Bacterial diversity amplifies nutrient‐based plant–soil feedbacks

Rhizospheric crosstalk: A mechanistic overview of how plant secondary metabolites alleviate abiotic stresses

Plants often encounter incompatible growing conditions, such as drought, extreme temperatures, salinity, and heavy metals, which negatively impact their growth and development, resulting in reduced yield and, in severe cases, plant death. These stresses trigger the synthesis of plant secondary metabolites (PSMs), which help plants develop strategies to deter enemies, combat pathogens, outcompete competitors, and overcome environmental restraints. PSMs are released into the rhizosphere and play crucial roles in plant defense and communication. The multifunctionality of PSMs offers new insights into the plant intricate adaptive responses, which can refine our understanding of plant tolerance mechanisms in challenging environments. Thus, elucidating the chemical composition and functions of plant-derived specialized metabolites in the rhizosphere is the key to understanding interactions in this belowground environment. In this review, we aim to elucidate how PSMs exudation shapes the activities and abundance of the rhizosphere microbiome. We also highlight key environmental factors that regulate the structure and diversity of microbial communities. Finally, we discuss various preventive roles of PSMs, exploring how plants recruit microbes preemptively to mitigate diverse abiotic stresses. Additionally, we emphasize the significant contribution of phenolic compounds to the antioxidant defense response in plants, regulated through the shikimate pathway and is considered as a distinctive plant stress resilience component as compared to other PSMs under abiotic stress. Collectively, this study reveals the significance of understanding the multifaceted crosstalk between PSMs and the microbiome, which will facilitate the potential for developing methods to manipulate PSMs-microbiome interaction with predictive outcomes for sustainable crop production.

Identity and timing of protist inoculation affect plant performance largely irrespective of changes in the rhizosphere microbial community

Bacterivorous soil protists can have positive impacts on plant performance, making them attractive targets for novel strategies to improve crop production. However, we generally lack the knowledge required to make informed choices regarding the protist species to be used or the optimal conditions for such amendments. Here, we examined how identity, diversity, and timing of inoculation of well-described protists impacted plant development and rhizosphere microbiome assembly. We first studied the impact of individual inoculation of six well-characterized protists on lettuce growth, with Cercomonas sp. S24D2 emerging as the strain with the largest impact on plant growth. In a second step, we created a three-protist species mixture inoculant by adding two protist species (Acanthamoeba sp. C13D2 and a heterolobosean isolate S18D10), based on differences in their feeding patterns. We then inoculated Cercomonas sp. either individually or in the protist mixture to lettuce plants 1 week before, simultaneously with, or 1 week after seedling transfer. We monitored plant growth and nutrient content, as well as impacts on the resident soil and rhizosphere microbiome composition. We found that early protist inoculation provided the greatest increase in aboveground biomass compared to the non-inoculated control. Single- and mixed-species inoculations had similar impacts on plant development and only minor impacts on prokaryotic community composition. While early inoculation seems to be the most promising timing for eliciting the positive effects of protist amendments, further, more systematic studies will be necessary to determine the conditions and ecological interactions that yield consistent and predictable improvements in plant performance.

IMPORTANCE

The application of microorganisms, including bacterivorous soil protists, has been increasingly suggested as a sustainable agricultural approach. While positive impacts of the presence of predatory protists have been generally reported, the effects of the selected species and amendment conditions are largely unknown. Here, we examined how identity, diversity, and timing of inoculation of well-described protists impacted plant development and rhizosphere microbiome assembly. One species emerged as the one having the strongest impact in our specific system. This result highlights the importance of species selection for optimal outcome, but also suggests a huge potential in the barely investigated protist diversity for targeted application. Furthermore, the application of the inoculants before plant transfer showed the strongest effects on plants, providing some useful and new insights on the optimal time for such amendments.

Changes in Plant Biomass Are Driven by Persisting Plant Species, but Species Gains Drive Nematode Carbon Dynamics

Global change drivers, such as shrub encroachment, alter above- and belowground communities, and the consequences of these changes for ecosystem functioning are largely unknown. We used the modified Price equation to quantify how the presence of shrubs alters the richness, composition, and abundance of plant and nematode communities and the resulting effects on ecosystem functioning (i.e., plant biomass and nematode carbon [C] metabolism) on the Qinghai-Tibet Plateau. Plots with shrubs had increased plant biomass (mostly due to persisting plant species producing more biomass) and nematode C metabolism (mostly due to increases in nematode species richness). The strength of the species richness effect on plant biomass was positively associated with the strength of the species richness on nematode C metabolism. Increases in the biomass of persisting species and species gains promote plant biomass and nematode C metabolism, respectively, which may accelerate decomposition and C turnover on the Qinghai-Tibet Plateau.

Soil chemical factors contributing to differences in bacterial communities among tea field soils and their relationships with tea quality

Introduction

Soil chemical properties and bacterial communities play key roles in shaping tea plant nutrient status and quality. While the relationships between soil bacterial communities and plant nutrient status have been investigated, the specific role by which soil bacterial communities interacted with soil properties to influence tea plant nutrients and quality remained underexplored.

Methods

In this study, different soil types were collected from tea gardens and designated as soil A (pH 3.41), soil B (pH 3.75), soil C (pH 4.16), soil D (pH 4.17) and soil E (pH 5.56) based on the initial soil pH. We conducted pot cultivation of tea plant 'Yabukita' to investigate how soil chemical factors affect bacterial communities and their influences on the nutrient status and quality of tea plants, and finally explored the complex relationships between soil bacterial features and tea quality.

Results and discussion

The results showed that soil bacterial α-diversity was higher level in soils D and E, with distinct β-diversity patterns separating higher pH soils (D and E) from lower pH soils (A, B, and C). The dominant amplicon sequence variants (ASVs) in soils were Proteobacteria (28.12%), Actinobacteriota (25.65%), Firmicutes (9.99%) at phylum level, and Acidothermaceae (7.24%), Solirubrobacteraceae (4.85%), and Acetobacteraceae (4.50%) at family level. Soil pH, exchangeable Mg2+, and Ca2+ were identified as key factors shaping bacterial community composition and positively correlated with bacterial diversity. Differentially abundant ASVs (DAAs) among all soils were also identified including the phylum Firmicutes and families such as Paenibacillaceae, Alicyclobacillaceae, JG36-TzT-191, KF-JG30-C25, and Acidobacteriaceae_subgroup1. Besides, the nutrient content of tea new leaves varied significantly among soil types and harvests. Combined with Mantel-test association analysis, soil chemical properties and soil bacterial communities were jointly correlated with the contents of total nitrogen, potassium, calcium, aluminum, magnesium, free amino acids, and caffeine in tea new leaves. These findings highlight the dynamic interactions between soil properties, bacterial communities, and tea nutrients, emphasizing the importance of optimizing soil health and bacterial networks to improve tea quality.

Mechanisms and Impact of Rhizosphere Microbial Metabolites on Crop Health, Traits, Functional Components: A Comprehensive Review

Current agricultural practices face numerous challenges, including declining soil fertility and heavy reliance on chemical inputs. Rhizosphere microbial metabolites have emerged as promising agents for enhancing crop health and yield in a sustainable manner. These metabolites, including phytohormones, antibiotics, and volatile organic compounds, play critical roles in promoting plant growth, boosting resistance to pathogens, and improving resilience to environmental stresses. This review comprehensively outlines the mechanisms through which rhizosphere microbial metabolites influence crop health, traits, functional components, and yield. It also discusses the potential applications of microbial secondary metabolites in biofertilizers and highlights the challenges associated with their production and practical use. Measures to overcome these challenges are proposed, alongside an exploration of the future development of the functional fertilizer industry. The findings presented here provide a scientific basis for utilizing rhizosphere microbial metabolites to enhance agricultural sustainability, offering new strategies for future crop management. Integrating these microbial strategies could lead to increased crop productivity, improved quality, and reduced dependence on synthetic chemical inputs, thereby supporting a more environmentally friendly and resilient agricultural system.

Maize/soybean intercropping with nitrogen supply levels increases maize yield and nitrogen uptake by influencing the rhizosphere bacterial diversity of soil

Introduction

Intercropping practices play a crucial role in enhancing and maintaining the biodiversity and resiliency of agroecosystems, as well as promoting stable and high crop yields. Yet the relationships between soil nitrogen, microbes, and yield in maize cultivated under maize/soybean intercropping systems remain unclear.

Methods

To fill that knowledge gap, here we collected maize rhizosphere soil at the staminate stage after 6 consecutive years of maize/soybean intercropping, to investigate how intercropping and nitrogen application rates affected nitrogen utilization by crops and soil microbial community composition and function. We also examined correlations of those responses with yields, to clarify the main ways that yield is enhanced via intercropping and by nitrogenous fertilizer gradient changes generated by different nitrogen application rates.

Results

The amount of applied fertilizer was 240 kg N ha-1 was best for obtaining a high maize yield and also led to the greatest nitrogen-use efficiency and bacterial diversity. Under the same N application rate, intercropping increased the maize yield by 31.17% and soil nitrogen (total, ammonium and nitrate nitrogen) by 14.53%, on average, in comparison to monocropping. The enrichment of Gemmatimonas and Bradyrhizobium significantly increased the soil nitrogen content, and a greater relative abundance of Sphingomonas and Gemmatimonas increased the maize yield, whereas enrichment of Candidatus_Udaeobacter and Bradyrhizobium decreased it. The benefits of intercropping mainly arise from augmenting the abundance of beneficial microorganisms and enhancing the efficiency of N use by crop plants.

Discussion

This study's findings are of key importance to bolster the stability of agro-ecosystems, to guide the scientific rational use of nitrogen fertilizers, and to provide a sound theoretical basis for achieving the optimal management of intensive crop-planting patterns and green sustainable development.

Can plants build their niche through modulation of soil microbial activities linked with nitrogen cycling? A test with Arabidopsis thaliana

In natural systems, different plant species have been shown to modulate specific nitrogen (N) cycling processes so as to meet their N demand, thereby potentially influencing their own niche. This phenomenon might go beyond plant interactions with symbiotic microorganisms and affect the much less explored plant interactions with free-living microorganisms involved in soil N cycling, such as nitrifiers and denitrifiers. Here, we investigated variability in the modulation of soil nitrifying and denitrifying enzyme activities (NEA and DEA, respectively), and their ratio (NEA : DEA), across 193 Arabidopsis thaliana accessions. We studied the genetic and environmental determinants of such plant-soil interactions, and effects on plant biomass production in the next generation. We found that NEA, DEA, and NEA : DEA varied c. 30-, 15- and 60-fold, respectively, among A. thaliana genotypes and were related to genes linked with stress response, flowering, and nitrate nutrition, as well as to soil parameters at the geographic origin of the analysed genotypes. Moreover, plant-mediated N cycling activities correlated with the aboveground biomass of next-generation plants in home vs away nonautoclaved soil, suggesting a transgenerational impact of soil biotic conditioning on plant performance. Altogether, these findings suggest that nutrient-based plant niche construction may be much more widespread than previously thought.

Macrogenomics-Based Analysis of the Effects of Intercropped Soybean Photosynthetic Characteristics and Nitrogen-Assimilating Enzyme Activities on Yield at Different Nitrogen Levels

Currently, China's soybean self-sufficiency rate is only 15%, highlighting the soybean crisis and the supply chain risks that pose a major threat to China's food security. Thus, it has become imperative to step up efforts to boost soybean production capacity while promoting the green and sustainable development of regional farmland ecosystems. In this context, the present study comprehensively investigated the effects of intercropping and nitrogen application rate on soybean yield, as well as the changes in gradients generated by different levels of nitrogen application. Based on six consecutive years of maize-soybean intercropping planting patterns, the inter-root soils of soybeans were collected at the flowering stage and evaluated for soil nitrogen content, nitrogen-assimilating enzyme activities, and microbial community composition of soybean, which were correlated with yield, to clarify the main pathways and modes of intercropping effects. The N2 level (80 kg·ha-1) was favourable for higher yield. In comparison to monocropping, the intercropping reduced yield by 9.65-13.01%, photosynthetic characteristics by 1.33-7.31%, and plant nitrogen-assimilating enzyme activities by 8.08-32.01% at the same level of N application. Likewise, soil urease and catalase activities were reduced by 9.22 and 1.80%, while soil nitrogen content declined by an average of 6.38%. Gemmatimonas and Bradyrhizobium enrichment significantly increased soil nitrogen content, photosynthetic characteristics, and soybean yield, while it was reduced by Candidatus_Udaeobacter and Candidatus_Solibacte enrichment. The results of this study provide a theoretical basis for further optimising maize-soybean intercropping, which is crucial for enhancing the agricultural production structure and improving the overall soybean production capacity.

Site properties, environmental factors, and crop identify influence soil bacterial communities more than municipal biosolid application

Reducing the environmental impact of Canadian field crop agriculture, including the reliance on conventional synthesised fertilisers, are key societal targets for establishing long-term sustainable practices. Municipal biosolids (MSB) are an abundant, residual organic material, rich in phosphate, nitrogen and other oligo-nutrients, that could be used in conjunction with conventional fertilisers to decrease their use. Though MBS have previously been shown to be an effective fertiliser substitute for different crops, including corn and soybean, there remain key knowledge gaps concerning the impact of MBS on the resident soil bacterial communities in agro-ecosystems. We hypothesised that the MBS fertiliser amendment would not significantly impact the structure or function of the soil bacterial communities, nor contribute to the spread of human pathogenic bacteria, in corn or soybean agricultural systems. In field experiments, fertiliser regimes for both crops were amended with MBS, and compared to corn and soybean plots with standard fertiliser treatments. We repeated this across four different agricultural sites in Quebec, over 2021 and 2022. We sampled MBS-treated, and untreated soils, and identified the composition of the soil bacterial communities via 16S rRNA metabarcoding. We found no indication that the MBS fertiliser amendment altered the structure of the soil bacterial communities, but rather that the soil type and crop identities were the most significant factors in structuring the bacterial communities. Moreover, there was no evidence that the MBS-treated soils were enriched in potential human bacterial pathogens over the two years of our study. Our analysis indicates that not only can MBS function as substitutes for conventional, synthesised fertilisers, but that they also do not disrupt the structure of the resident soil bacterial communities in the short term. Finally, we suggest that the use of MBS in agro-ecosystems poses no greater concern to the public than existing soil bacterial communities. This highlights the significant role MBS could potentially have in reducing the use of conventional industrial fertilisers and improving agricultural production, without risking environmental contamination.

Bacterially enhanced plant-growing media for controlled environment agriculture

Microbe-plant interactions in the root zone not only shape crop performance in soil but also in hydroponic cultivation systems. The biological and physicochemical properties of the plant-growing medium determine the root-associated microbial community and influence bacterial inoculation effectiveness, which affects plant growth. This study investigated the combined impact of plant-growing media composition and bacterial community inoculation on the root-associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Ten plant-growing media were composed of varying raw materials, including black peat, white peat, coir pith, wood fibre, composted bark, green waste compost, perlite and sand. In addition, five different bacterial community inocula (BCI S1-5) were collected from the roots of lettuce obtained at different farms. After inoculation and cultivation inside a vertical farm, lettuce root-associated bacterial community structures, diversity and compositions were determined by evaluating 16S rRNA gene sequences. The study revealed distinct bacterial community structures among experimental replicates, highlighting the influence of raw material variations on root-associated bacterial communities, even at the batch level. However, bacterial community inoculation allowed modulation of the root-associated bacterial communities independently from the plant-growing medium composition. Bacterial diversity was identified as a key determinant of plant growth performance with green waste compost introducing Bacilli and Actinobacteria, and bacterial community inoculum S3 introducing Pseudomonas, which positively correlated with plant growth. These findings challenge the prevailing notion of hydroponic cultivation systems as sterile environments and highlight the significance of proper plant-growing media raw material selection and bacterial community inoculation in shaping root-associated microbiomes that provide stability through microbial diversity. This study supports the concept of creating bacterially enhanced plant-growing media to promote plant growth in controlled environment agriculture.

Phyllosphere microbial associations improve plant reproductive success

The above-ground (phyllosphere) plant microbiome is increasingly recognized as an important component of plant health. We hypothesized that phyllosphere bacterial recruitment may be disrupted in a greenhouse setting, and that adding a bacterial amendment would therefore benefit the health and growth of host plants. Using a newly developed synthetic phyllosphere bacterial microbiome for tomato (Solanum lycopersicum), we tested this hypothesis across multiple trials by manipulating microbial inoculation of leaves and measuring subsequent plant growth and reproductive success, comparing results from plants grown in both greenhouse and field settings. We confirmed that greenhouse-grown plants have a relatively depauperate phyllosphere bacterial microbiome, which both makes them an ideal system for testing the impact of phyllosphere communities on plant health and important targets for microbial amendments as we move towards increased agricultural sustainability. We find that the addition of the synthetic microbial community early in greenhouse growth leads to an increase in fruit production in this setting, implicating the phyllosphere microbiome as a key component of plant fitness and emphasizing the role that these bacterial microbiomes likely play in the ecology and evolution of plant communities.

Peanut-based Rotation Stabilized Diazotrophic Communities and Increased Subsequent Wheat Yield

The introduction of legumes into rotations can improve nitrogen use efficiency and crop yield; however, its microbial mechanism involved remains unclear. This study aimed to explore the temporal impact of peanut introduction on microorganisms related to nitrogen metabolism in rotation systems. In this study, the dynamics of diazotrophic communities in two crop seasons and wheat yields of two rotation systems: winter wheat - summer maize (WM) and spring peanut → winter wheat - summer maize (PWM) in the North China Plain were investigated. Our results showed that peanut introduction increased wheat yield and biomass by 11.6% (p < 0.05) and 8.9%, respectively. Lower Chao1 and Shannon indexes of the diazotrophic communities were detected in soils that sampling in June compared with those sampling in September, although no difference was found between WM and PWM. Principal co-ordinates analysis (PCoA) showed that rotation system significantly changed the diazotrophic community structures (PERMANOVA; p < 0.05). Compared with WM, the genera of Azotobacter, Skermanella, Azohydromonas, Rhodomicrobium, Azospirillum, Unclassified_f_Opitutaceae, and Unclassified_f_Rhodospirillaceae were significantly enriched (p < 0.05) in PWM. Furthermore, rotation system and sampling time significantly influenced soil properties, which significantly correlated with the top 15 genera in relative abundance. Partial least squares path modeling (PLS-PM) analysis further showed that the diazotrophic community diversity (alpha- and beta-diversity) and soil properties (pH, SOC and TN) significantly affected wheat yield. In conclusion, legume inclusion has the potential to stabilize diazotrophic community structure at the temporal scales and increase subsequent crop yield.

Engineering multifunctional rhizosphere probiotics using consortia of Bacillus amyloliquefaciens transposon insertion mutants

While bacterial diversity is beneficial for the functioning of rhizosphere microbiomes, multi-species bioinoculants often fail to promote plant growth. One potential reason for this is that competition between different species of inoculated consortia members creates conflicts for their survival and functioning. To circumvent this, we used transposon insertion mutagenesis to increase the functional diversity within Bacillus amyloliquefaciens bacterial species and tested if we could improve plant growth promotion by assembling consortia of highly clonal but phenotypically dissimilar mutants. While most insertion mutations were harmful, some significantly improved B. amyloliquefaciens plant growth promotion traits relative to the wild-type strain. Eight phenotypically distinct mutants were selected to test if their functioning could be improved by applying them as multifunctional consortia. We found that B. amyloliquefaciens consortium richness correlated positively with plant root colonization and protection from Ralstonia solanacearum phytopathogenic bacterium. Crucially, 8-mutant consortium consisting of phenotypically dissimilar mutants performed better than randomly assembled 8-mutant consortia, suggesting that improvements were likely driven by consortia multifunctionality instead of consortia richness. Together, our results suggest that increasing intra-species phenotypic diversity could be an effective way to improve probiotic consortium functioning and plant growth promotion in agricultural systems.

Biodiversity of the beneficial soil-borne fungi steered by Trichoderma-amended biofertilizers stimulates plant production

The soil microbiota is critical to plant performance. Improving the ability of plant-associated soil probiotics is thus essential for establishing dependable and sustainable crop yields. Although fertilizer applications may provide an effective way of steering soil microbes, it is still unknown how the positive effects of soil-borne probiotics can be maximized and how their effects are mediated. This work aims to seek the ecological mechanisms involved in cabbage growth using bio-organic fertilizers. We conducted a long-term field experiment in which we amended soil with non-sterilized organic or sterilized organic fertilizer either containing Trichoderma guizhouense NJAU4742 or lacking this inoculum and tracked cabbage plant growth and the soil fungal community. Trichoderma-amended bio-organic fertilizers significantly increased cabbage plant biomass and this effect was attributed to changes in the resident fungal community composition, including an increase in the relative abundance and number of indigenous soil growth-promoting fungal taxa. We specifically highlight the fundamental role of the biodiversity and population density of these plant-beneficial fungal taxa in improving plant growth. Together, our results suggest that the beneficial effects of bio-organic fertilizer seem to be a combination of the biological inoculum within the organic amendment as well as the indirect promotion through effects on the diversity and composition of the soil resident plant-beneficial fungal microbiome.

Potential of growth-promoting bacteria in maize (Zea mays L.) varies according to soil moisture

Climate change has caused irregularities in water distribution, which affect the soil drying-wetting cycle and the development of economically important agricultural crops. Therefore, the use of plant growth-promoting bacteria (PGPB) emerges as an efficient strategy to mitigate negative impacts on crop yield. We hypothesized that the use of PGPB (in consortium or not) had potential to promote maize (Zea mays L.) growth under a soil moisture gradient in both non-sterile and sterile soils. Thirty PGPB strains were characterized for direct plant growth-promotion and drought tolerance induction mechanisms and were used in two independent experiments. Four soil water contents were used to simulate a severe drought (30% of field capacity [FC]), moderate drought (50% of FC), no drought (80% of FC) and, finally, a water gradient comprising the three mentioned soil water contents (80%, 50%, and 30% of FC). Two bacteria strains (BS28-7 Arthrobacter sp. and BS43 Streptomyces alboflavus), in addition to three consortia (BC2, BC4 and BCV) stood out in maize growth performance in experiment 1 and were used in experiment 2. Overall, under moderate drought, inoculation with BS43 surpassed the control treatment in root dry mass and nutrient uptake. Considering the water gradient treatment (80-50-30% of FC), the greatest total biomass was found in the uninoculated treatment when compared to BS28-7, BC2, and BCV. The greatest development of Z. mays L. was only observed under constant water stress conditions in the presence of PGPB. This is the first report that demonstrated the negative effect of individual inoculation of Arthrobacter sp. and the consortium of this strain with Streptomyces alboflavus on the growth of Z. mays L. based on a soil moisture gradient; however, future studies are needed for further validation.

Soil Chemistry and Soil History Significantly Structure Oomycete Communities in Brassicaceae Crop Rotations

Oomycetes are critically important in soil microbial communities, especially for agriculture, where they are responsible for major declines in yields. Unfortunately, oomycetes are vastly understudied compared to bacteria and fungi. As such, our understanding of how oomycete biodiversity and community structure vary through time in the soil remains poor. Soil history established by previous crops is one factor known to structure other soil microbes, but this has not been investigated for its influence on oomycetes. In this study, we established three different soil histories in field trials; the following year, these plots were planted with five different Brassicaceae crops. We hypothesized that the previously established soil histories would structure different oomycete communities, regardless of their current Brassicaceae crop host, in both the roots and rhizosphere. We used a nested internal transcribed spacer amplicon strategy incorporated with MiSeq metabarcoding, where the sequencing data was used to infer amplicon sequence variants of the oomycetes present in each sample. This allowed us to determine the impact of different soil histories on the structure and biodiversity of the oomycete root and rhizosphere communities from the five different Brassicaceae crops. We found that each soil history structured distinct oomycete rhizosphere communities, regardless of different Brassicaceae crop hosts, while soil chemistry structured the oomycete communities more during a dry year. Interestingly, soil history appeared specific to oomycetes but was less influential for bacterial communities previously identified from the same samples. These results advance our understanding of how different agricultural practices and inputs can alter edaphic factors to impact future oomycete communities. Examining how different soil histories endure and impact oomycete biodiversity will help clarify how these important communities may be assembled in agricultural soils. IMPORTANCE Oomycetes cause global plant diseases that result in substantial losses, yet they are highly understudied compared to other microbes, like fungi and bacteria. We wanted to investigate how past soil events, like changing crops in rotation, would impact subsequent oomycete communities. We planted different oilseed crops in three different soil histories and found that each soil history structured a distinct oomycete community regardless of which new oilseed crop was planted, e.g., oomycete communities from last year's lentil plots were still detected the following year regardless of which new oilseed crops we planted. This study demonstrated how different agricultural practices can impact future microbial communities differently. Our results also highlight the need for continued monitoring of oomycete biodiversity and quantification.

Responses of diversity and arsenic-transforming functional genes of soil microorganisms to arsenic hyperaccumulator (Pteris vittata L.)/pomegranate (Punica granatum L.) intercropping

Intercropping of arsenic (As) hyperaccumulator (Pteris vittata L.) with crops can reduce the As concentration in soil and the resulting ecological and health risks, while maintaining certain economic benefits. However, it is still unclear how As-transforming functional bacteria and dominant bacteria in the rhizosphere of P. vittata affect the microbial properties of crop rhizosphere soil, as well as how As concentration and speciation change in crop rhizosphere soil under intercropping. This is of great significance for understanding the biogeochemical cycle of As in soil and crops. This study aimed to use high-throughput sequencing and quantitative polymerase chain reaction (qPCR) to analyze the effects of different rhizosphere isolation patterns on the bacterial diversity and the copy number of As-transforming functional genes in pomegranate (Punica granatum L.) rhizosphere soil. The results showed that the abundance of bacteria in the rhizosphere soil of pomegranate increased by 16.3 %, and the soil bacterial community structure significantly changed. C_Alphaproteobacteria and o_Rhizobiales bacteria significantly accumulated in the rhizosphere of pomegranate. The copy number of As methylation (arsM) gene in pomegranate rhizosphere soil significantly increased by 63.37 %. The concentrations of nonspecifically sorbed As (F1), As associated with amorphous Fe (hydr)oxides (F3), and the total As (FT) decreased; the proportion of As (III) in pomegranate rhizosphere soil decreased; and the proportion of As (V) increased in pomegranate rhizosphere soil. c_Alphaproteobacteria and o_Rhizobiales accumulated in crop rhizosphere soil under the intercropping of P. vittata with crops. Also, the copy number of As methylation functional genes in crop rhizosphere soil significantly increased, which could reduce As (III) proportion in crop rhizosphere soil. These changes favored simultaneous agricultural production and soil remediation. The results provided the theoretical basis and practical guidance for the safe utilization of As-contaminated soil in the intercropping of As-hyperaccumulator and cash crops.

Nitrate transporter MdNRT2.4 interacts with rhizosphere bacteria to enhance nitrate uptake in apple rootstocks

Plants have developed complex mechanisms to adapt to changing nitrate (NO3-) concentrations and can recruit microbes to boost nitrogen absorption. However, little is known about the relationship between functional genes and the rhizosphere microbiome in NO3- uptake of apple rootstocks. Here, we found that variation in Malus domestica NO3- transporter (MdNRT2.4) expression contributes to nitrate uptake divergence between two apple rootstocks. Overexpression of MdNRT2.4 in apple seedlings significantly improved tolerance to low nitrogen via increasing net NO3- influx at the root surface. However, inhibiting the root plasma membrane H+-ATPase activity abolished NO3- uptake and led to NO3- release, suggesting that MdNRT2.4 encodes an H+-coupled nitrate transporter. Surprisingly, the nitrogen concentration of MdNRT2.4-overexpressing apple seedlings in unsterilized nitrogen-poor soil was higher than that in sterilized nitrogen-poor soil. Using 16S ribosomal RNA gene profiling to characterize the rhizosphere microbiota, we found that MdNRT2.4-overexpressing apple seedlings recruited more bacterial taxa with nitrogen metabolic functions, especially Rhizobiaceae. We isolated a bacterial isolate ARR11 from the apple rhizosphere soil and identified it as Rhizobium. Inoculation with ARR11 improved apple seedling growth in nitrogen-poor soils, compared with uninoculated seedlings. Together, our results highlight the interaction of host plant genes with the rhizosphere microbiota for host plant nutrient uptake.

Elucidating the microbiome of the sustainable peat replacers composts and nature management residues

Sustainable peat alternatives, such as composts and management residues, are considered to have beneficial microbiological characteristics compared to peat-based substrates. Studies comparing microbiological characteristics of these three types of biomass are, however, lacking. This study examined if and how microbiological characteristics of subtypes of composts and management residues differ from peat-based substrates, and how feedstock and (bio)chemical characteristics drive these characteristics. In addition, microbiome characteristics were evaluated that may contribute to plant growth and health. These characteristics include: genera associated with known beneficial or harmful microorganisms, microbial diversity, functional diversity/activity, microbial biomass, fungal to bacterial ratio and inoculation efficiency with the biocontrol fungus Trichoderma harzianum. Bacterial and fungal communities were studied using 16S rRNA and ITS2 gene metabarcoding, community-level physiological profiling (Biolog EcoPlates) and PLFA analysis. Inoculation with T. harzianum was assessed using qPCR. Samples of feedstock-based subtypes of composts and peat-based substrates showed similar microbial community compositions, while subtypes based on management residues were more variable in their microbial community composition. For management residues, a classification based on pH and hemicellulose content may be relevant for bacterial and fungal communities, respectively. Green composts, vegetable, fruit and garden composts and woody composts show the most potential to enhance plant growth or to suppress pathogens for non-acidophilic plants, while grass clippings, chopped heath and woody fractions of compost show the most potential for blends for calcifuge plants. Fungal biomass was a suitable predictor for inoculation efficiency of composts and management residues.

Plant-microbe interactions in the rhizosphere via a circular metabolic economy

Chemical exchange often serves as the first step in plant-microbe interactions and exchanges of various signals, nutrients, and metabolites continue throughout the interaction. Here, we highlight the role of metabolite exchanges and metabolic crosstalk in the microbiome-root-shoot-environment nexus. Roots secret a diverse set of metabolites; this assortment of root exudates, including secondary metabolites such as benzoxazinoids, coumarins, flavonoids, indolic compounds, and terpenes, shapes the rhizosphere microbiome. In turn, the rhizosphere microbiome affects plant growth and defense. These inter-kingdom chemical interactions are based on a metabolic circular economy, a seemingly wasteless system in which rhizosphere members exchange (i.e. consume, reuse, and redesign) metabolites. This review also describes the recently discovered phenomenon "Systemically Induced Root Exudation of Metabolites" in which the rhizosphere microbiome governs plant metabolism by inducing systemic responses that shift the metabolic profiles of root exudates. Metabolic exchange in the rhizosphere is based on chemical gradients that form specific microhabitats for microbial colonization and we describe recently developed high-resolution methods to study chemical interactions in the rhizosphere. Finally, we propose an action plan to advance the metabolic circular economy in the rhizosphere for sustainable solutions to the cumulative degradation of soil health in agricultural lands.

Brassicaceae host plants mask the feedback from the previous year's soil history on bacterial communities, except when they experience drought

Soil history operates through time to influence the structure and biodiversity of soil bacterial communities. Examining how different soil histories endure will help clarify the rules of bacterial community assembly. In this study, we established three different soil histories in field trials; the following year these plots were planted with five different Brassicaceae species. We hypothesized that the previously established soil histories would continue to structure the subsequent Brassicaceae bacterial root and rhizosphere communities. We used a MiSeq 16S rRNA metabarcoding strategy to determine the impact of different soil histories on the structure and biodiversity of the bacterial root and rhizosphere communities from the five different Brassicaceae host plants. We found that the Brassicaceae hosts were consistently significant factors in structuring the bacterial communities. Four host plants (Sinapis alba, Brassica napus, B. juncea, B. carinata) formed similar bacterial communities, regardless of different soil histories. Camelina sativa host plants structured phylogenetically distinct bacterial communities compared to the other hosts, particularly in their roots. Soil history established the previous year was only a significant factor for bacterial community structure when the feedback of the Brassicaceae host plants was weakened, potentially due to limited soil moisture during a dry year. Understanding how soil history is involved in the structure and biodiversity of bacterial communities through time is a limitation in microbial ecology and is required for employing microbiome technologies in improving agricultural systems. This article is protected by copyright. All rights reserved.

An insight to rhizosphere bacterial community composition and structure of consecutive winter-initiated sugarcane ratoon crop in Southern China

BACKGROUND

Ratooning in sugarcane is a crucial strategy for ensuring the long-term sustainability of the sugarcane industry. Knowledge gap relating to the interaction between rhizosphere microbiome and ratooning crop, particularly the impact of different sugarcane cultivars on the rhizosphere microbiome in consecutive ratooning, requires additional research. The response of two different sugarcane cultivars, viz ZZ-1 and ZZ-13, were evaluated in consecutive ratooning towards the rhizosphere microbial community and cane morphological characters.

RESULTS

Significant changes in the rhizosphere microbiome were observed in the second ratooning over the years. Several important genera were observed in high abundance during the second ratooning, including Burkholderia, Sphingomonas, Bradyzhizobium, and Acidothermus. Cultivar ZZ-13 caused more alterations in the rhizosphere microbiome than ZZ-1, resulting in a more favorable rhizosphere environment for sugarcane growth. The genotypes also varied in terms of nutrients and enzyme activity over the years. There were significant differences between the genotypes and year for number of stalks and yield was significant for genotypes, years and genotype × year.

CONCLUSION

This finding will help to understand thorough interactions between rhizosphere microorganisms and ratoon sugarcane and lay the foundation for promoting and maximizing yield as far as possible. In the future, this work can serve as guidance in sugarcane husbandry, mainly in Guangxi, China.

Evaluation of maize/peanut intercropping effects on microbial assembly, root exudates and peanut nitrogen uptake

Legume/cereal intercropping has been widely studied within ecosystem function, owing to its overyield potential, predominantly by dinitrogen (N₂) fixation. In our 2-year peanut/maize intercropping field experiment, land equivalent ratio (LER) showed an average yield-increase by 41.48%. Performance index of intercropped peanut (IP) functional leaves exhibited significant improvement (2.02-fold). Moreover, IP increased dry nodule weight by 58.82% as compared to mono-cropped. Also, the ratio of nodules to aboveground biomass in IP reduced by 65.8%. In pot experiment, higher urease activity was found in rhizosphere (22.73%). The abundance of Rhizobium and niƒH gene in the rhizosphere of IP were significantly enhanced by 71.91% and 208%, respectively. To analyze root exudates, we performed hydroponic coculture, the proportion of total isoflavonoids in peanut root exudates were increased distinctly by 22.4%. Our findings certainly helped in filling one the information gaps, that how intercropping increases nitrogen fixation in rhizosphere. Lastly, it can further facilitate to understand functional significance of intercropping system for agricultural ecological sustainability and efficient resource utilization.

Response of leaf stoichiometry of Potentilla anserina to elevation in China's Qilian Mountains

Plants adapt to changes in elevation by regulating their leaf ecological stoichiometry. Potentilla anserina L. that grows rapidly under poor or even bare soil conditions has become an important ground cover plant for ecological restoration. However, its leaf ecological stoichiometry has been given little attention, resulting in an insufficient understanding of its environmental adaptability and growth strategies. The objective of this study was to compare the leaf stoichiometry of P. anserina at different elevations (2,400, 2,600, 2,800, 3,000, 3,200, 3,500, and 3,800 m) in the middle eastern part of Qilian Mountains. With an increase in elevation, leaf carbon concentration [(C)_leaf] significantly decreased, with the maximum value of 446.04 g·kg^-1 (2,400 m) and the minimum value of 396.78 g·kg^-1 (3,500 m). Leaf nitrogen concentration [(N)_leaf] also increased with an increase in elevation, and its maximum and minimum values were 37.57 g·kg^-1 (3,500 m) and 23.71 g·kg^-1 (2,800 m), respectively. Leaf phosphorus concentration [(P)_leaf] was the highest (2.79 g·kg^-1) at 2,400 m and the lowest (0.91 g·kg^-1) at 2,800 m. The [C]_leaf/[N]_leaf decreased with an increase in elevation, while [N]_leaf/[P]_leaf showed an opposite trend. The mean annual temperature, mean annual precipitation, soil pH, organic carbon, nitrogen, and phosphorus at different elevations mainly affected [C]_leaf, [N]_leaf, and [P]_leaf. The growth of P. anserina in the study area was mainly limited by P, and this limitation was stronger with increased elevation. Progressively reducing P loss at high elevation is of great significance to the survival of P. anserina in this specific region.

Resistance and Not Plant Fruit Traits Determine Root-Associated Bacterial Community Composition along a Domestication Gradient in Tomato

Soil bacterial communities are involved in multiple ecosystem services, key in determining plant productivity. Crop domestication and intensive agricultural practices often disrupt species interactions with unknown consequences for rhizosphere microbiomes. This study evaluates whether variation in plant traits along a domestication gradient determines the composition of root-associated bacterial communities; and whether these changes are related to targeted plant traits (e.g., fruit traits) or are side effects of less-often-targeted traits (e.g., resistance) during crop breeding. For this purpose, 18 tomato varieties (wild and modern species) differing in fruit and resistance traits were grown in a field experiment, and their root-associated bacterial communities were characterised. Root-associated bacterial community composition was influenced by plant resistance traits and genotype relatedness. When only considering domesticated tomatoes, the effect of resistance on bacterial OTU composition increases, while the effect due to phylogenetic relatedness decreases. Furthermore, bacterial diversity positively correlated with plant resistance traits. These results suggest that resistance traits not selected during domestication are related to the capacity of tomato varieties to associate with different bacterial groups. Taken together, these results evidence the relationship between plant traits and bacterial communities, pointing out the potential of breeding to affect plant microbiomes.

Introduction of probiotic bacterial consortia promotes plant growth via impacts on the resident rhizosphere microbiome

Plant growth depends on a range of functions provided by their associated rhizosphere microbiome, including nutrient mineralization, hormone co-regulation and pathogen suppression. Improving the ability of plant-associated microbiomes to deliver these functions is thus important for developing robust and sustainable crop production. However, it is yet unclear how beneficial effects of probiotic microbial inoculants can be optimized and how their effects are mediated. Here, we sought to enhance tomato plant growth by targeted introduction of probiotic bacterial consortia consisting of up to eight plant-associated Pseudomonas strains. We found that the effect of probiotic consortium inoculation was richness-dependent: consortia that contained more Pseudomonas strains reached higher densities in the tomato rhizosphere and had clearer beneficial effects on multiple plant growth characteristics. Crucially, these effects were best explained by changes in the resident community diversity, composition and increase in the relative abundance of initially rare taxa, instead of introduction of plant-beneficial traits into the existing community along with probiotic consortia. Together, our results suggest that beneficial effects of microbial introductions can be driven indirectly through effects on the diversity and composition of the resident plant rhizosphere microbiome.

Effects of Sugarcane and Soybean Intercropping on the Nitrogen-Fixing Bacterial Community in the Rhizosphere

Intercropping between sugarcane and soybean is widely used to increase crop yield and promote the sustainable development of the sugarcane industry. However, our understanding of the soil microenvironment in intercropping systems, especially the effect of crop varieties on rhizosphere soil bacterial communities, remains poor. We selected two excellent sugarcane cultivars, Zhongzhe1 (ZZ1) and Zhongzhe9 (ZZ9), from Guangxi and the local soybean variety GUIZAO2 from Guangxi for field interplanting experiments. These two cultivars of sugarcane have good drought resistance. Rhizosphere soil samples were collected from the two intercropping systems to measure physicochemical properties and soil enzyme activities and to extract total soil DNA for high-throughput sequencing. We found that the diversity of the rhizosphere bacterial community was significantly different between the two intercropping systems. Compared with ZZ1, the ZZ9 intercropping system enriched the nitrogen-fixing bacteria, increasing the available nitrogen content by 18% compared with that with ZZ1. In addition, ZZ9 intercropping with soybean formed a more compact rhizosphere environment than ZZ1, thus providing favorable conditions for sugarcane growth. These results provide guidance for the sugarcane industry, especially for the management of sugarcane and soybean intercropping in Guangxi, China.

Antibiotic resistance development and human health risks during wastewater reuse and biosolids application in agriculture

The reuse of treated wastewater (TWW) and sewage sludge are considered as solutions to the limited water resource and sludge disposal issues, respectively. The associated environmental and human health risks need to be analyzed to assess whether they are safe solutions or not. This paper discusses issues that relate to the accumulation of antibiotics and antibiotic resistance (AR) determinants in agricultural lands and crops, following TWW irrigation and biosolid amendment. Exposure assessment and dose-response assessment are the two important aspects of risk assessment discussed in this paper. Finally, research gaps in current knowledge that are relevant to a comprehensive and quantitative AR risk assessment were identified which includes: 1.) Studies on soil conditions that increase the frequency of horizontal gene transfer (HGT) between native soil resistome and pathogenic microbes in biosolids and TWW 2.) Holistic studies that examine the accumulation or dissipation of antibiotics, antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) from the irrigation/biosolids application stage to crop consumption stage 3.) The influences of soil environmental conditions (e.g. salinity, nutrients) on the fate of ARB and ARGs in soil and translocation in edible plants 4.) The development of dose-response models that explicitly incorporate the potential for ARGs transfer between microbes when quantifying the risks of infection due to ARB.

Effect of Two Different Sugarcane Cultivars on Rhizosphere Bacterial Communities of Sugarcane and Soybean Upon Intercropping

Intercropping of soybean and sugarcane is an important strategy to promote sustainable development of the sugarcane industry. In fact, our understanding of the interaction between the rhizosphere and bacterial communities in the intercropping system is still evolving; particularly, the influence of different sugarcane varieties on rhizosphere bacterial communities in the intercropping process with soybean, still needs further research. Here, we evaluated the response of sugarcane varieties ZZ1 and ZZ9 to the root bacterial community during intercropping with soybean. We found that when ZZ9 was intercropped with soybean, the bacterial diversity increased significantly as compared to that when ZZ1 was used. ZZ9 played a major role in changing the bacterial environment of the root system by affecting the diversity of rhizosphere bacteria, forming a rhizosphere environment more conducive to the growth of sugarcane. In addition, our study found that ZZ1 and ZZ9 had differed significantly in their utilization of nutrients. For example, nutrients were affected by different functional genes in processes such as denitrification, P-uptake and transport, inorganic P-solubilization, and organic P-mineralization. These results are significant in terms of providing guidance to the sugarcane industry, particularly for the intercropping of sugarcane and soybean in Guangxi, China.

Potential for Mycorrhizae-Assisted Phytoremediation of Phosphorus for Improved Water Quality

During this 6th Great Extinction, freshwater quality is imperiled by upland terrestrial practices. Phosphorus, a macronutrient critical for life, can be a concerning contaminant when excessively present in waterways due to its stimulation of algal and cyanobacterial blooms, with consequences for ecosystem functioning, water use, and human and animal health. Landscape patterns from residential, industrial and agricultural practices release phosphorus at alarming rates and concentrations threaten watershed communities. In an effort to reconcile the anthropogenic effects of phosphorus pollution, several strategies are available to land managers. These include source reduction, contamination event prevention and interception. A total of 80% of terrestrial plants host mycorrhizae which facilitate increased phosphorus uptake and thus removal from soil and water. This symbiotic relationship between fungi and plants facilitates a several-fold increase in phosphorus uptake. It is surprising how little this relationship has been encouraged to mitigate phosphorus for water quality improvement. This paper explores how facilitating this symbiosis in different landscape and land-use contexts can help reduce the application of fertility amendments, prevent non-point source leaching and erosion, and intercept remineralized phosphorus before it enters surface water ecosystems. This literature survey offers promising insights into how mycorrhizae can aid ecological restoration to reconcile humans' damage to Earth's freshwater. We also identify areas where research is needed.

Effects of residual S-metolachlor in soil on the phyllosphere microbial communities of wheat (Triticum aestivum L.)

S-metolachlor (S-ME) is a widely used chiral herbicide that can cause potential ecological risks via long-term usage. In this work, we chose a model plant, wheat, as the test material to determine the effects of applying 10 mg/kg S-ME to soil on its fresh weight, chlorophyll and malondialdehyde (MDA) content, and superoxide dismutase (SOD) activity and the diversity and structural composition of the phyllosphere microorganisms after 7 and 14 days of exposure. Our work showed that this concentration of residual S-ME in soil only slightly decreased plant biomass and had little effect on lipid peroxidation, the antioxidant enzyme system and chlorophyll content. Interestingly, although the test concentration of S-ME did not exert strong inhibitory effects on the physiological activities of wheat, it decreased the diversity of phyllosphere microbial communities and changed their structure, indicating that microorganisms were more sensitive stress indicators. S-ME reduced the colonization by some beneficial bacteria related to plant nitrogen fixation among the phyllosphere microorganisms, which influenced the growth and yield of wheat because these bacteria contribute to plant fitness. In addition, S-ME affected the association between the host and the composition of the phyllosphere microbial communities under different growth conditions. Our work provides insights into the ecological implications of the effects of herbicides on the phyllosphere microbiome.

Spatial variation of the soil bacterial community in major apple producing regions of China

AIMS

In China, apple production areas are largely from the coastal to inland areas and across varied climate zones. However, the relationship among soil micro-organisms, environmental factors and fruit quality has not been clearly confirmed in orchards. Here we attempted to identify the variation of soil bacteria in the main apple producing regions and reveal the relationship among climatic factor, soil properties, soil bacterial community and fruit quality.

METHODS AND RESULTS

Sixty soil samples were collected from six main apple producing areas in China. We examined the soil bacteria using bacterial 16S rRNA gene amplicon profiling. The results show that the soil bacterial diversity of apple orchards varied from the Bohai Bay Region to the Loess Plateau Region. Proteobacteria, Acidobacteria and Actinobacteria were the predominant taxa at the phylum level for all six areas. In the Bohai Bay and the Loess Plateau region, which are the two largest apple producing areas, Proteobacteria and Actinobacteria had the highest relative abundance, respectively. Furthermore, soil bacterial diversity showed positive correlation with the mean annual temperature (MAT), soil organic matter (SOM) and pH. Excluding a direct effect on the apple fruit quality, MAT exerted an indirect influence through soil SOM and pH to alter the relative abundance of dominant taxa and shift the bacterial diversity, which affects the apple fruit titratable acids and soluble solids.

CONCLUSIONS

Geographic variables underlie apple orchard soil bacterial communities vary according to spatial scale. Environmental factors exert an indirect effect on apple fruit quality via shaping soil bacterial community.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides a list of bacteria associated with environmental factors and the ecological attributes of their interactions in apple orchards, which will improve our ability to promote soil bacterial functional capabilities in order to reduce the fertilizer input and enhance the fruit quality.

Structure of Bacterial Communities in Phosphorus-Enriched Rhizosphere Soils

Although phytoremediation is the main method for P-removal and maintaining ecosystem balance in geological phosphorus-enriched soils (PES), little is known about the structure and function of microbial communities in PES. Interactions between plants and soil microorganisms mainly occur in the rhizosphere. The aim of this work was to investigate the composition and diversity of bacterial communities found in rhizosphere soils associated with the following three dominant plant species: Erianthus rufipilus, Coriaria nepalensis, and Pinus yunnanensis. In addition, we compared these rhizosphere bacterial communities with those derived from bulk soils and grassland plots in PES from the Dianchi Lake basin of southwestern China. The Illumina MiSeq platform for high-throughput sequencing of 16S rRNA was used for the taxonomy and the analysis of soil bacterial communities. The results showed higher bacterial diversity and nutrient content in rhizosphere soils as compared with bulk soils. Rhizosphere bacteria were predominantly comprised of Proteobacteria (24.43%) and Acidobacteria (21.09%), followed by Verrucomicrobia (19.48%) and Planctomycetes (9.20%). A comparison of rhizosphere soils of the selected plant species in our study and the grassland plots showed that Acidobacteria were the most abundant in the rhizosphere soil of E. rufipilus; Bradyrhizobiaceae and Rhizobiaceae in the order Rhizobiales from C. nepalensis were found to have the greatest abundance; and Verrucomicrobia and Planctomycetes were in higher abundance in P. yunnanensis rhizosphere soils and in grassland plots. A redundancy analysis revealed that bacterial abundance and diversity were mainly influenced by soil water content, soil organic matter, and total nitrogen.

Long-Term Nutrient Enrichment of an Oligotroph-Dominated Wetland Increases Bacterial Diversity in Bulk Soils and Plant Rhizospheres

In nutrient-limited conditions, plants rely on rhizosphere microbial members to facilitate nutrient acquisition, and in return, plants provide carbon resources to these root-associated microorganisms. However, atmospheric nutrient deposition can affect plant-microbe relationships by changing soil bacterial composition and by reducing cooperation between microbial taxa and plants. To examine how long-term nutrient addition shapes rhizosphere community composition, we compared traits associated with bacterial (fast-growing copiotrophs, slow-growing oligotrophs) and plant (C3 forb, C4 grass) communities residing in a nutrient-poor wetland ecosystem. Results revealed that oligotrophic taxa dominated soil bacterial communities and that fertilization increased the presence of oligotrophs in bulk and rhizosphere communities. Additionally, bacterial species diversity was greatest in fertilized soils, particularly in bulk soils. Nutrient enrichment (fertilized versus unfertilized) and plant association (bulk versus rhizosphere) determined bacterial community composition; bacterial community structure associated with plant functional group (grass versus forb) was similar within treatments but differed between fertilization treatments. The core forb microbiome consisted of 602 unique taxa, and the core grass microbiome consisted of 372 unique taxa. Forb rhizospheres were enriched in potentially disease-suppressive bacterial taxa, and grass rhizospheres were enriched in bacterial taxa associated with complex carbon decomposition. Results from this study demonstrate that fertilization serves as a strong environmental filter on the soil microbiome, which leads to distinct rhizosphere communities and can shift plant effects on the rhizosphere microbiome. These taxonomic shifts within plant rhizospheres could have implications for plant health and ecosystem functions associated with carbon and nitrogen cycling.IMPORTANCE Over the last century, humans have substantially altered nitrogen and phosphorus cycling. Use of synthetic fertilizer and burning of fossil fuels and biomass have increased nitrogen and phosphorus deposition, which results in unintended fertilization of historically low-nutrient ecosystems. With increased nutrient availability, plant biodiversity is expected to decline, and the abundance of copiotrophic taxa is anticipated to increase in bacterial communities. Here, we address how bacterial communities associated with different plant functional types (forb, grass) shift due to long-term nutrient enrichment. Unlike other studies, results revealed an increase in bacterial diversity, particularly of oligotrophic bacteria in fertilized plots. We observed that nutrient addition strongly determines forb and grass rhizosphere composition, which could indicate different metabolic preferences in the bacterial communities. This study highlights how long-term fertilization of oligotroph-dominated wetlands could alter diversity and metabolism of rhizosphere bacterial communities in unexpected ways.

Rhizosphere Microbiome Assembly and Its Impact on Plant Growth

Microorganisms colonizing the plant rhizosphere provide a number of beneficial functions for their host. Although an increasing number of investigations clarified the great functional capabilities of rhizosphere microbial communities, the understanding of the precise mechanisms underlying the impact of rhizosphere microbiome assemblies is still limited. Also, not much is known about the various beneficial functions of the rhizosphere microbiome. In this review, we summarize the current knowledge of biotic and abiotic factors that shape the rhizosphere microbiome as well as the rhizosphere microbiome traits that are beneficial to plants growth and disease-resistance. We give particular emphasis on the impact of plant root metabolites on rhizosphere microbiome assemblies and on how the microbiome contributes to plant growth, yield, and disease-resistance. Finally, we introduce a new perspective and a novel method showing how a synthetic microbial community construction provides an effective approach to unravel the plant-microbes and microbes-microbes interplays.

More Than the Sum of Its Parts: Microbiome Biodiversity as a Driver of Plant Growth and Soil Health

Microorganisms drive several processes needed for robust plant growth and health. Harnessing microbial functions is thus key to productive and sustainable food production. Molecular methods have led to a greater understanding of the soil microbiome composition. However, translating species or gene composition into microbiome functionality remains a challenge. Community ecology concepts such as the biodiversity–ecosystem functioning framework may help predict the assembly and function of plant-associated soil microbiomes. Higher diversity can increase the number and resilience of plant-beneficial functions that can be coexpressed and unlock the expression of plant-beneficial traits that are hard to obtain from any species in isolation. We combine well-established community ecology concepts with molecular microbiology into a workable framework that may enable us to predict and enhance soil microbiome functionality to promote robust plant growth in a global change context.

Apple rootstocks of different nitrogen tolerance affect the rhizosphere bacterial community composition

AIMS

To select apple rootstocks that are tolerant to low nitrogen and reveal the relationship between the rhizosphere bacterial communities and the low nitrogen tolerance of the apple rootstock.

METHODS AND RESULTS

In total, 235 lines of hybrids of Malus robusta Rehd. × M.9 with low nitrogen stress were cultivated in pots in a greenhouse equipped with a drip irrigation system, and growth characteristics, photosynthesis traits and mineral elements were monitored. The bacterial community structure of the rhizosphere from different rootstocks was determined via Illumina MiSeq sequencing. This study selected three low nitrogen-tolerant (NT) lines that had higher nitrogen concentration, and higher photosynthesis rate than the three low nitrogen-sensitive (NS) lines. The bacterial community structure significantly differed (P ≤ 0·001) among the rootstocks. The bacterial phyla Proteobacteria and Actinobacteria were the dominant groups in the rhizosphere and presented higher abundance in the NT rhizosphere. The N concentration in the apple rootstocks exhibited highly positive Pearson correlations with the bacterial genera Sphingomonas, Pseudoxanthomonas, Bacillus and Acinetobacter, and negative correlations with the bacterial genera Pseudarthrobacter and Bradyrhizobium.

CONCLUSIONS

This study showed that investigated rootstocks achieved increased nitrogen concentration by enhancing their photosynthetic production capacity and shaping their rhizobacteria community structure.

SIGNIFICANCE AND IMPACT OF THE STUDY

The findings provide a basis for studying the mechanisms of resistance to low nitrogen stress in apple rootstocks. Based on these beneficial bacteria, microbial inoculants can be developed for use in sustainable agricultural and horticultural production.

Belowground Interactions Impact the Soil Bacterial Community, Soil Fertility, and Crop Yield in Maize/Peanut Intercropping Systems

Intercropping has been widely used to control disease and improve yield in agriculture. In this study, maize and peanut were used for non-separation intercropping (NS), semi-separation intercropping (SS) using a nylon net, and complete separation intercropping (CS) using a plastic sheet. In field experiments, two-year land equivalent ratios (LERs) showed yield advantages due to belowground interactions when using NS and SS patterns as compared to monoculture. In contrast, intercropping without belowground interactions (CS) showed a yield disadvantage. Meanwhile, in pot experiments, belowground interactions (found in NS and SS) improved levels of soil-available nutrients (nitrogen (N) and phosphorus (P)) and enzymes (urease and acid phosphomonoesterase) as compared to intercropping without belowground interactions (CS). Soil bacterial community assay showed that soil bacterial communities in the NS and SS crops clustered together and were considerably different from the CS crops. The diversity of bacterial communities was significantly improved in soils with NS and SS. The abundance of beneficial bacteria, which have the functions of P-solubilization, pathogen suppression, and N-cycling, was improved in maize and peanut soils due to belowground interactions through intercropping. Among these bacteria, numbers of Bacillus, Brevibacillusbrevis, and Paenibacillus were mainly increased in the maize rhizosphere. Burkholderia, Pseudomonas, and Rhizobium were mainly increased in the peanut rhizosphere. In conclusion, using maize and peanut intercropping, belowground interactions increased the numbers of beneficial bacteria in the soil and improved the diversity of the bacterial community, which was conducive to improving soil nutrient (N and P) supply capacity and soil microecosystem stability.

Understanding and exploiting plant beneficial microbes

After a century of incremental research, technological advances, coupled with a need for sustainable crop yield increases, have reinvigorated the study of beneficial plant-microbe interactions with attention focused on how microbiomes alter plant phenotypes. We review recent advances in plant microbiome research, and describe potential applications for increasing crop productivity. The phylogenetic diversity of plant microbiomes is increasingly well characterized, and their functional diversity is becoming more accessible. Large culture collections are available for controlled experimentation, with more to come. Genetic resources are being brought to bear on questions of microbiome function. We expect that microbial amendments of varying complexities will expose rules governing beneficial plant-microbe interactions contributing to plant growth promotion and disease resistance, enabling more sustainable agriculture.

The Potential of Hyperspectral Patterns of Winter Wheat to Detect Changes in Soil Microbial Community Composition

Reliable information on soil status and crop health is crucial for detecting and mitigating disasters like pollution or minimizing impact from soil-borne diseases. While infestation with an aggressive soil pathogen can be detected via reflected light spectra, it is unknown to what extent hyperspectral reflectance could be used to detect overall changes in soil biodiversity. We tested the hypotheses that spectra can be used to (1) separate plants growing with microbial communities from different farms; (2) to separate plants growing in different microbial communities due to different land use; and (3) separate plants according to microbial species loss. We measured hyperspectral reflectance patterns of winter wheat plants growing in sterilized soils inoculated with microbial suspensions under controlled conditions. Microbial communities varied due to geographical distance, land use and microbial species loss caused by serial dilution. After 3 months of growth in the presence of microbes from the two different farms plant hyperspectral reflectance patterns differed significantly from each other, while within farms the effects of land use via microbes on plant reflectance spectra were weak. Species loss via dilution on the other hand affected a number of spectral indices for some of the soils. Spectral reflectance can be indicative of differences in microbial communities, with the Renormalized Difference Vegetation Index the most common responding index. Also, a positive correlation was found between the Normalized Difference Vegetation Index and the bacterial species richness, which suggests that plants perform better with higher microbial diversity. There is considerable variation between the soil origins and currently it is not possible yet to make sufficient reliable predictions about the soil microbial community based on the spectral reflectance. We conclude that measuring plant hyperspectral reflectance has potential for detecting changes in microbial communities yet due to its sensitivity high replication is necessary and a strict sampling design to exclude other 'noise' factors.

The Potential of Hyperspectral Patterns of Winter Wheat to Detect Changes in Soil Microbial Community Composition

Reliable information on soil status and crop health is crucial for detecting and mitigating disasters like pollution or minimizing impact from soil-borne diseases. While infestation with an aggressive soil pathogen can be detected via reflected light spectra, it is unknown to what extent hyperspectral reflectance could be used to detect overall changes in soil biodiversity. We tested the hypotheses that spectra can be used to (1) separate plants growing with microbial communities from different farms; (2) to separate plants growing in different microbial communities due to different land use; and (3) separate plants according to microbial species loss. We measured hyperspectral reflectance patterns of winter wheat plants growing in sterilized soils inoculated with microbial suspensions under controlled conditions. Microbial communities varied due to geographical distance, land use and microbial species loss caused by serial dilution. After 3 months of growth in the presence of microbes from the two different farms plant hyperspectral reflectance patterns differed significantly from each other, while within farms the effects of land use via microbes on plant reflectance spectra were weak. Species loss via dilution on the other hand affected a number of spectral indices for some of the soils. Spectral reflectance can be indicative of differences in microbial communities, with the Renormalized Difference Vegetation Index the most common responding index. Also, a positive correlation was found between the Normalized Difference Vegetation Index and the bacterial species richness, which suggests that plants perform better with higher microbial diversity. There is considerable variation between the soil origins and currently it is not possible yet to make sufficient reliable predictions about the soil microbial community based on the spectral reflectance. We conclude that measuring plant hyperspectral reflectance has potential for detecting changes in microbial communities yet due to its sensitivity high replication is necessary and a strict sampling design to exclude other 'noise' factors.