Plant Beneficial Microbes Research Articles

Microbe-Responsive Proteomes During Plant–Microbe Interactions Between Rice Genotypes and the Multifunctional Methylobacterium oryzae CBMB20

BackgroundRice is colonized by plant growth promoting bacteria such as Methylobacterium leading to mutually beneficial plant–microbe interactions. As modulators of the rice developmental process, Methylobacterium influences seed germination, growth, health, and development. However, little is known about the complex molecular responsive mechanisms modulating microbe-driven rice development. The application of proteomics to rice-microbe interactions helps us elucidate dynamic proteomic responses mediating this association.ResultsIn this study, a total of 3908 proteins were detected across all treatments of which the non-inoculated IR29 and FL478 share up to 88% similar proteins. However, intrinsic differences appear in IR29 and FL478 as evident in the differentially abundant proteins (DAPs) and their associated gene ontology terms (GO). Successful colonization of M. oryzae CBMB20 in rice resulted to dynamic shifts in proteomes of both IR29 and FL478. The GO terms of DAPs for biological process in IR29 shifts in abundance from response to stimulus, cellular amino acid metabolic process, regulation of biological process and translation to cofactor metabolic process (6.31%), translation (5.41%) and photosynthesis (5.41%). FL478 showed a different shift from translation-related to response to stimulus (9%) and organic acid metabolic acid (8%). Both rice genotypes also showed a diversification of GO terms due to the inoculation of M. oryzae CBMB20. Specific proteins such as peptidyl-prolyl cis–trans isomerase (A2WJU9), thiamine thiazole synthase (A2YM28), and alanine—tRNA ligase (B8B4H5) upregulated in IR29 and FL478 indicate key mechanisms of M. oryzae CBMB20 mediated plant growth promotion in rice.ConclusionsInteraction of Methylobacterium oryzae CBMB20 to rice results in a dynamic, similar, and plant genotype-specific proteomic changes supporting associated growth and development. The multifaceted CBMB20 expands the gene ontology terms and increases the abundance of proteins associated with photosynthesis, diverse metabolic processes, protein synthesis and cell differentiation and fate potentially attributed to the growth and development of the host plant. The specific proteins and their functional relevance help us understand how CBMB20 mediate growth and development in their host under normal conditions and potentially link subsequent responses when the host plants are exposed to biotic and abiotic stresses.

Epigenetic control is involved in molecular dialogue in plant-microbe symbiosis.

This article is a Commentary on Vigneaud et al. (2023), 238: 2561–2577.

Metabolomic evaluation of PGPR defence priming in wheat (Triticum aestivum L.) cultivars infected with Puccinia striiformis f. sp. tritici (stripe rust).

Plant-microbe interactions are a phenomenal display of symbiotic/parasitic relationships between living organisms. Plant growth-promoting rhizobacteria (PGPR) are some of the most widely investigated plant-beneficial microbes due to their capabilities in stimulating plant growth and development and conferring protection to plants against biotic and abiotic stresses. As such, PGPR-mediated plant priming/induced systemic resistance (ISR) has become a hot topic among researchers, particularly with prospects of applications in sustainable agriculture. The current study applies untargeted ultra-high performance liquid chromatography-high-definition mass spectrometry (UHPLC-HDMS) to investigate PGPR-based metabolic reconfigurations in the metabolome of primed wheat plants against Puccinia striiformis f. sp. tricti (Pst). A seed bio-priming approach was adopted, where seeds were coated with two PGPR strains namely Bacillus subtilis and Paenibacillus alvei (T22) and grown under controlled conditions in a glasshouse. The plants were infected with Pst one-week post-germination, followed by weekly harvesting of leaf material. Subsequent metabolite extraction was carried out for analysis on a UHPLC-HDMS system for data acquisition. The data was chemometrically processed to reveal the underlying trends and data structures as well as potential signatory biomarkers for priming against Pst. Results showed notable metabolic reprogramming in primary and secondary metabolism, where the amino acid and organic acid content of primed-control, primed-challenged and non-primed-challenged plants were differentially reprogrammed. Similar trends were observed from the secondary metabolism, in which primed plants (particularly primed-challenged) showed an up-regulation of phenolic compounds (flavonoids, hydroxycinnamic acids-HCAs- and HCA amides) compared to the non-primed plants. The metabolomics-based semi-quantitative and qualitative assessment of the plant metabolomes revealed a time-dependent metabolic reprogramming in primed-challenged and primed-unchallenged plants, indicating the metabolic adaptations of the plants to stripe rust infection over time.

Fragmentation disrupts microbial effects on native plant community productivity

Abstract Anthropogenic habitat fragmentation—the breaking up of natural landscapes—is a pervasive threat to biodiversity and ecosystem function world‐wide. Fragmentation results in a mosaic of remnant native habitat patches embedded in human‐modified habitat known as the ‘matrix’. By introducing novel environmental conditions in matrix habitats and reducing connectivity of native habitats, fragmentation can dramatically change how organisms experience their environment. The effects of fragmentation can be especially important in urban landscapes, which are expanding across the globe. Despite this surging threat and the importance of microbiomes for ecosystem services, we know very little about how fragmentation affects microbiomes and even less about their consequences for plant–microbe interactions in urban landscapes. By combining field surveys, microbiome sequencing and experimental mesocosms, we (1) investigated how microbial community diversity, composition and functional profiles differed between 15 native pine rockland fragments and the adjacent urban matrix habitat, (2) identified habitat attributes that explained significant variation in microbial diversity of native core habitat compared to urban matrix and (3) tested how changes in urbanized and low connectivity microbiomes affected plant community productivity. We found urban and native microbiomes differed substantively in diversity, composition and functional profiles, including symbiotic fungi decreasing 81% and pathogens increasing 327% in the urban matrix compared to native habitat. Furthermore, fungal diversity rapidly declined as native habitats became increasingly isolated, with ~50% of variation across the landscape explained by habitat connectivity alone. Interestingly, microbiomes from native habitats increased plant productivity by ~300% while urban matrix microbiomes had no effect, suggesting that urbanization may decouple beneficial plant–microbe interactions. In addition, microbial diversity within native habitats explained significant variation in plant community productivity, with higher productivity linked to more diverse microbiomes from more connected, larger fragments. Synthesis. Taken together, our study not only documents significant changes in microbial diversity, composition and functions in the urban matrix, but also supports that two aspects of habitat fragmentation—the introduction of a novel urban matrix and reduced habitat connectivity—disrupt microbial effects on plant community productivity, highlighting preservation of native microbiomes as critical for productivity in remnant fragments.

Microbial Marvels in Cotton Farming: Unveiling the Potential of Plant Beneficial Microbes for Enhanced Growth and Disease Resistance in Pakistan

Cotton is a crucial cash crop in Pakistan, playing a pivotal role in the country's economy, agricultural sector, and employment opportunities. Its cultivation spans over 3 million hectares, primarily concentrated in the Punjab and Sindh provinces. Cotton production in Pakistan contributes significantly to the country's foreign exchange earnings, accounting for a substantial portion of its exports However, cotton pest and disease management is always a challenge as their impact change over time. The widespread use of agrochemicals and synthetic pesticides in major field crops poses significant threats to human and animal health, as well as environmental degradation. Use of beneficial microbes for sustainable cotton production can be a natural ally in the field, as they promote the plant growth as well as protect them from disease, insects and pests. They act as a reservoir of beneficial metabolites, enzymes, and nutrients, and they play a crucial role in biological pest control and disease resistance induction. Additionally, PGP rhizobacteria possess bioremediation potential, enabling them to phytoextract and detoxify pollutants and pesticides. Beneficial microorganisms like PGPR hold immense potential to replace and supplement these toxic chemicals, offering promising applications in organic farming and contributing to sustainable agricultural practices. Despite their potential, only a limited number of bio-formulations have been developed using PGPR strains with plant growth promotion, metabolite production, enzyme synthesis, nutrient mobilization, and biocontrol activities. An increasing body of evidence underscores the potential of diverse microorganisms to enhance plant productivity and yield within cropping systems. Unlocking the full benefits of these advantageous microbes requires a profound understanding of their role in promoting growth, specifically in the realms of fertilization and disease control, along with the elucidation of underlying mechanisms. It is imperative to confront challenges associated with the application of plant growth-promoting (PGP) microbes. This review focuses on the application of PGP microbes in the context of cotton production. Given the scarcity of information on beneficial microbes for cotton production, a comprehensive examination of current research becomes crucial, especially given the increasing interest in cotton inoculants, particularly in developing nations. The heightened attention towards PGP applications underscores the importance of advancing sustainable agricultural practices.

Trichoderma Species: Our Best Fungal Allies in the Biocontrol of Plant Diseases-A Review.

Biocontrol agents (BCA) have been an important tool in agriculture to prevent crop losses due to plant pathogens infections and to increase plant food production globally, diminishing the necessity for chemical pesticides and fertilizers and offering a more sustainable and environmentally friendly option. Fungi from the genus Trichoderma are among the most used and studied microorganisms as BCA due to the variety of biocontrol traits, such as parasitism, antibiosis, secondary metabolites (SM) production, and plant defense system induction. Several Trichoderma species are well-known mycoparasites. However, some of those species can antagonize other organisms such as nematodes and plant pests, making this fungus a very versatile BCA. Trichoderma has been used in agriculture as part of innovative bioformulations, either just Trichoderma species or in combination with other plant-beneficial microbes, such as plant growth-promoting bacteria (PGPB). Here, we review the most recent literature regarding the biocontrol studies about six of the most used Trichoderma species, T. atroviride, T. harzianum, T. asperellum, T. virens, T. longibrachiatum, and T. viride, highlighting their biocontrol traits and the use of these fungal genera in Trichoderma-based formulations to control or prevent plant diseases, and their importance as a substitute for chemical pesticides and fertilizers.

Plant growth and microbial responses from urban agriculture soils amended with excavated local sediments and municipal composts

Abstract With increasing urbanization and critical issues of food insecurity emerging globally, urban agriculture is expanding as an agroecosystem with a distinct soil type. Growing food in cities is challenged by legacy contaminants in soils, which necessitates the use of imported, safe soils and composts. To promote the long-term sustainability of urban agriculture, we examined the agronomic potential of constructing safe, locally sourced soils to support food production. We collected composts from four municipal composting facilities in New York City: Big Reuse, Long Island City, Queens (BRL), New York Department of Sanitation, Fresh Kills, Staten Island (DNY), Lower Eastside Ecology Center (LES) and Queens Botanic Garden (QBG). We then created two types of constructed soils using each compost: 100% pure compost and a 50:50 blend of compost and clean excavated sediments from the New York City Clean Soil Bank. We then assessed the growth of tomato, pepper and kale in the constructed soils within a plant growth chamber facility. We found Clean Soil Bank sediments enhanced tomato aboveground biomass production by 98%, kale aboveground biomass production by 50% and pepper plant height by 52% when mixed with compost from BRL. At the same time, Clean Soil Bank Sediments decreased tomato plant height by 16% and aboveground biomass production by 29% in LES compost and tomato plant height by 18% in QBG compost, likely due to compost properties. The addition of Clean Soil Bank sediments showed no decline in the symbiosis of arbuscular mycorrhizal fungi across all composts, which is an important beneficial plant–microbe interaction in agroecosystems. A positive ecosystem service was found when Clean Soil Bank sediments were added to municipal composts, with up to a 74% decrease in greenhouse gas emissions of soil CO2 in BRL compost. The results indicate that urban agricultural soils can be constructed using clean, locally sourced materials, such as composted organic waste and excavated sediments from city development sites to support sustainable urban agriculture while enhancing ecosystem services.

Fermentation of White and Brown Rice Water Increases Plant Nutrients and Beneficial Microbes

The wastewater after washing rice grains is known as washed rice water (WRW). WRW is often recommended for reuse as plant fertilizer, but little is known about the difference in the nutrient and microbial contents of WRW between white and brown rice. The study aims to answer this question and determine how much the nutrient contents in the WRW would change with fermentation and how fermentation would affect the phosphorus (P)- and potassium (K)-solubilization bacteria in the WRW. Medium-grained rice was washed at a volumetric rice-to-water ratio of 1:3 for 90 seconds at 0.357 × g. WRW was then fermented for 0 (fresh), 3, 6, and 9 days. The rice grains and WRW were analyzed for pH, electrical conductivity (EC), carbon (C), nitrogen (N), sulfur (S), ammonium (NH4+), nitrate (NO3-), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), copper (Cu), zinc (Zn), and boron (B), as well as for total microbial population and P- and K-solubilizing bacteria. Brown rice grains had 26 to 324% higher P, K, Mg, and Zn than white rice. Nutrient contents in the WRW increased with increasing fermentation, except for C, which decreased with fermentation. At 9 days of fermentation, P, Ca, Mg, Cu, and B in the white rice water increased by 4 to 207%, which were also higher than in the brown rice water. The microbial population increased with fermentation for 3 days, then decreased after that, following the same C trend in the WRW from both rice types. P-and K-solubilization by bacteria in the WRW from both rice types increased with fermentation. The P solubilization was 25% higher in brown rice water, while the K solubilization was 67% higher in white rice water. Fermented rice water from white and brown rice was revealed to potentially improve plant growth and increase overall soil health due to their plant nutrient and microbial contents.

Ethylene: A Master Regulator of Plant-Microbe Interactions under Abiotic Stresses.

The plant phytohormone ethylene regulates numerous physiological processes and contributes to plant-microbe interactions. Plants induce ethylene production to ward off pathogens after recognition of conserved microbe-associated molecular patterns (MAMPs). However, plant immune responses against pathogens are essentially not different from those triggered by neutral and beneficial microbes. Recent studies indicate that ethylene is an important factor for beneficial plant-microbial association under abiotic stress such as salt and heat stress. The association of beneficial microbes with plants under abiotic stresses modulates ethylene levels which control the expression of ethylene-responsive genes (ERF), and ERFs further regulate the plant transcriptome, epi-transcriptome, Na+/K+ homeostasis and antioxidant defense mechanisms against reactive oxygen species (ROS). Understanding ethylene-dependent plant-microbe interactions is crucial for the development of new strategies aimed at enhancing plant tolerance to harsh environmental conditions. In this review, we underline the importance of ethylene in beneficial plant-microbe interaction under abiotic stresses.

Back to the roots: defining the core microbiome of Sorghum bicolor in agricultural field soils from the centre of origin.

Sorghum is a major staple crop in sub-Saharan Africa with yields severely impacted by biotic and abiotic factors. Here, we analysed the taxonomic diversity and biogeographical distribution of bacterial taxa of 48 agricultural fields along a transect of approximately 2000km across the Ethiopian sorghum belt, the centre of origin of sorghum. The ultimate goal is to identify-yet-unexplored-beneficial plant-microbe associations. Based on bulk soil bacterial communities and DArT-SNP analyses of 59 sorghum accessions, we selected three microbiologically distinct field soils and 12 sorghum genotypes, including commercial varieties, wild relatives, and farmer-preferred landraces. The results showed a core rhizosphere microbiome of 2125 amplicon sequence variants (ASVs), belonging to eight bacterial families consistently found across the three soil types and the 12 sorghum genotypes. Integration of the rhizosphere bacterial community analysis with DArT-SNP sorghum genotyping revealed the association of differentially abundant ASVs with sorghum genotypic traits, including the distinct recruitment of Pseudomonadaceae by the stay-green, drought-tolerant, and wild sorghum genotypes. Collectively, these results provide new insights into the core and accessory bacterial taxa in the sorghum rhizosphere in the centre of origin, setting a baseline for targeted isolation and functional characterization of putative beneficial rhizobacteria.

Seed coating with fungicide causes a beneficial shift in root‐associated microbiomes of mature soybean

AbstractWhile seed coating with fungicide is commonly used to control diseases in conventional soybean culture, the impact of fungicide seed coating on root‐associated microbial communities remains largely understudied. This hinders our assessment of the potential ecological and environmental risks of fungicide seed coating and our ability to improve plant health by using appropriate disease control practices. Here, we examined the diversity and composition of bacterial and fungal communities across root–soil compartments collected from a field experiment sown with fungicide‐coated or untreated seeds. The community structures significantly differed among the root–soil compartments. Fungicide seed coating demonstrated a greater effect on the structure of endophytic communities, including root endosphere and nodule, than the rhizosphere communities. A number of plant beneficial microbes responded positively to fungicide seed coating. Meanwhile, seed coating increased the absolute abundance of the nifH gene related to nitrogen fixation, especially in the root endosphere, from 2.63 to 18.30 ×108 copies g–1 dry root. Root‐associated microbes with coatings had a higher complexity of the microbial interkingdom cooccurrence network than those without coatings. Altogether, soybean [Glycine max (L.) Merr.] root‐associated microbiomes may have a high resilience under fungicide seed coating. At the mature stage of soybean, seed coating did not show any negative impact of residual fungicide on the root‐associated microecology, and it may pose a lower environmental risk than we have envisaged. Our results took a step forward in the responses of root‐associated microbiomes to the environment for legumes that have rarely been studied and provided new evidence of the eco‐friendly advantages of seed coatings in addition to agricultural output.

Australian native Glycine clandestina seed microbiota hosts a more diverse bacterial community than the domesticated soybean Glycine max

BackgroundPlant microbiome composition has been demonstrated to change during the domestication of wild plants and it is suggested that this has resulted in loss of plant beneficial microbes. Recently, the seed microbiome of native plants was demonstrated to harbour a more diverse microbiota and shared a common core microbiome with modern cultivars. In this study the composition of the seed-associated bacteria of Glycine clandestina is compared to seed-associated bacteria of Glycine max (soybean).ResultsThe seed microbiome of the native legume Glycine clandestina (crop wild relative; cwr) was more diverse than that of the domesticated Glycine max and was dominated by the bacterial class Gammaproteobacteria. Both the plant species (cwr vs domesticated) and individual seed accessions were identified as the main driver for this diversity and composition of the microbiota of all Glycine seed lots, with the effect of factor “plant species” exceeded that of “geographical location”. A core microbiome was identified between the two Glycine species. A high percentage of the Glycine microbiome was unculturable [G. clandestina (80.8%) and G. max (75.5%)] with only bacteria of a high relative abundance being culturable under the conditions of this study.ConclusionOur results provided novel insights into the structure and diversity of the native Glycine clandestina seed microbiome and how it compares to that of the domesticated crop Glycine max. Beyond that, it also increased our knowledge of the key microbial taxa associated with the core Glycine spp. microbiome, both wild and domesticated. The investigation of this commonality and diversity is a valuable and essential tool in understanding the use of native Glycine spp. for the discovery of new microbes that would be of benefit to domesticated Glycine max cultivars or any other economically important crops. This study has isolated microbes from a crop wild relative that are now available for testing in G. max for beneficial phenotypes.

Environmental interference of plant-microbe interactions.

Environmental stresses can compromise the interactions of plants with beneficial microbes. In the present review, experimental results showing that stresses negatively affect the abundance and/or functionality of plant beneficial microbes are summarized. It is proposed that the environmental interference of these plant-microbe interactions is explained by the stress-mediated induction of plant signalling pathways associated with defence hormones and reactive oxygen species. These plant responses are recognized to regulate beneficial microbes within plants. The direct negative effect of stresses on microbes may also contribute to the environmental regulation of these plant mutualisms. It is also posited that, in stress situations, beneficial microbes harbour mechanisms that contribute to maintain the mutualistic associations. Beneficial microbes produce effector proteins and increase the antioxidant levels in plants that counteract the detrimental effects of plant stress responses on them. In addition, they deliver specific stress-protective mechanisms that assist to their plant hosts to mitigate the negative effects of stresses. Our study contributes to understanding how environmental stresses affect plant-microbe interactions and highlights why beneficial microbes can still deliver benefits to plants in stressful environments.

Improvement of Photosynthetic Pigment Characteristics, Mineral Content, and Antioxidant Activity of Lettuce (Lactuca sativa L.) by Arbuscular Mycorrhizal Fungus and Seaweed Extract Foliar Application

Beneficial plant–microbe interaction for enhancing crop yield and quality is a sustainable way to achieve eco-friendly, desirable agricultural productions. The main objective of this experiment was to evaluate the individual and combined effects of an arbuscular mycorrhizal fungus (AMF) strain (Funneliformis mosseae) and a seaweed extract (SWE) derived from Ascophyllum nodosum, on the growth and physiological responses of lettuce (Lactuca sativa L.). Lettuce plants were inoculated with commercial AMF inoculum (5 g kg−1 soil), and SWE foliar application was done at three levels (0.5, 1.5, and 3 g L−1). The findings revealed that AMF along with SWE generated the greatest impact. In fact, co-application of AMF inoculation and 3 g L−1 SWE considerably enhanced root colonization, chlorophyll a, chlorophyll b, total chlorophyll, carotenoids, and mineral content in the shoots and roots (N, P, K, Ca, Fe, Zn, and Mn content) of lettuce plants. This combination improved initial fluorescence (F0), photochemical efficiency of PSII (FV/Fm) and Y(NO) and total antioxidant activity (TAA), whereas the maximum fluorescence, (Fm) and Y(II), showed the highest increase in lettuce plants treated with AMF and 1.5 g L−1 SWE. Furthermore, AMF inoculation along with SWE, at concentrations 1.5 and 3 g L−1, considerably enhanced variable fluorescence (FV) and the activity of water decomposition in electron donor photosystem II (FV/F0). As a result of these findings, it can be stated that the co-application of AMF and SWE positively improves the growth and development of lettuce plants.

Phytostimulants in sustainable agriculture

The consistent use of synthetic fertilizers and chemicals in traditional agriculture has not only compromised the fragile agroecosystems but has also adversely affected human, aquatic, and terrestrial life. The use of phytostimulants is an alternative eco-friendly approach that eliminates ecosystem disruption while maintaining agricultural productivity. Phytostimulants include living entities and materials, such as microorganisms and nanomaterials, which when applied to plants or to the rhizosphere, stimulate plant growth and induce tolerance to plants against biotic and abiotic stresses. In this review, we focus on plant growth-promoting rhizobacteria (PGPR), beneficial fungi, such as arbuscular mycorrhizal fungi (AMF) and plant growth-promoting fungi (PGPF), actinomycetes, cyanobacteria, azolla, and lichens, and their potential benefits in the crop improvement, and mitigation of abiotic and biotic stresses either alone or in combination. PGPR, AMF, and PGPF are plant beneficial microbes that can release phytohormones, such as indole acetic acid (IAA), gibberellic acid (GA), and cytokinins, promoting plant growth and improving soil health, and in addition, they also produce many secondary metabolites, antibiotics, and antioxidant compounds and help to combat biotic and abiotic stresses. Their ability to act as phytostimulator and a supplement of inorganic fertilizers is considered promising in practicing sustainable agriculture and organic farming. Glomalin is a proteinaceous product, produced by AMF, involved in soil aggregation and elevation of soil water holding capacity under stressed and unstressed conditions. The negative effects of continuous cropping can be mitigated by AMF biofertilization. The synergistic effects of PGPR and PGPF may be more effective. The mechanisms of control exercised by PGPF either direct or indirect to suppress plant diseases viz. by competing for space and nutrients, mycoparasitism, antibiosis, mycovirus-mediated cross-protection, and induced systemic resistance (ISR) have been discussed. The emerging role of cyanobacterial metabolites and the implication of nanofertilizers have been highlighted in sustainable agriculture.

Current Techniques to Study Beneficial Plant-Microbe Interactions.

Many different experimental approaches have been applied to elaborate and study the beneficial interactions between soil bacteria and plants. Some of these methods focus on changes to the plant and others are directed towards assessing the physiology and biochemistry of the beneficial plant growth-promoting bacteria (PGPB). Here, we provide an overview of some of the current techniques that have been employed to study the interaction of plants with PGPB. These techniques include the study of plant microbiomes; the use of DNA genome sequencing to understand the genes encoded by PGPB; the use of transcriptomics, proteomics, and metabolomics to study PGPB and plant gene expression; genome editing of PGPB; encapsulation of PGPB inoculants prior to their use to treat plants; imaging of plants and PGPB; PGPB nitrogenase assays; and the use of specialized growth chambers for growing and monitoring bacterially treated plants.

Cover crops enhance resource availability for soil microorganisms in a pecan orchard

Currently, there are substantial knowledge gaps on the impacts of cover crops on soil resources in tree cropping systems, wherein they are typically planted in interrow alleys and maintained for multiple years. While cover crops uptake soil nutrients and water, they can also prevent soil water evaporative losses and return nutrients to soils via decomposition of plant residues and stimulation of microbial nutrient cycling. This field sampling study examined variances in soil conditions across 5- and 7-year-old, cover cropped pecan orchards. We collected soil beneath cover crops and beneath adjacent trees, where soil was kept bare, to evaluate impacts of cover on the soil biota, nutrients, carbon, and their dynamics across a production season. We employed routine soil chemical analyses, phospholipid fatty acid (PLFA) analysis, and high throughput sequencing of 16 S rRNA genes and ITS regions for soils collected at four time points. We revealed that the cover cropped alley soils contained higher relative abundances of microbes that use labile soil substrates in resource rich conditions than did the tree row soils. Soil chemical analyses provided additional evidence that the cover crops did not deplete soil nutrients and reduce soil moisture, but rather, enhanced soil nutrient and moisture contents during many of the sampling time points. Notably, cover crop plant species correlated with soil nutrients and plant beneficial microbes, which may warrant consideration when selecting cover crop species. The tree row and cover cropped alley soils had different proportions of plant-beneficial mycorrhizal fungi. The tree rows supported higher numbers of ectomycorrhizal (ECM) fungi and alleys had higher relative abundances of arbuscular mycorrhizal (AM) fungi, suggesting potential benefits for tree species like pecan, which support dual colonization by AM and ECM Fungi. Altogether, the cover crops enhanced soil carbon, nutrients, and microbial populations in a pecan orchard and these impacts were frequently larger in a 7-year-old versus 5-year-old orchard.

Exploring the Corn Microbiome: A Detailed Review on Current Knowledge, Techniques, and Future Directions

In their natural environment, plants are colonized by a plethora of microorganisms. These diverse microorganisms interact with each other and the host to form a complex microbiome community. A growing body of research suggests that the microbiome has a significant impact on plant yield or health by promoting growth, stress tolerance, and resistance to pathogens. Although plant microbiomes have great potential for improving plant health and productivity, studies on crop microbiomes, especially in corn, have only recently started to be conducted. During the last few years, progress in next-generation sequencing technologies has enabled an increasing number of studies of corn-associated microbiomes and their dynamics with the plant. The composition and differentiation of microbial communities are affected not only by environmental factors and agricultural management but also by host phenotype and genotype. Although challenges remain in understanding the microbiome, the combination of beneficial plant microbes, microbial community interactions, and the optimization of the taxonomic composition of microbiomes determine the overall health and fitness of the plant and thus lead to more sustainable agriculture. In this review, we present an overview of the current knowledge and research on corn microbiomes using traditional culture-based approaches and next-generation amplicon or metagenomic profiling, discuss results from these approaches with an emphasis on the influence of environmental and host genetic factors on corn-microbe interactions, and outline future directions and challenges in corn microbiome research. A better understanding of the corn microbiome diversity, function, and microbiology will contribute to the improvement of crop health and productivity. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Glycyrrhiza uralensis Fisch. Root-associated microbiota: the multifaceted hubs associated with environmental factors, growth status and accumulation of secondary metabolites

Glycyrrhiza uralensis Fisch. is an important, perennial medicinal plant whose root microbiome is considered to play an important role in promoting accumulation of effective medicinal ingredients (liquiritin and glycrrhizic acid). Here, we report a comprehensive analysis of the microbial community structural composition and metabolite-plant-microbes association of G. uralensis Fisch. We collected both soil and rhizosphere samples of G. uralensis from different environmental conditions (cultivated and wild) and growth years (grown for one year and three years). Our data revealed higher species diversity in the wild group than in the cultivated group. The core rhizosphere microbiome of G. uralensis comprised 78 genera, including Bacillus, Pseudomonas, Rhizobium, some of which were potential plant beneficial microbes. Our results suggest that the growth of G. uralensis has a correlation with the root-associated microbiota assemblage. Integrated analysis among rhizosphere microbial taxa, plant gene expressions, and liquiritin and glycrrhizic acid accumulation showed that the liquiritin and glycrrhizic acid accumulation exhibited associations with the rhizosphere microbial composition at the genus level. The results provide valuable information to guide cultivation of G. uralensis, and potentially to harness the power of the root-associated microbiota to improve medicinal plant production.

Deterministic Process Dominated Belowground Community Assembly When Suffering Tomato Bacterial Wilt Disease

Soil microbial communities are closely associated with ecosystem functions. However, unravelling the complex nature of the microbial world and successfully utilizing all positive interactions for multipurpose environmental benefits is still a major challenge. Here, we describe the soil bacterial communities in different niches of healthy and diseased tomatoes under natural conditions. A higher abundance of the pathogen Ralstonia solanacearum and lower bacterial diversity were observed in the disease samples. The healthy tomato rhizosphere harbored more plant-beneficial microbes, including Bacillus and Streptomyces. Also, the co-occurrence network in the healthy rhizosphere samples was more complicated, so as to better adapt to the soil-borne pathogen invasion. Both the beta nearest-taxon-index (βNTI) and normalized stochasticity ratio (NST) analyses demonstrated that healthy rhizosphere communities were less phylogenetically clustered and mainly dominated by dispersal limitation, while homogeneous selection was the major assembly process driving the rhizosphere community of diseased samples. The results obtained with community assembly methods and co-occurrence network analysis revealed that healthy rhizosphere bacterial communities possessed potentially broader environmental stress (soil-borne pathogen stress) adaptability compared with diseased rhizosphere bacterial communities. In conclusion, this study contributed to widening our understanding of the potential mechanisms of soil bacterial community composition and assembly responding to soil-borne pathogen invasion.