different plant growth stages. Nonetheless, plant-microbe interactions involved in the alterations are scarcely studied. This study elucidated how the properties of the soil microbial community inhabiting the rhizosphere associated with lettuce (Lactuca sativa L. var. crispa "Red fire") change during plant growth stages. Lettuce plants were cultivated in control soil and soil with rye, hairy vetch (HV), and rye plus HV (rye + HV) cover crop amendments. Rhizosphere soil samples were collected at the mid-growth and mature stages of plant development. DNA was extracted from the soil, and the 16S rRNA region was amplified using polymerase chain reaction to analyze bacterial genes and community structures and functions. Cover crop amendments and plant growth stages increased or decreased the relative abundances of bacterial taxa at the genus level. Plant maturity decreased 16S rRNA gene expression and the number of bacterial operational taxonomic units in all treatments. The unique, core, and shared taxa with low relative abundances may be associated with improved lettuce Nup and lettuce shoot and root biomass at each plant growth stage under different cover crop amendments based on multivariate analysis between plant indicators and bacterial genera groups. This study revealed the importance of bacterial groups with low relative abundance in plant-microbe interactions; such bacteria may promote the cover crop application for high lettuce productivity.

Soil bacterial communities of paddy are dependent on root compartment niches but independent of growth stages from Mollisols of Northeast China

Introduction

Deep insights into adhering soil of root zones (rhizosphere and rhizoplane) microbial community could provide a better understanding of the plant-microbe relationship. To better understand the dynamics of these microbial assemblies over the plant life cycle in rhizodeposition along rice roots.

Methods

Here, we investigated bacterial distribution in bulk, rhizosphere, and rhizoplane soils at tillering, heading, and mature stage, from rice (Oryza sativa) fields of the Northeast China.

Results and Discussion

Our results revealed that soil bacterial α-diversity and community composition were significantly affected by root compartment niches but not by temporal change. Compared to rhizoplane soils in the same period, bulk in the heading and rhizosphere in the mature had the largest increase in Shannon's index, with 11.02 and 14.49% increases, respectively. Proteobacteria, Chloroflexi, Bacteroidetes, and Acidobacteria are predominant across all soil samples, bulk soil had more phyla increased across the growing season than that of root related-compartments. Deterministic mechanisms had a stronger impact on the bacterial community in the compartments connected to the roots, with the relative importance of the bulk soil, rhizoplane and rhizosphere at 83, 100, and 56%, respectively. Because of ecological niche drivers, the bacterial networks in bulk soils exhibit more complex networks than rhizosphere and rhizoplane soils, reflected by more nodes, edges, and connections. More module hub and connector were observed in bulk (6) and rhizoplane (5) networks than in rhizosphere (2). We also detected shifts from bulk to rhizoplane soils in some functional guilds of bacteria, which changed from sulfur and nitrogen utilization to more carbon and iron cycling processes. Taken together, our results suggest distinct bacterial network structure and distribution patterns among rhizosphere, rhizoplane, and bulk soils, which could possibly result in potential functional differentiation. And the potential functional differentiation may be influenced by plant root secretions, which still needs to be further explored.

Carbon source utilization pattern of soil bacterial microbiome of bambara groundnut rhizosphere at the different growth stages determines soil fertility

The diversity of microbes in the soil of plants is important for sustainable agriculture as these microbes are important in carrying out different functional processes to improve the soil and invariably plant growth. Inversely the presence of the crop also affects the types of microbial communities in the soil. In this study, bambara groundnut was grown during the planting season in South Africa, from November to March 2014/2015 and 2015/2016 and soil samples were taken after every 4 weeks after planting. Soil samples were taken 15 cm deep from 2 different landraces named VBR and VL. Microbial diversity was determined by soil microbial Carbon Source Utilization Profiles (CSUP) using BIOLOG™ GN2 plates. The abundance and richness of the soil microbes was also determined using the Shannon-Weaver and Evenness diversity indices. The diversity of the soil microbial population changed over the stages of plant growth, according to cluster analysis. Bacterial abundance and diversity were higher at 4 and 8 weeks after planting (WAP). The microbial abundance (richness index) in this study ranged from 0.64 to 0.94 with cultivar VL2 at 8 WAP being the highest while bulk soil (control), R2 was the lowest. The Shannon-Weaver index varied between 2.19 and 4.00 with the lowest corresponding to control while the highest was VL2 at 8 WAP. Carbon sources utilized by bacterial communities spread across the 96 carbon sources. The highest utilization of carboxylic acids, ester, amino acids and polymers and carbohydrates was found in the bacterial communities of the different landraces across growth stages. The highest utilization of alcohols, amides, amines, aromatic chemicals, brominated chemicals and phosphorylated chemicals was found in the control landraces. This indicates that the soil samples between 4 WAP and 12 WAP were richer in diversity of microbial species and their abundance. This soil diversity and richness is an indicator of the quality of the soil in order to increase crop yields and agricultural production.

Treatment with atypical rhizobia, Pararhizobium giardinii and Ochrobactrum sp. modulate the rhizospheric bacterial community, and enhances Lens culinaris growth in fallow-soil

Diazotrophic nodule isolates are acknowledged promoters of plant growth and rhizospheric community. Consequently, in the lentil agroecosystem, inoculation of atypical rhizobial isolates could be a viable alternative to chemical fertilizers for fallow land usage optimization. The aim of this study is to evaluate and select the rhizobial isolates of lentil nodules with plant-growth-promoting (PGP) attributes and to elucidate their application in rice-fallow soil for determining the growth of lentils and its impact on the rhizospheric bacterial community. Lentil's nodule isolates were identified and screened for their PGP attributes, biofilm, exopolysaccharide (EPS) formation, and early plant growth promotion. The pot experiment with the selected atypical rhizobial isolates Pararhizobium giardinii (P1) and Ochrobactrum sp. (42S) significantly enhanced germination, vigour index, nodule formation (P1 60%, 42S 42% increase), nodule fresh weight, shoot length (65% P1 & 35% 42S), and chlorophyll content as compared to the uninoculated control treatment. The genes for nitrogen fixation nifH and nifK were detected in both isolates. Scanning Electron Microscopy (SEM) revealed successful root and nodule colonization by both isolates, while Transmission Electron Microscopy (TEM) displayed nitrogen-fixing zones within root nodules. Proteobacteria predominated in the lentil rhizosphere of all the treatments. Whereas, application of either P1 or 42S increased Rhizobium, Mesorhizobium, and Bradyrhizobium genra, thus positively modulating rhizospheric community structure. The correlation network analysis revealed an abundance of some interdependent bacterial genera with a possible role in overall plant growth. Functional genes for siderophore biosynthesis and ABC transporter were positively modulated by application of either P1 or 42S. This study showed the significant effect of P. giardinii P1 and Ochrobactrum sp. 42S of L. culinaris on lentil growth, improving fallowsoil health for optimum usage, and modulated rhizospheric community structure which strongly manifest prospects of low-cost, eco-friendly and sustainable biofertilizers.

Relationship between nitrifying microorganisms and other microorganisms residing in the maize rhizosphere

The microbial network of rhizosphere is unique as a result of root exudate. Insights into the relationship that exists with the energy metabolic functional groups will help in biofertilizer production. We hypothesize that there exists a relationship between nitrifying microorganisms and other energy metabolic functional microbial groups in the maize rhizosphere across different growth stages. Nucleospin soil DNA extraction kit was used to extract DNA from soil samples collected from maize rhizosphere. The 16S metagenomics sequencing was carried out on Illumina Miseq. The sequence obtained was analyzed on MG-RAST. Nitrospira genera were the most abundant in the nitrifying community. Nitrifying microorganisms were more than each of the studied functional groups except for nitrogen-fixing bacteria. Also, majority of the microorganisms were noticed at the fruiting stage and there was variation in the microbial structure across different growth stages. The result showed that there exists a substantial amount of both negative and positive correlation within the nitrifying microorganisms, and between them and other energy metabolic functional groups. The knowledge obtained from this study will help improve the growth and development of maize through modification of the rhizosphere microbial community structure.

Bacterial Communities in the Rhizosphere at Different Growth Stages of Maize Cultivated in Soil Under Conventional and Conservation Agricultural Practices

Farmers in Mexico till soil intensively, remove crop residues for fodder and grow maize often in monoculture. Conservation agriculture (CA), including minimal tillage, crop residue retention and crop diversification, is proposed as a more sustainable alternative. In this study, we determined the effect of agricultural practices and the developing maize rhizosphere on soil bacterial communities. Bulk and maize (Zea mays L.) rhizosphere soil under conventional practices (CP) and CA were sampled during the vegetative, flowering and grain filling stage, and 16S rRNA metabarcoding was used to assess bacterial diversity and community structure. The functional diversity was inferred from the bacterial taxa using PICRUSt. Conservation agriculture positively affected taxonomic and functional diversity compared to CP. The agricultural practice was the most important factor in defining the structure of bacterial communities, even more so than rhizosphere and plant growth stage. The rhizosphere enriched fast growing copiotrophic bacteria, such as Rhizobiales, Sphingomonadales, Xanthomonadales, and Burkholderiales, while in the bulk soil of CP other copiotrophs were enriched, e.g., Halomonas and Bacillus. The bacterial community in the maize bulk soil resembled each other more than in the rhizosphere of CA and CP. The bacterial community structure, and taxonomic and functional diversity in the maize rhizosphere changed with maize development and the differences between the bulk soil and the rhizosphere were more accentuated when the plant aged. Although agricultural practices did not alter the effect of the rhizosphere on the soil bacterial communities in the flowering and grain filling stage, they did in the vegetative stage.

IMPORTANCE We studied the effect of sustainable conservation agricultural practices versus intensive conventional ones on the soil microbial diversity, potential functionality, and community assembly in rhizosphere of maize cultivated in a semiarid environment. We found that conservation agriculture practices increased the diversity of soil microbial species and functions and strongly affected how they were structured compared to conventional practices. Microbes affected by the roots of maize, the rhizobiome, were different and more diverse than in the surrounding soil and their diversity increased when the plant grew. The agricultural practices affected the maize rhizobiome only in the early stages of growth, but this might have an important impact on the development of maize plant.

Rhizosphere Tripartite Interactions and PGPR-Mediated Metabolic Reprogramming towards ISR and Plant Priming: A Metabolomics Review

Plant growth-promoting rhizobacteria (PGPR) are beneficial microorganisms colonising the rhizosphere. PGPR are involved in plant growth promotion and plant priming against biotic and abiotic stresses. Plant-microbe interactions occur through chemical communications in the rhizosphere and a tripartite interaction mechanism between plants, pathogenic microbes and plant-beneficial microbes has been defined. However, comprehensive information on the rhizosphere communications between plants and microbes, the tripartite interactions and the biochemical implications of these interactions on the plant metabolome is minimal and not yet widely available nor well understood. Furthermore, the mechanistic nature of PGPR effects on induced systemic resistance (ISR) and priming in plants at the molecular and metabolic levels is yet to be fully elucidated. As such, research investigating chemical communication in the rhizosphere is currently underway. Over the past decades, metabolomics approaches have been extensively used in describing the detailed metabolome of organisms and have allowed the understanding of metabolic reprogramming in plants due to tripartite interactions. Here, we review communication systems between plants and microorganisms in the rhizosphere that lead to plant growth stimulation and priming/induced resistance and the applications of metabolomics in understanding these complex tripartite interactions.

Responses of Phosphate-Solubilizing Microorganisms Mediated Phosphorus Cycling to Drought-Flood Abrupt Alternation in Summer Maize Field Soil

Soil microbial communities are essential to phosphorus (P) cycling, especially in the process of insoluble phosphorus solubilization for plant P uptake. Phosphate-solubilizing microorganisms (PSM) are the dominant driving forces. The PSM mediated soil P cycling is easily affected by water condition changes due to extreme hydrological events. Previous studies basically focused on the effects of droughts, floods, or drying-rewetting on P cycling, while few focused on drought-flood abrupt alternation (DFAA), especially through microbial activities. This study explored the DFAA effects on P cycling mediated by PSM and P metabolism-related genes in summer maize field soil. Field control experiments were conducted to simulate two levels of DFAA (light drought-moderate flood, moderate drought-moderate flood) during two summer maize growing periods (seeding-jointing stage, tasseling-grain filling stage). Results showed that the relative abundance of phosphate-solubilizing bacteria (PSB) and phosphate-solubilizing fungi (PSF) increased after DFAA compared to the control system (CS), and PSF has lower resistance but higher resilience to DFAA than PSB. Significant differences can be found on the genera Pseudomonas, Arthrobacter, and Penicillium, and the P metabolism-related gene K21195 under DFAA. The DFAA also led to unstable and dispersed structure of the farmland ecosystem network related to P cycling, with persistent influences until the mature stage of summer maize. This study provides references for understanding the micro process on P cycling under DFAA in topsoil, which could further guide the DFAA regulations.

Dynamic changes in rhizosphere fungi in different developmental stages of wheat in a confined and isolated environment

As the core food crop of a bioregenerative life support system (BLSS), wheat is susceptible to pathogen infection due to the lack of effective microbial communities in the confined and isolated environment. Therefore, a thorough understanding of the dynamic changes in wheat rhizosphere fungi is of great significance for improving wheat production and ensuring the stability of the BLSS. In the current study, we collected samples of rhizosphere fungi in the four growth stages of wheat grown in the "Lunar Palace 365" experiment. We employed bioinformatics methods to analyze the samples' species composition characteristics, community network characteristics, and FUNGuild function analysis. We found that the species composition of rhizosphere fungi in the wheat at the tillering stage changed greatly in the closed and isolated environment, while the species composition in the seedling, flowering, and mature stage were relatively stable. The results of the FUNGuild function analysis showed that the functions of rhizosphere fungi changed during wheat development. The rhizosphere fungal community was centered on Ascomycota, Mortierellomycota, and Chytridiomycota, and the community showed the characteristics of a "small world" arrangement. The stage of wheat seedlings is characterized by a greater abundance, diversity, and complexity of the network of interactions in the rhizosphere mycorrhiza community, while the tillering stage exhibited a greater clustering coefficient. Based on the changes in species composition, guild function regulation, and community structure differences of the wheat rhizosphere fungi in the BLSS, our study identified the critical fungal species during wheat development, providing a reference for ensuring the health and yield of plants in the BLSS system. KEY POINTS: • The diversity, composition, FUNguild, and network structure of rhizosphere fungi were analyzed. • Ascomycota, Mortierellomycota, and Chytridiomycota were the center of the rhizosphere fungal community network. • The effects of different wheat developmental stages on the community composition, function, and network structure of rhizosphere fungi were examined.

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.

Early response of soil fungal communities to the conversion of monoculture cropland to a temperate agroforestry system

Background

Alley-cropping systems in the temperate zone are a type of agroforestry in which rows of fast-growing trees are alternated with rows of annual crops. With numerous environmental benefits, temperate agroforestry is considered a promising alternative to conventional agriculture and soil fungi may play a key in maintaining productivity of these systems. Agroforestry systems that are established for more than 10 years have shown to increase the fungal biomass and impact the composition of soil fungal communities. Investigations of soil fungi in younger temperate agroforestry systems are scarce and the temporal dynamic of these changes is not understood.

Methods

Our study was conducted in a young poplar-based alley cropping and adjacent monoculture cropland system in an Arenosol soil in north-west Germany. We investigated the temporal dynamics of fungal populations after the establishment of agroforestry by collecting soil samples half, one, and one and a half years after conversion of cropland to agroforestry. Samples were collected within the agroforestry tree row, at 1, 7, and 24 m distance from the tree row within the crop row, and in an adjacent conventional monoculture cropland. The biomass of soil fungi, Asco-, and Basidiomycota was determined by real-time PCR. Soil fungal community composition and diversity were obtained from amplicon sequencing.

Results

Differences in the community composition of soil fungi in the tree row and arable land were detected as early as half a year following the conversion of monoculture cropland to agroforestry. In the tree row, soil fungal communities in the plots strongly diverged with the age of the system. The presence of young trees did not affect the biomass of soil fungi.

Conclusions

The composition of soil fungal communities responded rapidly to the integration of trees into arable land through agroforestry, whereas the fungal biomass was not affected during the first one and a half years after planting the trees. Fungal communities under the trees gradually diversified. Adaptation to spatially heterogeneous belowground biomass of the trees and understory vegetation or stochastic phenomena due to limited exchange among fungal populations may account for this effect; long-term monitoring might help unravelling the cause.

Local Network Properties of Soil and Rhizosphere Microbial Communities in Potato Plantations Treated with a Biological Product Are Important Predictors of Crop Yield

Understanding the effectiveness and potential mechanism of action of agricultural biological products under different soil profiles and crops will allow more precise product recommendations based on local conditions and will ultimately result in increased crop yield. This study aimed to use bulk soil and rhizosphere microbial composition and structure to evaluate the potential effect of a Bacillus amyloliquefaciens inoculant (strain QST713) on potatoes and to explore its relationship with crop yield. We implemented next-generation sequencing (NGS) and bioinformatics approaches to assess the bacterial and fungal biodiversity in 185 soil samples, distributed over four different time points—from planting to harvest—from three different geographical locations in the United States. In addition to location and sampling time (which includes the difference between bulk soil and rhizosphere) as the main variables defining the microbiome composition, the microbial inoculant applied as a treatment also had a small but significant effect in fungal communities and a marginally significant effect in bacterial communities. However, treatment preserved the native communities without causing a detectable long-lasting effect on the alpha- and beta-diversity patterns after harvest. Using information about the application of the microbial inoculant and considering microbiome composition and structure data, we were able to train a Random Forest model to estimate if a bulk soil or rhizosphere sample came from a low- or high-yield block with relatively high accuracy (84.6%), concluding that the structure of fungal communities gives us more information as an estimator of potato yield than the structure of bacterial communities.

IMPORTANCE Our results reinforce the notion that each cultivar on each location recruits a unique microbial community and that these communities are modulated by the vegetative growth stage of the plant. Moreover, inoculation of a Bacillus amyloliquefaciens strain QST713-based product on potatoes also changed the abundance of specific taxonomic groups and the structure of local networks in those locations where the product caused an increase in the yield. The data obtained, from in-field assays, allowed training a predictive model to estimate the yield of a certain block, identifying microbiome variables—especially those related to microbial community structure—even with a higher predictive power than the geographical location of the block (that is, the principal determinant of microbial beta-diversity). The methods described here can be replicated to fit new models in any other crop and to evaluate the effect of any agricultural input in the composition and structure of the soil microbiome.

Shifts in the rhizobiome during consecutive in planta enrichment for phosphate-solubilizing bacteria differentially affect maize P status

Phosphorus (P) is despite its omnipresence in soils often unavailable for plants. Rhizobacteria able to solubilize P are therefore crucial to avoid P deficiency. Selection for phosphate-solubilizing bacteria (PSB) is frequently done in vitro; however, rhizosphere competence is herein overlooked. Therefore, we developed an in planta enrichment concept enabling simultaneous microbial selection for P-solubilization and rhizosphere competence. We used an ecologically relevant combination of iron- and aluminium phosphate to select for PSB in maize (Zea mays L.). In each consecutive enrichment, plant roots were inoculated with rhizobacterial suspensions from plants that had grown in substrate with insoluble P. To assess the plants' P statuses, non-destructive multispectral imaging was used for quantifying anthocyanins, a proxy for maize's P status. After the third consecutive enrichment, plants supplied with insoluble P and inoculated with rhizobacterial suspensions showed a P status similar to plants supplied with soluble P. A parallel metabarcoding approach uncovered that the improved P status in the third enrichment coincided with a shift in the rhizobiome towards bacteria with plant growth-promoting and P-solubilizing capacities. Finally, further consecutive enrichment led to a functional relapse hallmarked by plants with a low P status and a second shift in the rhizobiome at the level of Azospirillaceae and Rhizobiaceae.

Tillage, Mulching and Nitrogen Fertilization Differentially Affects Soil Microbial Biomass, Microbial Populations and Bacterial Diversity in a Maize Cropping System

Determination of biologically active components of the soil organic matter, such as soil microbial biomass carbon (C) and nitrogen (N) can be used as indicators for variations in soil productivity due to changes in soil management. Soil agronomic management practices bring about changes in the physical and chemical properties of the soil, resulting in variations in soil microbial biomass and microbial diversity. The effects of tillage, mulch and inorganic fertilizers on soil microbial biomass C and N, microbial populations and bacterial diversity were determined from the treatment combinations which had been applied for 5 years in Central Kenyan Highlands. The test crop used was maize (Zea mays L.). The study involved conventional and minimum tillage systems, mulching and inorganic fertilizers (120 kg N/ha). Tillage (P < 0.001), mulch (P < 0.001), and fertilizer (P = 0.009) significantly affected soil microbial biomass C and N whereby minimum tillage and mulch increased soil microbial biomass C and N. Interestingly, minimum tillage and mulch recorded the highest bacteria and fungi CFUs compared to conventional tillage and inorganic fertilizers. Only fertilizer and mulch (P < 0.001) had significant effect on actinobacteria CFUs. Amplified ribosomal DNA analysis (ARDRA) showed that the highest genetic distance of 0.611 was recorded between treatments conventional tillage + no mulch + no NPK fertilizer and conventional tillage + no mulch + NPK fertilizer. The results demonstrate that minimum tillage and mulching are attractive soil agronomic management practices since they increase soil microbial biomass and bacterial diversity in agricultural soils.

Pseudomonas entomophila PE3 and its exopolysaccharides as biostimulants for enhancing growth, yield and tolerance responses of sunflower under saline conditions

Evaluation of plant growth promoting bacteria and the associated metabolites under saline conditions can be a potential eco-friendly remediation and productivity enhancement strategy. Salt-tolerant Pseudomonas entomophila PE3 was isolated from saline soil and screened for plant growth promoting (PGP) traits. The isolate produced indole acetic acid (IAA), gibberellic acid (GA), exopolysaccharides (EPS) and siderophore along with the potential to solubilize potassium (K), zinc (Zn) and phosphorus (P). Maximum stimulation of PGP attributes was recorded at 2% NaCl concentration. To determine the role of EPS, their composition was analyzed (at different salt concentrations) and comparison was done to determine the changes upon exposure to salinity. EPS was found to be rich in carbohydrates, proteins and phenolic compounds. The extracted EPS were also found to possess salt-tolerance properties including antioxidant, hydroxyl scavenging activity, reducing power, emulsification and flocculation potential, and Na⁺ accumulation ability. Interestingly, the salt tolerance properties of EPS were enhanced upon exposure to salinity (2% NaCl). Finally, EPS based bioformulation of isolate PE3 was checked through field assay in saline soil. With promising results on growth promotion and improved salinity tolerance attributes of inoculated sunflower plants, the bioformulation of PE3 amended with EPS can be a breakthrough for remediation of saline-agroecosystems.

Vegetation drives the structure of active microbial communities on an acidogenic mine tailings deposit

Plant-microbe associations are increasingly recognized as an inextricable part of plant biology and biogeochemistry. Microbes play an essential role in the survival and development of plants, allowing them to thrive in diverse environments. The composition of the rhizosphere soil microbial communities is largely influenced by edaphic conditions and plant species. In order to decipher how environmental conditions on a mine site can influence the dynamics of microbial communities, we characterized the rhizosphere soil microbial communities associated with paper birch, speckled alder, and spruce that had naturally colonized an acidogenic mine tailings deposit containing heavy metals. The study site, which had been largely undisturbed for five decades, had highly variable vegetation density; with some areas remaining almost barren, and others having a few stands or large thickets of mature trees. Using Illumina sequencing and ordination analyses (redundancy analysis and principal coordinate analysis), our study showed that soil bacterial and fungal community structures correlated mainly with vegetation density, and plant species. Tailings without any vegetation were the most different in bacterial community structure, compared to all other areas on the mine site, as well as an adjacent natural forest (comparison plot). The bacterial genera Acidiferrobacter and Leptospirillum were more abundant in tailings without vegetation than in any of the other sites, while Bradyrhizobium sp. were more abundant in areas of the tailings deposit having higher vegetation density. Frankia sp. is equally represented in each of the vegetation densities and Pseudomonas sp. present a greater relative abundance in boreal forest. Furthermore, alder rhizosphere showed a greater relative abundance of Bradyrhizobium sp. (in comparison with birch and spruce) as well as Haliangium sp. (in comparison with birch). In contrast, fungal community structures were similar across the tailings deposit regardless of vegetation density, showing a greater relative abundance of Hypocrea sp. Tailings deposit fungal communities were distinct from those found in boreal forest soils. Alder rhizosphere had greater relative abundances of Hypocrea sp. and Thelephora sp., while birch rhizosphere were more often associated with Mollisia sp. Our results indicate that, with increasing vegetation density on the mine site, the bacterial communities associated with the individual deciduous or coniferous species studied were increasingly similar to the bacterial communities found in the adjacent forest. In order to properly assess and restore disturbed sites, it is important to characterize and understand the plant-microbe associations that occur since they likely improve plant fitness in these harsh environments.

Optimization of microbial assisted phytoremediation of soils contaminated with pesticides

580 microbial strains were isolated from the rhizosphere of the plants Cucurbita pepo L. and Xanthium strumarium grown on soil contaminated with dichlorodiphenyltrichloroethane (DDT) and its metabolites. During the cultivation, two bacterial strains were selected because of their ability to grow on media containing 0.5-5.0 mg L^-1 of dichlorodiphenyldichloroethylene (DDE) as the sole carbon source. They were identified as Bacillus vallismortis and Bacillus aryabhattai. Both of these species were shown to have a high capacity for the utilization of DDE - more than 90% of which was consumed after 21 days of cultivation. Laboratory experiments were carried out then to assess the possibility of using these strains for the decontamination of organochlorine pesticides (OCPs) contaminated soils. Inoculation of C. pepo and X. strumarium with our isolates B. vallismortis and B. aryabhattai resulted in a reduction of the pollutant stress to the plants as shown by an increase both in aboveground and in root biomass. The microorganisms enhanced the uptake and phytostabilization potential of C. pepo and X. strumarium and can be applied for the treatment of DDE contaminated soils.

Life in mine tailings: microbial population structure across the bulk soil, rhizosphere, and roots of boreal species colonizing mine tailings in northwestern Québec

Purpose

Mining activities have negative effects on soil characteristics and can result in low pH, high heavy metal content, and limited levels of essential nutrients. A tailings storage area located in northwestern Québec showed natural colonization by plants from the adjacent natural environment. The objective of the study was to determine the main edaphic parameters that structured microbial populations associated with the indigenous woody plants that had naturally colonized the site.

Methods

Microbial populations were studied in the bulk soil, the rhizosphere, and inside plant roots using Illumina sequencing, ordination analysis (i.e., redundancy analysis (RDA) and principal coordinates analysis (PCoA)), ternary plotting, and statistical analysis (MANOVA).

Results

The main variables that drove the microbial community patterns were plant species and the tailings pH. Indeed, the main bacterial classes were Gammaproteobacteria and Deltaproteobacteria in both the rhizosphere and root endosphere. Analysis revealed that some dominant operational taxonomic units (e.g., Pseudomonas sp., Acinetobacter sp., and Delftia sp.) were present in increased proportions in roots for each plant species under study. This study also revealed that many of the most abundant fungal genera (e.g., Claussenomyces, Eupenicillium, and Trichoderma) were more abundant in the rhizosphere than in the root endosphere.

Conclusions

This comprehensive study of the microbial community dynamics in the bulk soil, rhizosphere, and root endosphere of boreal trees and shrubs could be beneficial in facilitating the rehabilitation of disturbed ecosystems.

Revealing structure and assembly for rhizophyte-endophyte diazotrophic community in mangrove ecosystem after introduced Sonneratia apetala and Laguncularia racemosa

Biological nitrogen fixation (BNF) mediated by diazotrophic communities is a major source of bioavailable nitrogen in mangrove wetlands, which plays important roles in maintaining the health and stability of mangrove ecosystems. Recent large-scale mangrove afforestation activities have drawn great attention due to introduced mangrove species and their potential impacts on bio-functionalities of local ecosystems. However, the effects of introduced mangrove species on diazotrophic communities remain unclear. Here, we analyzed rhizosphere and endosphere diazotrophic communities between native mangrove species (Avicennia marina) and introduced mangrove species (Sonneratia apetala and Laguncularia racemose) by sequencing nifH gene amplicons. Our results showed that S. apetala and L. racemose introduction significantly (P < 0.05) increased nutrition components (e.g., total carbon and total nitrogen) in rhizosphere, as well as the diazotrophs richness in rhizosphere and endosphere. The relative abundance of clusters III diazotrophs in the rhizosphere and Rhizobium in the endosphere were significantly increased with L. racemosa or S. apetala introduction. Fe and pH were the main environmental factors driving the divergence of endophyte-rhizophyte diazotrophs between native and introduced mangroves. The correlation-based network analyses indicated that the interaction among rhizophyte-endophyte diazotrophs is more harmonious in native mangrove, while there exist more competition in introduced mangroves. These findings expand our current understanding of BNF in mangrove afforestation, and providing new perspectives to sustainable management of mangrove ecosystem.

Effects of Drought-Flood Abrupt Alternation on the Growth of Summer Maize

Climate change, especially precipitation change, will significantly change soil moisture, which then influences root growth, further affecting yield and grain quality. Previous studies focused on the drought or flood effects on summer maize growth. However, few studied the effects of drought-flood abrupt alternation (DFAA) on the growth of summer maize. We explored the DFAA impacts on the roots, leaf area index (LAI), yield, and grain quality in field. The main results show that DFAA had different impacts on the summer maize growth in the seeding-jointing stage (SJS) and tasseling-grain filling stage (TGS). In general, the DFAA reduced the yield. Roots at the depth of 40 cm had obviously positive impacts on the yield. The DFAA reduced the LAI and promoted the maximum LAI achieving in advance. The grain crude protein augmented under DFAA. The drought had evidently negative impacts on the grain crude fat in the TGS, while it had no obvious influence in the SJS. DFAA had no apparent impact on the grain crude starch. These results could provide some references for the effects and adaptation-strategies study of extreme climate events and their impacts on growth of summer maize.

Bacterial rhizosphere community profile at different growth stages of Umorok (Capsicum chinense) and its response to the root exudates

The role of microflora is an indispensable part of the living organisms. Plants actively recruit specific microbial community to establish favorable habitat with the distinct microbiome, essentially unique for each species, offering new opportunities for plant growth and productivity. Umorok, an indigenous chili variety of northeastern India, production is highly affected by various factors; therefore, rhizosphere bacteria and their relationship with the root exudates released were analyzed to demonstrate rhizosphere bacterial impact on plant growth and health. Culturable and metagenomic bacterial DNA was characterized and the chemical nature of the root exudate was analyzed using chemotaxis assay after its basic analysis in HPLC. Juvenile stage exhibited diverse bacterial species of gammaproteobacteria, alphaproteobacteria, and actinobacteria but lacked the betaproteobacteria while the microbial diversity was reduced in flowering and fruiting stages. However, every growth stage maintained a similar amount of bacterial population regardless of diversity. The population of Pseudomonas, Bacillus, and Burkholderia species was increased several folds in flowering and fruiting stage. Further, the chemotaxis assay unveiled the advantage of root exudate chemical composition for specific microbial recruitment. The chemical composition analysis of root exudates showed substantial variation in the concentration of organic acids, phenolics, and flavonoids that are favoring unique bacterial species. Thus, root exudates confer and limit the related microbial population besides typical plant-bacterial synergetic association. This study emphasized information about the type of microbial load present in each growth stage, which is essential to develop a microbial consortia package for Umorok overall crop improvement.

Bacterial communities associated to Chilean altiplanic native plants from the Andean grasslands soils

The rhizosphere is considered the primary place for soil microbiome differentiation and plays a key role in plant survival, especially for those subjected to environmental stress. Using high-throughput sequencing of the 16S rRNA gene, we analyzed and compared soil bacterial communities associated to four of the most abundant high altitude native plant species of the Chilean Andean grasslands. We examined three soil compartments: the rhizosphere (bacteria firmly attached to the roots), the rhizosphere-surrounding soil (bacteria loosely attached to the roots) and the bulk soil (plant-free soil). The rhizosphere microbiome was in all cases the least diverse, exposing that the bulk soil was a more complex environment. Taxonomic analysis revealed an abrupt change between the rhizosphere and the rest of the non-rhizospheric soils. Thus, while rhizobacterial communities were enriched in Proteobacteria (mainly Alphaproteobacteria), Actinobacteria (mostly Blastocatellia) dominated in bulk soils. Finally, we detected certain taxonomic rhizosphere signatures, which could be attributed to a particular genotype. Overall, our results indicate that the thin layer of soil surrounding the roots constitute a distinctive soil environment. This study contributes to expand the knowledge about soil bacterial communities in the Chilean highlands and takes the first step to understand the processes that might lead to the rhizosphere differentiation in that area.

Bacterial diversity in soils of different Hungarian karst areas

Karst areas have great environmental importance as sources of subsurface water and often maintain very sensitive ecosystems. In recent years, increasing number of microbiological studies focused on the bacterial communities of karst soils. In this study, diversity examinations on two distinct Hungarian karst areas, Aggtelek and Tapolca, were performed using parallel cultivation and molecular cloning methods. The phylogenetic affiliation of bacterial strains and molecular clones was determined based on their 16S rRNA gene sequences. Bacterial isolates were identified as members of the phyla Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. Besides the taxa identified by cultivation, members of the phyla Chloroflexi, Cyanobacteria, Acidobacteria, Verrucomicrobia, and Gemmatimonadetes were detected by the cloning. The difference in the composition of soil bacterial communities was related to geographic locations and soil types. Both the highest and the lowest bacterial diversities were detected in samples from Aggtelek National Park, characterized by Leptic Luvisol and Rendzic Leptosol soil types. The difference in the composition of bacterial communities between Rendzic Leptosol and Leptic Phaeozem soil types at Tapolca could be the result of human impacts.

Nitrogen Fixation in Cereals

Cereals such as maize, rice, wheat and sorghum are the most important crops for human nutrition. Like other plants, cereals associate with diverse bacteria (including nitrogen-fixing bacteria called diazotrophs) and fungi. As large amounts of chemical fertilizers are used in cereals, it has always been desirable to promote biological nitrogen fixation in such crops. The quest for nitrogen fixation in cereals started long ago with the isolation of nitrogen-fixing bacteria from different plants. The sources of diazotrophs in cereals may be seeds, soils, and even irrigation water and diazotrophs have been found on roots or as endophytes. Recently, culture-independent molecular approaches have revealed that some rhizobia are found in cereal plants and that bacterial nitrogenase genes are expressed in plants. Since the levels of nitrogen-fixation attained with nitrogen-fixing bacteria in cereals are not high enough to support the plant’s needs and never as good as those obtained with chemical fertilizers or with rhizobium in symbiosis with legumes, it has been the aim of different studies to increase nitrogen-fixation in cereals. In many cases, these efforts have not been successful. However, new diazotroph mutants with enhanced capabilities to excrete ammonium are being successfully used to promote plant growth as commensal bacteria. In addition, there are ambitious projects supported by different funding agencies that are trying to genetically modify maize and other cereals to enhance diazotroph colonization or to fix nitrogen or to form nodules with nitrogen-fixing symbiotic rhizobia.

Rhizosphere Bacterial Communities Differ According to Fertilizer Regimes and Cabbage (Brassica oleracea var. capitata L.) Harvest Time, but Not Aphid Herbivory

Rhizosphere microbial communities are known to be highly diverse and strongly dependent on various attributes of the host plant, such as species, nutritional status, and growth stage. High-throughput 16S rRNA gene amplicon sequencing has been used to characterize the rhizosphere bacterial community of many important crop species, but this is the first study to date to characterize the bacterial and archaeal community of Brassica oleracea var. capitata. The study also tested the response of the bacterial community to fertilizer type (organic or synthetic) and N dosage (high or low), in addition to plant age (9 or 12 weeks) and aphid (Myzus persicae) herbivory (present/absent). The impact of aboveground herbivory on belowground microbial communities has received little attention in the literature, and since the type (organic or mineral) and amount of fertilizer applications are known to affect M. percicae populations, these treatments were applied at agricultural rates to test for synergistic effects on the soil bacterial community. Fertilizer type and plant growth were found to result in significantly different rhizosphere bacterial communities, while there was no effect of aphid herbivory. Several operational taxonomic units were identified as varying significantly in abundance between the treatment groups and age cohorts. These included members of the S-oxidizing genus Thiobacillus, which was significantly more abundant in organically fertilized 12-week-old cabbages, and the N-fixing cyanobacteria Phormidium, which appeared to decline in synthetically fertilized soils relative to controls. These responses may be an effect of accumulating root-derived glucosinolates in the B. oleracea rhizosphere and increased N-availability, respectively.

Community structure and plant growth-promoting potential of cultivable bacteria isolated from Cameroon soil

Exploiting native plant growth-promoting rhizobacteria (PGPR) in Cameroonian agro-ecosystems provides a means to improve plant-microbe interactions that may enhance ecosystem sustainability and agricultural productivity in an environmentally eco-friendly way. Consequently, we aimed to investigate the community structure and functional PGPR diversity of maize grown in Cameroon. Native bacteria isolated from Cameroon maize rhizosphere soil were identified by partial 16S rRNA gene sequencing and screened for traits particularly relevant for Cameroon low-fertility soil conditions, such as their abilities to tolerate high concentrations of salt, and their plant growth- promoting potential. Genetic and functional diversity was characterized according to their phylogenetic affiliation. A total of 143 bacteria were identified and assigned to 3 phyla (Actinobacteria, Firmicutes and Proteobacteria), 13 families and 20 genera. Bacillus (31.5%), Arthrobacter (17.5%), and Sinomonas (13.3%) were the most abundant genera identified among all the isolates. Based on their in vitro characterization, 88.1% were salt tolerant at 2% NaCl, but only 16.8% could tolerate 8% NaCl, 50.4% solubilized phosphate, 10.5% possessed the nifH gene, and 19.6% produced siderophores. Six isolates affiliated to the most abundant genera identified in this work, Bacillus and Arthrobacter, carrying multiple or only single tested traits were selected to evaluate their growth- promoting potential in an in vitro maize germination assay. Three strains possessing multiple traits induced significantly increased hypocotyl and root length of maize seeds compared to non-inoculated control seeds. Our results indicate the potential of selected indigenous Cameroon rhizobacteria to enhance maize growth.

Drought and host selection influence bacterial community dynamics in the grass root microbiome

Root endophytes have been shown to have important roles in determining host fitness under periods of drought stress, and yet the effect of drought on the broader root endosphere bacterial community remains largely uncharacterized. In this study, we present phylogenetic profiles of bacterial communities associated with drought-treated root and rhizosphere tissues of 18 species of plants with varying degrees of drought tolerance belonging to the Poaceae family, including important crop plants. Through 16S rRNA gene profiling across two distinct watering regimes and two developmental time points, we demonstrate that there is a strong correlation between host phylogenetic distance and the microbiome dissimilarity within root tissues, and that drought weakens this correlation by inducing conserved shifts in bacterial community composition. We identify a significant enrichment in a wide variety of Actinobacteria during drought within the roots of all hosts, and demonstrate that this enrichment is higher within the root than it is in the surrounding environments. Furthermore, we show that this observed enrichment is the result of an absolute increase in Actinobacterial abundance and that previously hypothesized mechanisms for observed enrichments in Actinobacteria in drought-treated soils are unlikely to fully account for the phenomena observed here within the plant root.

The Value of a Comparative Approach to Understand the Complex Interplay between Microbiota and Host Immunity

The eukaryote immune system evolved and continues to evolve within a microbial world, and as such is critically shaped by-and in some cases even reliant upon-the presence of host-associated microbial species. There are clear examples of adaptations that allow the host to simultaneously tolerate and/or promote growth of symbiotic microbiota while protecting itself against pathogens, but the relationship between immunity and the microbiome reaches far beyond simple recognition and includes complex cross talk between host and microbe as well as direct microbiome-mediated protection against pathogens. Here, we present a broad but brief overview of how the microbiome is controlled by and interacts with diverse immune systems, with the goal of identifying questions that can be better addressed by taking a comparative approach across plants and animals and different types of immunity. As two key examples of such an approach, we focus on data examining the importance of early exposure on microbiome tolerance and immune system development and function, and the importance of transmission among hosts in shaping the potential coevolution between, and long-term stability of, host-microbiome associations. Then, by comparing existing evidence across short-lived plants, mouse model systems and humans, and insects, we highlight areas of microbiome research that are strong in some systems and absent in others with the hope of guiding future research that will allow for broad-scale comparisons moving forward. We argue that such an approach will not only help with identification of generalities in host-microbiome-immune interactions but also improve our understanding of the role of the microbiome in host health.

Rhizosphere effect is stronger than PAH concentration on shaping spatial bacterial assemblages along centimetre-scale depth gradients

At centimetre scale, soil bacterial assemblages are shaped by both abiotic (edaphic characteristics and pollutants) and biotic parameters. In a rhizobox experiment carried out on planted industrial soil contaminated with polycyclic aromatic hydrocarbons (PAHs), we previously showed that pollution was distributed randomly with hot and cold spots. Therefore, in the present study, we investigated the effect of this patchy PAH distribution on the bacterial community assemblage and compared it with that of root depth gradients found in the rhizosphere of either alfalfa or ryegrass. Sequencing of 16S rRNA amplicons revealed a higher bacterial diversity in ryegrass rhizosphere and enrichment in specific taxa by the 2 plant species. Indeed, Bacteroidetes, Firmicutes, and Gammaproteobacteria were globally favored in alfalfa, whereas Acidimicrobiia, Chloroflexi, Alpha-, and Betaproteobacteria were globally favored in ryegrass rhizosphere. The presence of alfalfa created depth gradients of root biomass, carbohydrate, and pH, and actually shaped the bacterial assemblage, favoring Actinobacteria near the surface and Gemmatimonadetes and Proteobacteria at greater depths. Contrarily, the bacterial assemblage was homogeneous all along depths of the ryegrass root system. With both plant species, the PAH content and random distribution had no significant effect on bacterial assemblage. Globally, at centimeter scale, bacterial community assemblages were mostly shaped by soil physical and chemical depth gradients induced by root growth but not by patchy PAH content.

Long-Term Rock Phosphate Fertilization Impacts the Microbial Communities of Maize Rhizosphere

Phosphate fertilization is a common practice in agriculture worldwide, and several commercial products are widely used. Triple superphosphate (TSP) is an excellent soluble phosphorus (P) source. However, its high cost of production makes the long-term use of crude rock phosphate (RP) a more attractive alternative in developing countries, albeit its influence on plant-associated microbiota remains unclear. Here, we compared long-term effects of TSP and RP fertilization on the structure of maize rhizosphere microbial community using next generation sequencing. Proteobacteria were dominant in all conditions, whereas Oxalobacteraceae (mainly Massilia and Herbaspirillum) was enriched in the RP-amended soil. Klebsiella was the second most abundant taxon in the RP-treated soil. Burkholderia sp. and Bacillus sp. were enriched in the RP-amended soil when compared to the TSP-treated soil. Regarding fungi, Glomeromycota showed highest abundance in RP-amended soils, and the main genera were Scutellospora and Racocetra. These taxa are already described as important for P solubilization/acquisition in RP-fertilized soil. Maize grown on TSP and RP-treated soil presented similar productivity, and a positive correlation was detected for P content and the microbial community of the soils. The results suggest changes of the microbial community composition associated to the type of phosphate fertilization. Whilst it is not possible to establish causality relations, our data highlights a few candidate taxa that could be involved in RP solubilization and plant growth promotion. Moreover, this can represent a shorter path for further studies aiming the isolation and validation of the taxa described here concerning P release on the soil plant system and their use as bioinoculants.

Metagenomic analyses of bacterial endophytes associated with the phyllosphere of a Bt maize cultivar and its isogenic parental line from South Africa

Genetic modification of maize with Bacillus thuringiensis (Bt) cry proteins may predispose shifts in the bacterial endophytes' community associated with maize shoots. In this study, the diversity of bacterial endophytes associated with a Bt maize genotype (Mon810) and its isogenic non-transgenic parental line were investigated at pre-flowering (50 days) and post-flowering (90 days) developmental stages. PCR-DGGE and high throughput sequencing on the Illumina MiSeq sequencer were used to characterize bacterial 16S rRNA gene diversity in leaves, stems, seeds and tassels. PCR-DGGE profile revealed similarity as well as differences between bacterial communities of shoots in both cultivars and at both developmental stages. A total of 1771 operational taxonomic units (OTUs) were obtained from the MiSeq and assigned into 14 phyla, 27 classes, 58 orders, 116 families and 247 genera. Differences in alpha and beta diversity measures of OTUs between the phyllospheres of both genotypes were not significant (P > .05) at all developmental stages. In all cultivars, OTU diversity reduced with plant development. OTUs belonging to the phyla Proteobacteria were dominant in all maize phyllospheres. The class Gammaproteobacteria was dominant in Bt maize while, Alphaproteobacteria and Actinobacteria were dominant in non-Bt maize phyllospheres. Differences in the abundance of some genera, including Acidovorax, Burkerholderia, Brachybacterium, Enterobacter and Rhodococcus, whose species are known beneficial endophytes were observed between cultivars. Hierarchical cluster analysis further suggests that the bacterial endophyte communities of both maize genotypes associate differently (are dissimilar). Overall, the results suggest that bacterial endophytes community differed more across developmental stages than between maize genotypes.

Successive soybean-monoculture cropping assembles rhizosphere microbial communities for the soil suppression of soybean cyst nematode

One of the mechanisms of disease suppressiveness in soils is long-term monoculture (LTM) cropping to dissuade pathogen infestation. However, the linkage between monoculturing and microbial community assemblage in the rhizosphere for disease suppression remains unclear. To decipher this potential relationship, soil samples were collected from seven locations in northeastern China, where LTM (6-38 yr) and short-term monoculture (STM ≤ 5 yr) cropping of soybean showed varying degrees of soil suppressiveness to the soybean cyst nematode (SCN; Heterodera glycines). Using high-throughput pyrosequencing to examine bacterial 16S rRNA and fungal ITS1 genes, we observed substantial variation in the species richness and relative abundance of taxa in the rhizosphere across different sampling sites. At the genus level, the genera Pseudomonas, Purpureocillium and Pochonia, which have been documented to suppress SCN in earlier studies, were much more abundant in LTM soils than in STM soils. Moreover, the relative abundance of several bacterial and fungal genera with metabolic, biocidal and parasitic activities was also monitored in the rhizosphere. In this study, we provide additional evidence that plants shift the structural and functional composition of the rhizosphere microbiota to suppress pathogen infection in LTM cropping soils.

Diversity of root-associated arbuscular mycorrhizal fungal communities in a rubber tree plantation chronosequence in Northeast Thailand

Rubber tree (Hevea brasiliensis) is of major economic importance in Southeast Asia and for small land holders in Thailand in particular. Due to the high value of latex, plantations are expanding into unsuitable areas, such as the northeast province of Thailand where soil fertility is very low and therefore appropriate management practices are of primary importance. Arbuscular mycorrhizal fungi (AMF) contribute to plant growth through a range of mechanisms and could play a key role in a more sustainable management of the rubber plantations. We described the diversity of AMF associated with rubber tree roots in Northeast Thailand in relation to tree age and soil parameters along a chronosequence of rubber tree plantations. Cassava fields were included for comparison. Rubber tree and cassava roots harbored high diversity of AMF (111 Virtual Taxa, VT), including 20 novel VT. AMF VT richness per sample was consistently high (per site mean 16 to 21 VT per sample) along the chronosequence and was not related to soil properties. The composition of AMF communities differed between cassava and rubber tree plantations and was influenced by soil texture and nutrient content (sand, K, P, Ca). AMF community composition gradually shifted with the age of the trees. Our results suggest that the high diversity of AMF in this region is potentially significant for maintaining high functionality of AMF communities.

Endophytic fungus Phomopsis liquidambari and different doses of N-fertilizer alter microbial community structure and function in rhizosphere of rice

Microbial community structure and functions of rhizosphere soil of rice were investigated after applying low and high doses of nitrogenous fertilizer and Phomopsis liquidambari. Average well color development, substrate richness, catabolic diversity and soil enzymes activities varied after applying N-fertilizer and P. liquidambari and were greater in P. liquidambari treated soil than only N-fertilization. Multivariate analysis distinctly separated the catabolic and enzymes activity profile which statistically proved alteration of microbial functional diversity. Nitrogen fertilizer altered microbial community structure revealed by the increased content of total PLFAs, specific subgroup marker PLFAs except fungal PLFAs and by the decreased ratio of G(+)/G(-), sat/monunsat, iso/anteiso, F/B except trans/cis while P. liquidambari inoculation enhanced N-fertilization effect except increased fungal PLFA and decreased trans/cis. PCA using identified marker PLFAs revealed definite discrimination among the treatments which further statistically confirmed structural changed of microbial community. Nitrogenase activity representative of N-fixing community decreased in N-fertilizer treatment while P. liquidambari inoculation increased. In short, application of P. liquidambari with low doses of N-fertilizer improved rice growth and reduced N-fertilizer requirement by increasing enzymes activities involved in C, N and P cycling, structural and functional diversity of microbes, nitrogenase activity involved in N2 fixation and accumulation of total-N.

Proliferation of the biocontrol agent Fusarium oxysporum f. sp. strigae and its impact on indigenous rhizosphere fungal communities in maize under different agro-ecologies

Our objectives were to (1) monitor the proliferation of the biocontrol agent (BCA) Fusarium oxysporum f. sp. strigae strain "Foxy-2", an effective soil-borne BCA against the parasitic weed Striga hermonthica, in the rhizosphere of maize under different agro-ecologies, and (2) investigate its impact on indigenous rhizosphere fungal community abundance and composition. Field experiments were conducted in Busia and Homa Bay districts in western Kenya during two cropping seasons to account for effects of soil type, climate, growth stage and seasonality. Maize seeds were coated with or without "Foxy-2" and soils were artificially infested with S. hermonthica seeds. One treatment with nitrogen rich organic residues (Tithonia diversifolia) was established to compensate hypothesized resource competition between "Foxy-2" and the indigenous fungal community. Rhizosphere soil samples collected at three growth stages (i.e., EC30, EC60, EC90) of maize were subjected to abundance measurement of "Foxy-2" and total indigenous fungi using quantitative polymerase chain reaction (qPCR) analysis. Terminal restriction fragment length polymorphism (TRFLP) analysis was used to assess potential alterations in the fungal community composition in response to "Foxy-2" presence. "Foxy-2" proliferated stronger in the soils with a sandy clay texture (Busia) than in those with a loamy sand texture (Homa Bay) and revealed slightly higher abundance in the second season. "Foxy-2" had, however, only a transient suppressive effect on total indigenous fungal abundance which ceased in the second season and was further markedly compensated after addition of T. diversifolia residues. Likewise, community structure of the indigenous fungal community was mainly altered by maize growth stages, but not by "Foxy-2". In conclusion, no adverse effects of "Foxy-2" inoculation on indigenous fungal rhizosphere communities were observed corroborating the safety of this BCA under the given agro-ecologies.

The plant microbiome

Plant genomes contribute to the structure and function of the plant microbiome, a key determinant of plant health and productivity. High-throughput technologies are revealing interactions between these complex communities and their hosts in unprecedented detail.

Rhizosphere bacteria ofCostulariaspp. from ultramafic soils in New Caledonia: diversity, tolerance to extreme edaphic conditions, and role in plant growth and mineral nutrition

Rhizosphere bacteria were isolated from Costularia spp., pioneer sedges from ultramafic soils in New Caledonia, which is a hotspot of biodiversity in the South Pacific. Genus identification, ability to tolerate edaphic constraints, and plant-growth-promoting (PGP) properties were analysed. We found that 105colony-forming units per gram of root were dominated by Proteobacteria (69%) and comprised 21 genera, including Burkholderia (28%), Curtobacterium (15%), Bradyrhizobium (9%), Sphingomonas (8%), Rhizobium (7%), and Bacillus (5%). High proportions of bacteria tolerated many elements of the extreme edaphic conditions: 82% tolerated 100 μmol·L–1chromium, 70% 1 mmol·L–1nickel, 63% 10 mmol·L–1manganese, 24% 1 mmol·L–1cobalt, and 42% an unbalanced calcium/magnesium ratio (1/16). These strains also exhibited multiple PGP properties, including the ability to produce ammonia (65%), indole-3-acetic acid (60%), siderophores (52%), and 1-aminocyclopropane-1-carboxylate (ACC) deaminase (39%); as well as the capacity to solubilize phosphates (19%). The best-performing strains were inoculated with Sorghum sp. grown on ultramafic substrate. Three strains significantly enhanced the shoot biomass by up to 33%. The most successful strains influenced plant nutrition through the mobilization of metals in roots and a reduction of metal transfer to shoots. These results suggest a key role of these bacteria in plant growth, nutrition, and adaptation to the ultramafic constraints.

Physiological studies on endorhizospheric establishment of Azotobacter chroococcum in wheat

Ten strains of Azotobacter chroococcum were studied for their ability to invade the endorhizosphere of wheat. Strain W-5 exhibited ability to invade endorhizosphere as shown in the microscopic observations. This strain was compared with the strain OA-3 which did not invade the endorhizosphere zone. Strain W-5 showed higher production of cellulase and pectinase than OA-3. Both the strains induced defense enzymes in the host plant. However, induction of peroxidase and phenylalanine ammonia lyase activities (PAL) was higher in OA-3 than W-5. Quantitative differences in flavonoid like compounds obtained from root extracts and root exudates of plants inoculated with these strains were observed.