Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed

Plant growth promoting endophyte modulates soil ecological characteristics during the enhancement process of cadmium phytoremediation

Endophyte assisted phytoremediation of cadmium (Cd) contaminated soil represents a promising strategy. However, the precise soil ecological regulatory mechanisms by which endophyte enhance the Cd phytoextraction remain unclear. Here, we employed the plant growth promoting endophyte (PGPE) Pseudomonas sp. E3, which has been validated to effectively enhance Cd extraction in Solanum nigrum L., to investigate its regulatory mechanism on soil ecology. The results demonstrated that while PGPE inoculation resulted in minimal alterations to the physicochemical properties of the bulk soil, it led to a notable increase in acid phosphatase activity by 17.86% and urease activity by 24.85% in the rhizosphere soil. This, in turn, significantly raised the available nitrogen and phosphorus contents by 16.93% and 21.27%, respectively, in the rhizosphere soil. Additionally, PGPE inoculation effectively replenished the bioavailable fractions of Fe and Cd, which had been depleted due to root uptake. Importantly, the inoculation specifically augmented the abundance of biomarkers p_Patescibacteria, f_Saccharimonadales, and g_Saccharimonadales in the rhizosphere soil. These biomarkers exhibited a significant positive correlation with the available nutrient and metal element contents. Moreover, the co-occurrence network analysis demonstrated that the inoculation resulted in a simplified bacterial community network, which may have facilitated community synergism by displacing bacteria with a negative association. This regulation appears to occur independently of PGPE colonization. Overall, our findings suggested that PGPE also exerts a regulatory influence on soil ecological features, significantly aiding hyperaccumulators in nutrient acquisition and heavy metal accumulation.

Characteristics of Pinus hwangshanensis Rhizospheric Fungal Community along Huangshan Mountain's Elevation Gradients, China

Elevation gradients strongly influence the diversity pattern of soil microorganisms. To date, many studies have elucidated the response of soil microbes to changes in elevation gradients. However, the effects of these gradients on the assembly mechanisms and network complexity of rhizospheric microbial communities remain underexplored. To bridge this knowledge gap, this study assessed the response of rhizospheric fungal communities of Pinus hwangshanensis along different elevation gradients in the Huangshan Mountain scenic area with regard to diversity, community composition, and assembly mechanisms using high-throughput amplicon sequencing. The results revealed significant differences in rhizospheric fungal community composition across three elevation gradients. The soil organic matter and pH were the most relevant factors influencing the changes in rhizospheric fungal community composition. The rhizospheric fungal diversity was significantly lower at both low and high elevations compared to the medium elevation. The rhizospheric fungal community assembly showed a more deterministic process at low and high elevations than at the medium elevation, indicating that stronger environmental filtering contributed to reduced fungal diversity at the extremes of the elevation gradient. In addition, rhizospheric pathogens, particularly Dermateaceae, acted as keystone taxa, diminishing the stability of co-occurrence networks at the medium elevation. This study contributes to a more comprehensive understanding of rhizospheric fungal community patterns and their ecological functions along elevation gradients in mountainous regions.

Exploring the Rhizospheric Microbial Communities under Long-Term Precipitation Regime in Norway Spruce Seed Orchard

The rhizosphere is the hotspot for microbial enzyme activities and contributes to carbon cycling. Precipitation is an important component of global climate change that can profoundly alter belowground microbial communities. However, the impact of precipitation on conifer rhizospheric microbial populations has not been investigated in detail. In the present study, using high-throughput amplicon sequencing, we investigated the impact of precipitation on the rhizospheric soil microbial communities in two Norway Spruce clonal seed orchards, Lipová Lhota (L-site) and Prenet (P-site). P-site has received nearly double the precipitation than L-site for the last three decades. P-site documented higher soil water content with a significantly higher abundance of Aluminium (Al), Iron (Fe), Phosphorous (P), and Sulphur (S) than L-site. Rhizospheric soil metabolite profiling revealed an increased abundance of acids, carbohydrates, fatty acids, and alcohols in P-site. There was variance in the relative abundance of distinct microbiomes between the sites. A higher abundance of Proteobacteria, Acidobacteriota, Ascomycota, and Mortiellomycota was observed in P-site receiving high precipitation, while Bacteroidota, Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadota, and Basidiomycota were prevalent in L-site. The higher clustering coefficient of the microbial network in P-site suggested that the microbial community structure is highly interconnected and tends to cluster closely. The current study unveils the impact of precipitation variations on the spruce rhizospheric microbial association and opens new avenues for understanding the impact of global change on conifer rizospheric microbial associations.

Clubroot-Induced Changes in the Root and Rhizosphere Microbiome of Susceptible and Resistant Canola

Clubroot is a soilborne disease of canola (Brassica napus) and other crucifers caused by the obligate parasite Plasmodiophora brassicae. In western Canada, clubroot is usually managed by planting-resistant cultivars, but the emergence of resistance-breaking pathotypes of P. brassicae represents a major threat to sustainable canola production. The rhizosphere and root contain beneficial microorganisms that can improve plant health. In this study, we evaluated the effect of two P. brassicae isolates (termed A and B) with different levels of virulence on the root and rhizosphere microbiomes of clubroot-resistant and clubroot-susceptible canola. Additionally, potential biocontrol microorganisms were identified based on taxa antagonistic to clubroot. Although both P. brassicae isolates were classified as pathotype 3A, isolate A caused a higher disease severity index in the resistant canola genotype compared with isolate B. Metabarcoding analysis indicated a shift in the bacterial and fungal communities in response to inoculation with either field isolate. Root endophytic bacterial and fungal communities responded to changes in inoculation, isolate type, sampling time, and canola genotype. In contrast, fungal communities associated with the rhizosphere exhibited significant differences between sampling times, while bacterial communities associated with the rhizosphere exhibited low variability.

Differential effects of domesticated and wild Capsicum frutescens L. on microbial community assembly and metabolic functions in rhizosphere soil

Objective

Rhizosphere microorganisms play crucial roles in the growth and development of plants, disease resistance, and environmental adaptability. As the only wild pepper variety resource in China, domesticated Capsicum frutescens Linn. (Xiaomila) exhibits varying beneficial traits and affects rhizosphere microbial composition compared with its wild counterparts. In this study, we aimed to identify specific rhizosphere microbiome and metabolism patterns established during the domestication process.

Methods

The rhizosphere microbial diversity and composition of domesticated and wild C. frutescens were detected and analyzed by metagenomics. Non-targeted metabolomics were used to explore the differences of metabolites in rhizosphere soil between wild and domesticated C. frutescens.

Results

We found that the rhizosphere microbial diversity of domesticated variety was significantly different from that of the wild variety, with Massilia being its dominant bacteria. However, the abundance of certain beneficial microbes such as Gemmatimonas, Streptomyces, Rambibacter, and Lysobacter decreased significantly. The main metabolites identified in the wild variety included serylthreonine, deoxyloganic acid, vitamin C, among others. In contrast, those identified in the domesticated group were 4-hydroxy-l-glutamic acid and benzoic acid. Furthermore, the differentially enriched pathways were concentrated in tyrosine and tryptophan biosynthesis, histidine and purine-derived alkaloids biosynthesis, benzoic acid family, two-component system, etc.

Conclusion

This study revealed that C. frutescens established specific rhizosphere microbiota and metabolites during domestication, which has important significance for the efficient utilization of beneficial microorganisms in breeding and cultivation practices.

Green Roof Substrate Microbes Compose a Core Community of Stress-Tolerant Taxa

Extensive green roofs provide for many ecosystem services in urban environments. The efficacy of these services is influenced by the vegetation structure. Despite their key role in plant performance and productivity, but also their contribution to nitrogen fixation or carbon sequestration, green roof microbial communities have received little attention so far. No study included a spatiotemporal aspect to investigate the core microbiota residing in the substrates of extensive green roofs, although these key taxa are hypothesized to be amongst the most ecologically important taxa. Here, we identified the core microbiota residing in extensive green roof substrates and investigated whether microbial community composition is affected by the vegetation that is planted on extensive green roofs. Eleven green roofs from three different cities in Flanders (Belgium), planted either with a mixture of grasses, wildflowers and succulents (Sedum spp.; Sedum-herbs-grasses roofs) or solely species of Sedum (Sedum-moss roofs), were seasonally sampled to investigate prokaryotic and fungal communities via metabarcoding. Identifying the key microbial taxa revealed that most taxa are dominant phylotypes in soils worldwide. Many bacterial core taxa are capable of nitrogen fixation, and most fungal key taxa are stress-tolerant saprotrophs, endophytes, or both. Considering that soil microbes adapted to the local edaphic conditions have been found to improve plant fitness, further investigation of the core microbiome is warranted to determine the extent to which these stress-tolerant microbes are beneficial for the vegetational layer. Although Sedum-herbs-grasses roofs contained more plant species than Sedum-moss roofs, we observed no discriminant microbial communities between both roof types, likely due to sharing the same substrate textures and the vegetational layers that became more similar throughout time. Future studies are recommended to comprehensively characterize the vegetational layer and composition to examine the primary drivers of microbial community assembly processes.

Responses of microbial communities in rhizocompartments of king grass to phytoremediation of cadmium-contaminated soil

King grass has been recognized as a potential phytoremediation plant species due to its high biomass and resistance to heavy metals (HMs). However, the possible impacts of cadmium (Cd) contamination on rhizocompartments' microbial activities in association with king grass have not been extensively explored. The utilization of 16S rRNA gene and ITS sequencing was carried out to examine alterations in the bacterial and fungal communities in the rhizosphere and rhizoplane of king grass in response to low and high Cd stress. Results demonstrated that both bacterial and fungal communities' diversity and richness were negatively impacted by Cd stress, regardless of its concentration. However, evenness did not exhibit any significant response to either of the concentrations. Additionally, nonmetric multidimensional scaling (NMDS) ordination demonstrated a significant difference (p < 0.001) in microbial communities under different treatments. The abundance of bacterial taxa such as Steroibacter, Nitrospira, Pseudoxanthomonas, Cellvirio, Phenylobacterium, Mycobacterium, Pirellula and Aquicella was adversely affected under Cd stress while Flavobacterium, Gemmata, Thiobacillus and Gemmatimonas showed no prominent response, indicating their resistance to Cd stress. Like that, certain fungal taxa for instance, Cladosporium, Cercophora, Acremonium, Mortierella, Aspergillus, Penicillium, Glomus and Sebacina were also highly reduced by low and high Cd stress. In contrast, Fusarium, Thanatephorus, Botrytis and Curvularia did not show any response to Cd stress. The identified taxa may have a crucial role in the growth of king grass under heavy metal contamination, making them promising candidates for developing bioinoculants to encourage plant performance and phytoremediation capability in HM-contaminated soils.

Influence of the Antibiotic Oxytetracycline on the Morphometric Characteristics and Endophytic Bacterial Community of Lettuce (Lactuca sativa L.)

Antibiotics enter the soil with compost prepared from livestock manures and other sources. There is concern that they may influence plant growth and cause antibiotic resistance in soil and plant endospheric microbiomes. In the present work, lettuce plants were cultivated in soil and hydroponics spiked with oxytetracycline (0, 15, and 300 mg × kg-1 and 0, 15, and 50 mg × L-1, respectively) during a 28-day greenhouse experiment. It was revealed that the antibiotic reduced the chlorophyll content, the biomass, and the length of the roots and stems by 1.4-4.7, 1.8-39, 2.5-3.2, and 1.8-6.3 times in soil and in hydroponics. The copy numbers of the tet(A) and tet(X) genes were revealed to be 4.51 × 103-1.58 × 105 and 8.36 × 106-1.07 × 108 copies × g-1, respectively, suggesting the potential migration of these genes from soil/hydroponics to plant roots and leaves. According to a non-metric multidimensional scaling (NMDS) analysis of the 16S rRNA amplicon sequencing data, endospheric bacterial communities were similar in leaves and roots independent of the growing substrate and antibiotic concentration. While soil bacterial communities were unaffected by the presence of antibiotics, hydroponic communities exhibited dependency, likely attributable to the absence of the mitigating effect of soil particle absorption.

Microbiome-Mediated Protection against Pathogens in Woody Plants

Pathogens, especially invasive species, have caused significant global ecological, economic, and social losses in forests. Plant disease research has traditionally focused on direct interactions between plants and pathogens in an appropriate environment. However, recent research indicates that the microbiome can interact with the plant host and pathogens to modulate plant resistance or pathogen pathogenicity, thereby altering the outcome of plant-pathogen interactions. Thus, this presents new opportunities for studying the microbial management of forest diseases. Compared to parallel studies on human and crop microbiomes, research into the forest tree microbiome and its critical role in forest disease progression has lagged. The rapid development of microbiome sequencing and analysis technologies has resulted in the rapid accumulation of a large body of evidence regarding the association between forest microbiomes and diseases. These data will aid the development of innovative, effective, and environmentally sustainable methods for the microbial management of forest diseases. Herein, we summarize the most recent findings on the dynamic structure and composition of forest tree microbiomes in belowground and aboveground plant tissues (i.e., rhizosphere, endosphere, and phyllosphere), as well as their pleiotropic impact on plant immunity and pathogen pathogenicity, highlighting representative examples of biological control agents used to modulate relevant tree microbiomes. Lastly, we discuss the potential application of forest tree microbiomes in disease control as well as their future prospects and challenges.

Genetic diversity of Actinidia spp. shapes the oomycete pattern associated with Kiwifruit Vine Decline Syndrome (KVDS)

Kiwifruit Vine Decline Syndrome (KVDS) is an important soil-borne disease for the Italian kiwifruit industry, causing €300,000 in economic losses in 2020 alone. So far, the organisms recognized as involved in the aetiology of KVDS mainly belong to the Oomycota. As no effective management strategies exist, a promising approach to overcoming KVDS is the use of resistant species as rootstocks or for inclusion in breeding programs. Several Actinidia genotypes showing different level of resistance to KVDS were grown in disease-promoting soils. A metabarcoding approach was set up to identify KVDS-associated oomycetes and investigate whether the main species involved may vary according to plant genotype. Our results clearly showed significant differences between the genotypes in terms of oomycetes present in both plant rhizosphere and endosphere, which were strongly correlated with the symptoms displayed. We found out that the resistance of Actinidia macrosperma to KVDS is related to its ability to shape the pathobiome, particularly as far as the endosphere is concerned. In our conditions, Phytophthora sp. was predominantly found in sensitive genotypes, whilst Globisporangium intermedium was mainly detected in asymptomatic plants, suggesting that the latter species could compete with the recruitment of Phytophthora sp. in plants with different levels of resistance, consequently, explaining the onset of symptoms and the resistance condition.

Home-field advantage affects the local adaptive interaction between Andropogon gerardii ecotypes and root-associated bacterial communities

Due to climate change, drought frequencies and severities are predicted to increase across the United States. Plant responses and adaptation to stresses depend on plant genetic and environmental factors. Understanding the effect of those factors on plant performance is required to predict species' responses to environmental change. We used reciprocal gardens planted with distinct regional ecotypes of the perennial grass Andropogon gerardii adapted to dry, mesic, and wet environments to characterize their rhizosphere communities using 16S rRNA metabarcode sequencing. Even though the local microbial pool was the main driver of these rhizosphere communities, the significant plant ecotypic effect highlighted active microbial recruitment in the rhizosphere, driven by ecotype or plant genetic background. Our data also suggest that ecotypes planted at their homesites were more successful in recruiting rhizosphere community members that were unique to the location. The link between the plants' homesite and the specific local microbes supported the "home field advantage" hypothesis. The unique homesite microbes may represent microbial specialists that are linked to plant stress responses. Furthermore, our data support ecotypic variation in the recruitment of congeneric but distinct bacterial variants, highlighting the nuanced plant ecotype effects on rhizosphere microbiome recruitment. These results improve our understanding of the complex plant host-soil microbe interactions and should facilitate further studies focused on exploring the functional potential of recruited microbes. Our study has the potential to aid in predicting grassland ecosystem responses to climate change and impact restoration management practices to promote grassland sustainability. IMPORTANCE In this study, we used reciprocal gardens located across a steep precipitation gradient to characterize rhizosphere communities of distinct dry, mesic, and wet regional ecotypes of the perennial grass Andropogon gerardii. We used 16S rRNA amplicon sequencing and focused oligotyping analysis and showed that even though location was the main driver of the microbial communities, ecotypes could potentially recruit distinct bacterial populations. We showed that different A. gerardii ecotypes were more successful in overall community recruitment and recruitment of microbes unique to the "home" environment, when growing at their "home site." We found evidence for "home-field advantage" interactions between the host and host-root-associated bacterial communities, and the capability of ecotypes to recruit specialized microbes that were potentially linked to plant stress responses. Our study aids in a better understanding of the factors that affect plant adaptation, improve management strategies, and predict grassland function under the changing climate.

Soil properties drive the bacterial community to cadmium contamination in the rhizosphere of two contrasting wheat (Triticum aestivum L.) genotypes

Cadmium (Cd) bioavailability in the rhizosphere makes an important difference in grain Cd accumulation in wheat. Here, pot experiments combined with 16S rRNA gene sequencing were conducted to compare the Cd bioavailability and bacterial community in the rhizosphere of two wheat (Triticum aestivum L.) genotypes, a low-Cd-accumulating genotype in grains (LT) and a high-Cd-accumulating genotype in grains (HT), grown on four different soils with Cd contamination. Results showed that there was non-significant difference in total Cd concentration among four soils. However, except for black soil, DTPA-Cd concentrations in HT rhizospheres were higher than those of LT in fluvisol, paddy soil and purple soil. Results of 16S rRNA gene sequencing showed that soil type (52.7%) was the strongest determinant of root-associated community, while there were still some differences in rhizosphere bacterial community composition between two wheat genotypes. Taxa specifically colonized in HT rhizosphere (Acidobacteria, Gemmatimonadetes, Bacteroidetes and Deltaproteobacteria) could participate in metal activation, whereas LT rhizosphere was highly enriched by plant growth-promoting taxa. In addition, PICRUSt2 analysis also predicted high relative abundances of imputed functional profiles related to membrane transport and amino acid metabolism in HT rhizosphere. These results revealed that the rhizosphere bacterial community may be an important factor regulating Cd uptake and accumulation in wheat and indicated that the high Cd-accumulating cultivar might improve Cd bioavailability in the rhizosphere by recruiting taxa related to Cd activation, thus promoting Cd uptake and accumulation.

Effects of a Nanonetwork-Structured Soil Conditioner on Microbial Community Structure

Fertilizer application can increase yields, but nutrient runoff may cause environmental pollution and affect soil quality. A network-structured nanocomposite used as a soil conditioner is beneficial to crops and soil. However, the relationship between the soil conditioner and soil microbes is unclear. We evaluated the soil conditioner's impact on nutrient loss, pepper growth, soil improvement, and, especially, microbial community structure. High-throughput sequencing was applied to study the microbial communities. The microbial community structures of the soil conditioner treatment and the CK were significantly different, including in diversity and richness. The predominant bacterial phyla were Pseudomonadota, Actinomycetota, and Bacteroidota. Acidobacteriota and Chloroflexi were found in significantly higher numbers in the soil conditioner treatment. Ascomycota was the dominant fungal phylum. The Mortierellomycota phylum was found in significantly lower numbers in the CK. The bacteria and fungi at the genus level were positively correlated with the available K, available N, and pH, but were negatively correlated with the available P. Our results showed that the loss of nutrients controlled by the soil conditioner increased available N, which improved soil properties. Therefore, the microorganisms in the improved soil were changed. This study provides a correlation between improvements in microorganisms and the network-structured soil conditioner, which can promote plant growth and soil improvement.

Environmental sporobiota: Occurrence, dissemination, and risks

Spore-forming bacteria known as sporobiota are widespread in diverse environments from terrestrial and aquatic habitats to industrial and healthcare systems. Studies on sporobiota have been mainly focused on food processing and clinical fields, while a large amount of sporobiota exist in natural environments. Due to their persistence and capabilities of transmitting virulence factors and antibiotic resistant genes, environmental sporobiota could pose significant health risks to humans. These risks could increase as global warming and environmental pollution has altered the life cycle of sporobiota. This review summarizes the current knowledge of environmental sporobiota, including their occurrence, characteristics, and functions. An interaction network among clinical-, food-related, and environment-related sporobiota is constructed. Recent and effective methods for detecting and disinfecting environmental sporobiota are also discussed. Key problems and future research needs for better understanding and reducing the risks of environmental sporobiota and sporobiome are proposed.

Uptake, translocation, bioaccumulation, and bioavailability of organophosphate esters in rice paddy and maize fields

Rice and maize are two main crops with different growth habits in Northeast China. To investigate the uptake, translocation, and accumulation of organophosphate esters (OPEs) in those two crops, we measured the OPE concentrations in their agricultural soil-crop systems during different growing seasons. OPE concentrations were higher in paddy (221 ± 62.0 ng/g) than in maize (149 ± 31.6 ng/g) soil, with higher OPE levels in the rhizosphere than in bulk soil for rice, and the opposite in maize. Two-step extractions were used to obtain the labile and stable adsorption components of OPEs. The stable-adsorbed OPEs were activated to be more bioavailable by root exudates as rice grew. OPEs in rice increased linearly with the growing period. The uptake and translocation processes of OPEs by crops were not well-explained by logK_ow alone, indicating other processes such as growth dilution are significant for understanding OPE levels in plant. The translocation factors of OPEs from nutritive to reproductive organs indicated that OPEs in rice seeds may follow the translocation from root to leaf and then transfer to grains. Two genera, Sphingomonas and Geobacter, associated with degradation of organophosphorus compounds were enriched in rhizosphere soils, indicating enhanced OPE degradation.

Age-Related Rhizosphere Analysis of Coffea arabica Plants

The analysis of large-scale sequence data has revealed that plants over time recruit certain microbes that are efficient colonizers of the rhizosphere. This enrichment phenomenon is especially seen in annual crops, but we suggest that there could have been some type of enrichment in perennial crops such as coffee plants. To verify this hypothesis, we performed a metagenomic and chemical analysis in rhizosphere with three different plant ages (young, mature, and old) and cultivated on the same farm. We verified that from mature to old plants, there was a decrease in diversity, particularly Fusarium and Plenodomus, while there was an increase in Aspergillus, Cladosporium, Metarhizium, and Pseudomonas. We also detected that the abundance of anti-microbials and ACC-deaminase grows as plants age, although denitrification and carbon fixation had reduced abundances. In summary, we detected an enrichment in the microbial community, especially in the great increase in the participation of Pseudomonas, passing from 50% of the relative abundance as the plants get older. Such enrichment can occur through the dynamics of nutrients such as magnesium and boron.

Acremoniumcapsici and A.guizhouense, two new members of Acremonium (Hypocreales, Sordariomycetes) isolated from the rhizosphere soil of Capsicumannuum

Two new species, Acremoniumcapsici and A.guizhouense, isolated from the rhizosphere soil of Capsicumannuum, are described and illustrated. Two-locus DNA sequences based on phylogeny, in combination with the morphology of the asexual morph, were used to characterize these species. In the phylogenetic tree, both new species clustered into a monophyletic clade with strong support, distinct from other previously known species of Acremonium. The new species differed from their allied species in their morphology.

Higher-Quality Pumpkin Cultivars Need to Recruit More Abundant Soil Microbes in Rhizospheres

Two different qualities of pumpkin, cultivars G1519 and G1511, were grown in the same environment under identical management. However, their qualities, such as the contents of total soluble solids, starch, protein, and vitamin C, were significantly different. Do rhizospheric microbes contribute to pumpkin quality? To answer this question, this study investigated the soil microbial compositions in the rhizospheres of different quality pumpkin cultivars to determine the differences in these soil microbial compositions and thus determine how soil microbes may affect pumpkin quality. Firstly, a randomized complete block design with two pumpkin cultivars and three replications was performed in this study. The soil microbial compositions and structures in the rhizospheres of the two pumpkin cultivars were analyzed using a high-throughput sequencing technique. In comparison with the low-quality pumpkin cultivar (G1519), higher microbial diversity and richness could be found in the rhizospheres of the high-quality pumpkin cultivar (G1511). The results showed that there were significant differences in the soil bacterial and fungal community compositions in the rhizospheres of the high- and low-quality pumpkin cultivars. Although the compositions and proportions of microorganisms were similar in the rhizospheres of the two pumpkin cultivars, the proportions of Basidiomycota and Micropsalliota in the G1519 rhizosphere were much higher than those in the G1511 rhizosphere. Furthermore, the fungal phylum and genus Rozellomycota and Unclassified_p__Rozellomycota were unique in the rhizosphere of the high-quality pumpkin cultivar (G1511). All the above results indicate that soil microbes were enriched differentially in the rhizospheres of the low- and high-quality pumpkin cultivars. In other words, more abundant soil microbes were recruited in the rhizosphere of the high-quality pumpkin cultivar as compared to that of the low-quality cultivar. Rozellomycota and Unclassified_p__Rozellomycota may be functional microorganisms relating to pumpkin quality.

Functionally-explicit sampling can answer key questions about the specificity of plant-microbe interactions

The rhizosphere is a nexus for plant-microbe interactions and, as a host-structured environment, a location of high activity for distinct microbes and plant species. Although our insights into this habitat have exploded in recent years, we are still limited in our ability to answer key questions about the specificity of these root-microbial relationships. In particular, it can be difficult to confirm or reject microbiome heritability in many plant systems and to pinpoint which microbial taxa are key to plant functioning. Like other host-structured environments, the rhizosphere is structurally, chemically, and biologically complex, driven largely by differences in root anatomy, location, and function. In this Correspondence, we describe a review of 377 "rhizosphere microbiome" research papers and demonstrate how matching a sampling method to the biological question can advance our understanding of host-microbe interactions in a functionally heterogeneous environment. We found that the vast majority of studies (92%) pool all roots from a root system during sampling, ignoring variation in microbial composition between roots of different function and limiting insight into key root-microbial relationships. Furthermore, approaches for removing root-associated microbes are highly variable and non-standard, complicating multi-study analyses. Our understanding of the strength and nature of host-microbe relationships in heterogenous host-microbiome environments can be clarified by targeting sampling to locations of high interaction. While the high complexity of the rhizosphere creates logistical challenges, we suggest that unambiguous language and refined approaches will improve our ability to match methods to research questions and advance our understanding of the specificity of plant-microbial interactions.

Long-term continuous mono-cropping of Macadamia integrifolia greatly affects soil physicochemical properties, rhizospheric bacterial diversity, and metabolite contents

Macadamia integrifolia is the most economically important Proteaceae crop known for its edible nuts. The present study was conducted to examine the effect of continuous cultivation (for 1, 5, and 20 years) of M. integrifolia on soil quality, bacterial diversity, and metabolites. Soil rhizospheres from three different Macadamia rhizosphere orchards, 1-year monoculture orchard (CK), 5-year monoculture orchard (Y5), and 20-year monoculture orchard (Y20), were analyzed through metagenomic and metabolomic profiling. The soil physicochemical properties, including organic matter, and available nutrients (P, N, and K) were first increased significantly (p &lt; 0.05) from the CK to the Y5 group and then decreased (p &lt; 0.05) from the Y5 to the Y20 group. The soil pH continuously decreased (p &lt; 0.05) over time from CK to Y20. Metagenomic profiling revealed that Actinobacteria, Acidobacteria, and Proteobacteria were the top three abundant phyla with their inconsistent relative abundance patterns from CK to Y20 (CK: 23.76%, Y5: 34. 06%, and Y20: 31.55%), (CK: 13.59%, Y5: 18.59%, and Y20: 21.35%), and (CK: 27.59%, Y5: 15.98%, and Y20: 17.08%), respectively. Furthermore, the Y5 rhizospheres had a higher number of beneficial bacterial genera belonging to Proteobacteria and Actinobacteria than the Y20 rhizospheres. The KEGG annotation analysis revealed that cellular processes, organism systems, metabolism, and genetic information were the most enriched functional categories. CAZy database screening indicated the highest enrichment of glycoside hydrolases following the glycoside transferases and carbohydrate-binding modules. Differential metabolite analysis revealed the highest number of metabolites (11) in the Y5 group than in the Y20 group (6). It is concluded that continuous monoculture of M. integrifolia improves the soil physicochemical properties, bacterial diversity, and metabolite contents in short-term planted orchards which, however, are deteriorated in long-term planted orchards.

Positive feedback between peanut and arbuscular mycorrhizal fungi with the application of hairy vetch in Ultisol

Multiple agricultural practices are being applied to increase crop yield in order to overcome the food shortage. Green manure has emerged as an appropriate practice to improve soil fertility and crop yield. However, the potential functions of arbuscular mycorrhizal fungi (AMF) in the below-ground ecosystems following the application of green manure in Ultisols remain largely unexplored. In this study, qPCR and high-throughput sequencing were used to investigate the response of AMF abundance and communities in different treatment groups, i.e., control (without fertilization), mineral fertilization (NPK), mineral fertilization with returning peanut straw (NPKS), and with green manure (hairy vetch; NPKG). The NPKG treatment significantly increased soil fertility compared to other treatment groups. Compared with control, the NPK, NPKS, and NPKG treatments increased peanut yield by 12.3, 13.1, and 25.4%, respectively. NPKS and NPKG treatments significantly altered the AMF community composition decreased the AMF diversity and increased AMF abundance compared to the control. The AMF network of the NPKG treatment group showed the highest complexity and stability compared to other treatment groups. The structural equation modeling revealed that the application of hairy vetch improved soil nutrients and peanut yield by increasing the soil AMF abundance and network stability. Overall, the results suggested that the application of hairy vetch might trigger positive feedback between the peanut and AMF community, contributing to fertility and yield improvement in the dryland of Ultisol.

The parameters determining hyperaccumulator rhizobacteria diversity depend on the study scale

Soils harbor some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. Numerous parameters, intrinsic to plant physiology, life history and the soil itself, can influence the structure of rhizomicrobial communities. While our knowledge of rhizosphere microbial diversity is increasing, opinion is divided as to whether the factors that most impact this diversity are abiotic, climatic or plant selection. Here we focused on the rhizosphere bacterial diversity of nickel hyperaccumulator plants (28 species from Mediterranean or tropical climates). We showed, by leveraging 16S Illumina sequencing of 153 ultramafic rhizosphere soils, that bacterial genetic diversity was highest in Mediterranean habitats where plant diversity was the lowest. Concerning those parameters driving this diversity, we demonstrated that climate drives bacterial diversity, in particular with the annual temperature variation. Focusing on each region, we underlined the substantial role of soil physicochemical parameters. Our results highlight the importance of considering spatial scale when explaining bacterial community diversity.

Salt-tolerant endophytic bacterium Enterobacter ludwigii B30 enhance bermudagrass growth under salt stress by modulating plant physiology and changing rhizosphere and root bacterial community

Osmotic and ionic induced salt stress suppresses plant growth. In a previous study, Enterobacter ludwigii B30, isolated from Paspalum vaginatum, improved seed germination, root length, and seedling length of bermudagrass (Cynodon dactylon) under salt stress. In this study, E. ludwigii B30 application improved fresh weight and dry weight, carotenoid and chlorophyll levels, catalase and superoxide dismutase activities, indole acetic acid content and K⁺ concentration. Without E. ludwigii B30 treatment, bermudagrass under salt stress decreased malondialdehyde and proline content, Y(NO) and Y(NPQ), Na⁺ concentration, 1-aminocyclopropane-1-carboxylate, and abscisic acid content. After E. ludwigii B30 inoculation, bacterial community richness and diversity in the rhizosphere increased compared with the rhizosphere adjacent to roots under salt stress. Turf quality and carotenoid content were positively correlated with the incidence of the phyla Chloroflexi and Fibrobacteres in rhizosphere soil, and indole acetic acid (IAA) level was positively correlated with the phyla Actinobacteria and Chloroflexi in the roots. Our results suggest that E. ludwigii B30 can improve the ability of bermudagrass to accumulate biomass, adjust osmosis, improve photosynthetic efficiency and selectively absorb ions for reducing salt stress-induced injury, while changing the bacterial community structure of the rhizosphere and bermudagrass roots. They also provide a foundation for understanding how the bermudagrass rhizosphere and root microorganisms respond to endophyte inoculation.

Changes of Microbial Diversity in Rhizosphere of Different Cadmium-Gradients Soil under Irrigation with Reclaimed Water

Water scarcity and the uneven distribution of water resources in China have resulted in water shortages for agricultural irrigation in arid and semi-arid areas. Reclaimed water used for agricultural irrigation has become an effective solution in the context of the global water shortage. In order to improve soil productivity and solve the shortage of water resources, we carried out reclaimed water irrigation experiments on polluted soil. Compared with full irrigation treatments, the EC value of reclaimed water under deficit irrigation treatments decreased by 2.89–42.90%, and the content of organic matter increased by 6.31–12.10%. The proportion of Acidobacteria community in soils with different cadmium concentration gradients irrigated with reclaimed water ranged from 13.6% to 30.5%, its relative abundance decreased with the increase of soil cadmium concentration. In particular, the relative abundance of Pseudomonas pathogens in deficit irrigation treatments was lower than that of the full irrigation treatments. RDA analysis showed that the environmental factors that played a leading role in the change of microbial community structure were organic matter and pH. Furthermore, the metabolic function potential of the rhizosphere soil bacterial community in deficit irrigation treatments was higher than that of full irrigation treatments with reclaimed water. This study proved that reclaimed water irrigation for cadmium contaminated soil did not aggravate the pollution level and promoted the soil ecological environment with better microbial community diversity.

Cultivar sensitivity of broomcorn millet (Panicum miliaceum L.) to nitrogen availability is associated with differences in photosynthetic physiology and nitrogen uptake

In order to explore the influences of low nitrogen (N) fertilizer on the growth performances of two broomcorn millet (Panicum miliaceum L.) cultivars with different N tolerances, the field experiment was carried out with a low-N-tolerant cultivar (BM 184) and a low-N-sensitive cultivar (BM 230) under three N levels (0, 75 and 150 kg N ha^-1) in the Loess Plateau, China. 150 kg N ha^-1 was conventional N application rate and considered as the control. Compared to typical N supply, low N fertilizer significantly weakened the photosynthetic capacity by increasing the light transmission ratio and decreasing leaf area index, resulting in reduced biomass accumulation. BM 184 held the longer duration of the biomass increase phase and larger relative growth rate than BM 230 as well as higher photosynthetic parameters (i.e., relative chlorophyll content, net photosynthetic rate, and transpiration rate) did under low N treatments. Such optimized physiological characteristics contributed to more effective N uptake and transportation from the stems, leaves, and sheaths to grains in the BM 184. Furthermore, compared with BM 230, BM 184 had higher rhizosphere soil fertility and soil enzyme activity under low N conditions; consequently, combined with the physiological characteristics for aboveground and soil nutrient status for belowground, higher productivity was obtained in BM 184 than that in BM 230 over the two years study. Overall, our results demonstrated that low-N-tolerant cultivar achieved reduced N fertilizer input with increased efficiency by optimizing growth performances in semi-arid cultivation areas.

Microbial Community Composition of the Antarctic Ecosystems: Review of the Bacteria, Fungi, and Archaea Identified through an NGS-Based Metagenomics Approach

Antarctica represents a unique environment, both due to the extreme meteorological and geological conditions that govern it and the relative isolation from human influences that have kept its environment largely undisturbed. However, recent trends in climate change dictate an unavoidable change in the global biodiversity as a whole, and pristine environments, such as Antarctica, allow us to study and monitor more closely the effects of the human impact. Additionally, due to its inaccessibility, Antarctica contains a plethora of yet uncultured and unidentified microorganisms with great potential for useful biological activities and production of metabolites, such as novel antibiotics, proteins, pigments, etc. In recent years, amplicon-based next-generation sequencing (NGS) has allowed for a fast and thorough examination of microbial communities to accelerate the efforts of unknown species identification. For these reasons, in this review, we present an overview of the archaea, bacteria, and fungi present on the Antarctic continent and the surrounding area (maritime Antarctica, sub-Antarctica, Southern Sea, etc.) that have recently been identified using amplicon-based NGS methods.

Brassica napus Bacterial Assembly Processes Vary with Plant Compartment and Growth Stage but Not between Lines

Holobiont bacterial community assembly processes are an essential element to understanding the plant microbiome. To elucidate these processes, leaf, root, and rhizosphere samples were collected from eight lines of Brassica napus in Saskatchewan over the course of 10 weeks. We then used ecological null modeling to disentangle the community assembly processes over the growing season in each plant part. The root was primarily dominated by stochastic community assembly processes, which is inconsistent with previous studies that suggest of a highly selective root environment. Leaf assembly processes were primarily stochastic as well. In contrast, the rhizosphere was a highly selective environment. The dominant rhizosphere selection process leads to more similar communities. Assembly processes in all plant compartments were dependent on plant growth stage with little line effect on community assembly. The foundations of assembly in the leaf were due to the harsh environment, leading to dominance of stochastic effects, whereas the stochastic effects in the root interior likely arise due to competitive exclusion or priority effects. Engineering canola microbiomes should occur during periods of strong selection assuming strong selection could promote beneficial bacteria. For example, engineering the microbiome to resist pathogens, which are typically aerially born, should focus on the flowering period, whereas microbiomes to enhance yield should likely be engineered postflowering as the rhizosphere is undergoing strong selection. IMPORTANCE In order to harness the microbiome for more sustainable crop production, we must first have a better understanding of microbial community assembly processes that occurring during plant development. This study examines the bacterial community assembly processes of the leaf, root, and rhizosphere of eight different lines of Brassica napus over the growing season. The influence of growth stage and B. napus line were examined in conjunction with the assembly processes. Understanding what influences the assembly processes of crops might allow for more targeted breeding efforts by working with the plant to manipulate the microbiome when it is undergoing the strongest selection pressure.

Enhanced anti-herbivore defense of tomato plants against Spodoptera litura by their rhizosphere bacteria

BACKGROUND

The use of beneficial microorganisms as an alternative for pest control has gained increasing attention. The objective of this study was to screen beneficial rhizosphere bacteria with the ability to enhance tomato anti-herbivore resistance.

RESULTS

Rhizosphere bacteria in tomato field from Fuqing, one of the four locations where rhizosphere bacteria were collected in Fujian, China, enhanced tomato resistance against the tobacco cutworm Spodoptera litura, an important polyphagous pest. Inoculation with the isolate T6-4 obtained from the rhizosphere of tomato field in Fuqing reduced leaf damage and weight gain of S. litura larvae fed on the leaves of inoculated tomato plants by 27% in relative to control. Analysis of 16S rRNA gene sequence identities indicated that the isolate T6-4 was closely related to Stenotrophomonas rhizophila supported with 99.37% sequence similarity. In the presence of S. litura infestation, inoculation with the bacterium led to increases by a 66.9% increase in protease inhibitor activity, 53% in peroxidase activity and 80% in polyphenol oxidase activity in the leaves of inoculated plants as compared to the un-inoculated control. Moreover, the expression levels of defense-related genes encoding allene oxide cyclase (AOC), allene oxide synthase (AOS), lipoxygenase D (LOXD) and proteinase inhibitor (PI-II) in tomato leaves were induced 2.2-, 1.7-, 1.4- and 2.7-fold, respectively by T6-4 inoculation.

CONCLUSION

These results showed that the tomato rhizosphere soils harbor beneficial bacteria that can systemically induce jasmonate-dependent anti-herbivore resistance in tomato plants.

Insights into the microbiome assembly during different growth stages and storage of strawberry plants

BACKGROUND

Microbiome assembly was identified as an important factor for plant growth and health, but this process is largely unknown, especially for the fruit microbiome. Therefore, we analyzed strawberry plants of two cultivars by focusing on microbiome tracking during the different growth stages and storage using amplicon sequencing, qPCR, and microscopic approaches.

RESULTS

Strawberry plants carried a highly diverse microbiome, therein the bacterial families Sphingomonadaceae (25%), Pseudomonadaceae (17%), and Burkholderiaceae (11%); and the fungal family Mycosphaerella (45%) were most abundant. All compartments were colonized by high number of bacteria and fungi (10⁷-10¹⁰ marker gene copies per g fresh weight), and were characterized by high microbial diversity (6049 and 1501 ASVs); both were higher for the belowground samples than in the phyllosphere. Compartment type was the main driver of microbial diversity, structure, and abundance (bacterial: 45%; fungal: 61%) when compared to the cultivar (1.6%; 2.2%). Microbiome assembly was strongly divided for belowground habitats and the phyllosphere; only a low proportion of the microbiome was transferred from soil via the rhizosphere to the phyllosphere. During fruit development, we observed the highest rates of microbial transfer from leaves and flowers to ripe fruits, where most of the bacteria occured inside the pulp. In postharvest fruits, microbial diversity decreased while the overall abundance increased. Developing postharvest decay caused by Botrytis cinerea decreased the diversity as well, and induced a reduction of potentially beneficial taxa.

CONCLUSION

Our findings provide insights into microbiome assembly in strawberry plants and highlight the importance of microbe transfer during fruit development and storage with potential implications for food health and safety.

Phosphate fertilization affects rhizosphere microbiome of maize and sorghum genotypes

Despite the lower reactivity of natural phosphates compared to soluble fertilizers, their P bioavailability can increase over the cultivation years, due to the physicochemical processes and the activity of soil microbiota. Therefore, this work aimed to evaluate the α and β diversity of the rhizosphere microbiota of maize and sorghum genotypes grown under different sources and doses of phosphate fertilizers. Four commercial maize and four sorghum genotypes were grown under field conditions with three levels of triple superphosphate (TSP) and two types of rock phosphate sources: phosphorite (RockP) and bayóvar (RP) during two seasons. Maize and sorghum presented a significant difference on the genetic β diversity of both rhizosferic bacterial and arbuscular mycorrhizal fungi. Moreover, P doses within each phosphate source formed two distinct groups for maize and sorghum, and six bacterial phyla were identified in both crops with significant difference in the relative abundance of Firmicutes and Proteobacteria. It was observed that RockP fertilization increased Firmicutes population while Proteobacteria was the most abundant phylum after TSP fertilization in maize. In sorghum, a significant impact of fertilization was observed on the Acidobacteria and Proteobacteria phyla. TSP fertilization increased the Acidobacteria population compared to no fertilized (P0) and RockP while Proteobacteria abundance in RockP was reduced compared to P0 and TSP, indicating a shift toward a more copiotrophic community. Our results suggested that the reactivity of P source is the predominant factor in bacterial community' structures in the maize and sorghum rhizosphere from the evaluated genotypes, followed by P source.

Unexpected diversity among small-scale sample replicates of defined plant root compartments

Community assembly processes determine patterns of species distribution and abundance which are central to the ecology of microbiomes. When studying plant root microbiome assembly, it is typical to sample at the whole plant root system scale. However, sampling at these relatively large spatial scales may hinder the observability of intermediate processes. To study the relative importance of these processes, we employed millimetre-scale sampling of the cell elongation zone of individual roots. Both the rhizosphere and rhizoplane microbiomes were examined in fibrous and taproot model systems, represented by wheat and faba bean, respectively. Like others, we found that the plant root microbiome assembly is mainly driven by plant selection. However, based on variability between replicate millimetre-scale samples and comparisons with randomized null models, we infer that either priority effects during early root colonization or variable selection among replicate plant roots also determines root microbiome assembly.

Temporal Dynamics of Rhizosphere Communities Across the Life Cycle of Panax notoginseng

Rhizosphere microbiome promotes plant growth; however, the succession of rhizosphere microbial community during the growth stages of perennial medicinal plant Panax notoginseng (P. notoginseng) is still unclear. Here, amplicon sequencing was performed to assess the succession characteristics of rhizosphere microbiomes during developmental stages. Results showed that bacterial and fungal communities were mainly shaped by the development stages. The microbial α-diversities first increased and then decreased with plant growth and the variation in microbial composition was active at the 3-year root growth (3YR) stage. The variation trend of cross-domain co-occurrence network complexity was similar to that of α-diversities. Cross-domain nodes decreased at the 3YR stage and fungal nodes increased at the 3YR stage. This study provided a detailed and systematic survey of rhizosphere microbiomes during the growth stages of P. notoginseng. The findings revealed that the development stages of P. notoginseng drove the temporal dynamics of rhizosphere communities. This study helps in harnessing the power of microbiomes to evaluate herbal medicine growth and provides valuable information to guide the microbial breeding of medical plants.

Plant growth promoting rhizobacterial diversity in potato grown soil in the Gwalior region of India

There seems to be meager studies with regards to rhizo and non-rhizo microbial association with potato plant from the central India. Present study was undertaken to evaluate the microbial diversity of rhizospheric and non-rhizospheric isolates from three varieties of potato viz Kufri sindhuri, Kufri lauvkar and Kufri chipsona-3 procured from the Central Potato Research Station, Maharajpura, Gwalior. A total of 130 bacterial forms were isolated, and amongst these forty isolates were further characterized on their morphological basis, and those showing some of PGPR characteristics were identified to species level using VITEK-2 method. Various bacterial populations were found in potato rhizosphere and dominant presence was those of Bacillus subtilis, Bacillus Megaterium and Lysinibacillus sphaericus. The non-rhizospheric soil was dominant in the forms like Aeromonas salmonicida, Morxella group and Bacillus coagulans. Highest bacterial diversity was found in the rhizosphere soil of different potato cultivars than in the non-rhizospheric soil of potato.

Wheat Genotype-Specific Recruitment of Rhizosphere Bacterial Microbiota Under Controlled Environments

Plants recruit beneficial microbial communities in the rhizosphere that are involved in a myriad of ecological services, such as improved soil quality, nutrient uptake, abiotic stress tolerance, and soil-borne disease suppression. Disease suppression caused by rhizosphere microbiomes has been important in managing soil-borne diseases in wheat. The low heritability of resistance in wheat to soil-borne diseases like Rhizoctonia root rot has made management of these diseases challenging, particularly in direct-seeded systems. Identification of wheat genotypes that recruit rhizosphere microbiomes that promote improved plant fitness and suppression of the pathogen could be an alternative approach to disease management through genetic improvement. Several growth chamber cycling experiments were conducted using six winter wheat genotypes (PI561725, PI561727, Eltan, Lewjain, Hill81, Madsen) to determine wheat genotypes that recruit suppressive microbiomes. At the end of the third cycle, suppression assays were done by inoculating R. solani into soils previously cultivated with specific wheat genotypes to test suppression of the pathogen by the microbiome. Microbiome composition was characterized by sequencing of 16S rDNA (V1-V3 region). Among the growth cycling lengths, 160-day growth cycles exhibited the most distinct rhizosphere microbiomes among the wheat genotypes. Suppression assays showed that rhizosphere microbiomes of different wheat genotypes resulted in significant differences in shoot length (value of p=0.018) and had an impact on the pathogenicity of R. solani, as observed in the reduced root disease scores (value of p=0.051). Furthermore, soils previously cultivated with the ALMT1 isogenic lines PI561725 and PI561727 exhibited better seedling vigor and reduced root disease. Microbiome analysis showed that Burkholderiales taxa, specifically Janthinobacterium, are differentially abundant in PI561727 and PI561725 cultivated soils and are associated with reduced root disease and better growth. This study demonstrates that specific wheat genotypes recruit different microbiomes in growth chamber conditions but the microbial community alterations were quite different from those previously observed in field plots, even though the same soils were used. Genotype selection or development appears to be a viable approach to controlling soil-borne diseases in a sustainable manner, and controlled environment assays can be used to see genetic differences but further work is needed to explain differences seen between growth chamber and field conditions.

No tillage and residue mulching method on bacterial community diversity regulation in a black soil region of Northeastern China

Soil microorganisms are important components of agricultural ecosystems; they are important in agricultural soil nutrient cycle and are easily affected by soil tillage. The response of soil microbial community to tillage is very complex, and the effect of the no tillage and residue mulching method on soil microbial diversity remains unclear. In 2019, the soil was collected from an experimental field after 10 years of continuous cultivation in the black soil area of the Sanjiang Plain in Northeastern China. In this study, the diversity and composition of the soil bacterial community and their relationship with soil properties were explored via high-throughput sequencing under no tillage with four residue mulching treatments. No tillage with 60% residue mulching (NTR3) significantly increased the alpha diversity of the rhizosphere soil bacteria and changed the composition of the bacterial community-consistent with changes in soil physicochemical properties. Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla in the sample soil. Soil physicochemical properties explained 80.6% of the changes in soil diversity and composition, of which soil organic carbon, soil pH, and soil temperature were the principal contributors. Our results suggest that no tillage and residue mulching is conducive to increasing soil organic carbon and soil nutrient content, which is a beneficial conservation tillage measure for black soil protection in Sanjiang Plain of Northeast China. The no tillage with residue mulching, especially 60% residue mulching, alters soil bacterial community and highlights the importance of soil physicochemical properties in shaping the diversity and composition of the soil bacterial community. Our findings contribute to a broad understanding of the effects of no tillage and residue mulching on bacterial community differences and provide a scientific basis for the optimization of no tillage measures and sustainable utilization of the black soil of the Sanjiang Plain in Northeastern China.

Can We Estimate Functionality of Soil Microbial Communities from Structure-Derived Predictions? A Reality Test in Agricultural Soils

Computational approaches that link bacterial 16S rRNA gene amplicon data to functional genes based on prokaryotic reference genomes have emerged. This study aims to validate or refute the applicability of the functional gene prediction tools for assessment and comparison of community functionality among experimental treatments, inducing either fast or slow responses in rhizosphere microbial community composition and function. Rhizosphere samples of wheat and barley were collected in two consecutive years at active and mature growth phases from organic and conventional farming plots with ambient or future-climate treatments of the Global Change Experimental Facility. Bacterial community composition was determined by 16S rRNA gene amplicon sequencing, and the activities of five extracellular enzymes involved in carbon (β-glucosidases, cellobiohydrolase, and xylosidase), nitrogen (N-acetylglucosaminidase), and phosphorus (acid phosphatase) cycles were determined. Structural community data were used to predict functional patterns of the rhizosphere communities using Tax4Fun and PanFP. Subsequently, the predictions were compared with the measured activities. Despite the fact that different treatments mainly drove either community composition (plant growth phase) or measured enzyme activities (farming system), the predictions mirrored patterns in the treatments in a qualitative but not quantitative way. Most of the discrepancies between measured and predicted values resulted from plant growth stages (fast community response), followed by farming management and climate (slower community response). Thus, our results suggest the applicability of the prediction tools for comparative investigations of soil community functionality in less-dynamic environmental systems. IMPORTANCE Linking soil microbial community structure to its functionality, which is important for maintaining health and services of an ecosystem, is still challenging. Besides great advances in structural community analysis, functional equivalents, such as metagenomics and metatranscriptomics, are still time and cost intensive. Recent computational approaches (Tax4Fun and PanFP) aim to predict functions from structural community data based on reference genomes. Although the usability of these tools has been confirmed with metagenomic data, a comparison between predicted and measured functions is so far missing. Thus, this study comprises an expansive reality test on the performance of these tools under different environmental conditions, including relevant global change factors (land use and climate). The work provides a valuable validation of the applicability of the prediction tools for comparison of soil community functions across different sufficiently established soil ecosystems and suggest their usability to unravel the broad spectrum of functions provided by a given community structure.

The remediation potential for PAHs of Verbascum sinuatum L. combined with an enhanced rhizosphere landscape: A full-scale mesocosm experiment

A full-scale mesocosm study was conducted to depict how integrated biological systems interact to adapt to contaminant stress and improve remediation of polycyclic aromatic hydrocarbons (PAHs)contaminated soils. The combination of Verbascum sinuatum L. and microbial consortium (fungi and bacteria) was employed along with three differently contaminated soils. After 240 days the highest PAHs removal (up to 68 %) and 6-rings compounds decrease was found in soil with lower pollution and cation exchange capacity. V. sinuatum showed a significant adaptability over time in terms of redox biology. Soil enzyme activities and microscopic evidences proved a rising plant-microorganisms association and a successful mycorrhization, arising from the inoculation of our consortia. In addition, an enhanced richness of PAHs degrading genes was achieved. Microbial co-metabolism, helped by the establishment of complex relationships with hosting plant, demonstrated to be suitable for the degradation of high molecular weight PAHs and represents a biotechnology with great prospects.

Soil type influence nutrient availability, microbial metabolic diversity, eubacterial and diazotroph abundance in chickpea rhizosphere

Rhizosphere microbial communities are dynamic and play a crucial role in diverse biochemical processes and nutrient cycling. Soil type and cultivar modulate the composition of rhizosphere microbial communities. Changes in the community composition significantly alter microbial function and ecological process. We examined the influence of soil type on eubacterial and diazotrophic community abundance and microbial metabolic potential in chickpea (cv. BG 372 and cv. BG 256) rhizosphere. The total eubacterial and diazotrophic community as estimated through 16 S rDNA and nifH gene copy numbers using qPCR showed the soil type influence with clear rhizosphere effect on gene abundance. PLFA study has shown the variation in microbial community structure with different soil types. Differential influence of soil types and cultivar on the ratio of Gram positive to Gram negative bacteria was observed with most rhizosphere soils corresponding to higher ratios than bulk soil. The rhizosphere microbial activities (urease, dehydrogenase, alkaline phosphatase and beta-glucosidase) were also assessed as an indicator of microbial metabolic diversity. Principal component analysis and K-means non-hierarchical cluster mapping grouped soils into three categories, each having different soil enzyme activity or edaphic drivers. Soil type and cultivar influence on average substrate utilization pattern analyzed through community level physiological profiling (CLPP) was higher for rhizosphere soils than bulk soils. The soil nutrient studies revealed that both soil type and cultivar influenced the available N, P, K and organic carbon content of rhizosphere soil. Our study signifies that soil type and cultivar jointly influenced soil microbial community abundance and their metabolic potential in chickpea rhizosphere.

Current Methods, Common Practices, and Perspectives in Tracking and Monitoring Bioinoculants in Soil

Microorganisms promised to lead the bio-based revolution for a more sustainable agriculture. Beneficial microorganisms could be a valid alternative to the use of chemical fertilizers or pesticides. However, the increasing use of microbial inoculants is also raising several questions about their efficacy and their effects on the autochthonous soil microorganisms. There are two major issues on the application of bioinoculants to soil: (i) their detection in soil, and the analysis of their persistence and fate; (ii) the monitoring of the impact of the introduced bioinoculant on native soil microbial communities. This review explores the strategies and methods that can be applied to the detection of microbial inoculants and to soil monitoring. The discussion includes a comprehensive critical assessment of the available tools, based on morpho-phenological, molecular, and microscopic analyses. The prospects for future development of protocols for regulatory or commercial purposes are also discussed, underlining the need for a multi-method (polyphasic) approach to ensure the necessary level of discrimination required to track and monitor bioinoculants in soil.

Overview of Approaches to Improve Rhizoremediation of Petroleum Hydrocarbon-Contaminated Soils

Soil contamination with petroleum hydrocarbons (PHCs) has become a global concern and has resulted from the intensification of industrial activities. This has created a serious environmental issue; therefore, there is a need to find solutions, including application of efficient remediation technologies or improvement of current techniques. Rhizoremediation is a green technology that has received global attention as a cost-effective and possibly efficient remediation technique for PHC-polluted soil. Rhizoremediation refers to the use of plants and their associated microbiota to clean up contaminated soils, where plant roots stimulate soil microbes to mineralize organic contaminants to H2O and CO2. However, this multipartite interaction is complicated because many biotic and abiotic factors can influence microbial processes in the soil, making the efficiency of rhizoremediation unpredictable. This review reports the current knowledge of rhizoremediation approaches that can accelerate the remediation of PHC-contaminated soil. Recent approaches discussed in this review include (1) selecting plants with desired characteristics suitable for rhizoremediation; (2) exploiting and manipulating the plant microbiome by using inoculants containing plant growth-promoting rhizobacteria (PGPR) or hydrocarbon-degrading microbes, or a combination of both types of organisms; (3) enhancing the understanding of how the host–plant assembles a beneficial microbiome, and how it functions, under pollutant stress. A better understanding of plant–microbiome interactions could lead to successful use of rhizoremediation for PHC-contaminated soil in the future.

Plant Compartments and Developmental Stages Modulate the Balance between Niche-Based and Neutral Processes in Soybean Microbiome

Understanding the dynamics of plant-associated microbial communities within agriculture is well documented. However, the ecological processes that assemble the plant microbiome are not well understood. This study elucidates the relative dominance of assembly processes across plant compartments (root, stem, and leaves) and developmental stages (emergence, growth, flowering, and maturation). Bacterial community composition and assembly processes were assessed using 16S rRNA gene amplicon sequencing. Null models that couple phylogenetic community composition and species distribution models were used to evaluate ecological assembly processes of bacterial communities. All models highlighted that the balance between the assembly process was modulated by compartments and developmental stages. Dispersal limitation dominated amongst the epiphytic communities and at the maturation stage. Homogeneous selection dominated assembly across plant compartments and development stages. Overall, both sets of models were mostly in agreement in predicting the prevailing assembly processes. Our results show, for the first time, that even though niche-based processes dominate in the plant environment, the relative influence of dispersal limitation in community assembly is important.

Functional assembly of root-associated microbial consortia improves nutrient efficiency and yield in soybean

Root-associated microbes are critical for plant growth and nutrient acquisition. However, scant information exists on optimizing communities of beneficial root-associated microbes or the mechanisms underlying their interactions with host plants. In this report, we demonstrate that root-associated microbes are critical influencers of host plant growth and nutrient acquisition. Three synthetic communities (SynComs) were constructed based on functional screening of 1,893 microbial strains isolated from root-associated compartments of soybean plants. Functional assemblage of SynComs promoted significant plant growth and nutrient acquisition under both N/P nutrient deficiency and sufficiency conditions. Field trials further revealed that application of SynComs stably and significantly promoted plant growth, facilitated N and P acquisition, and subsequently increased soybean yield. Among the tested communities, SynCom1 exhibited the greatest promotion effect, with yield increases of up to 36.1% observed in two field sites. Further RNA-seq implied that SynCom application systemically regulates N and P signaling networks at the transcriptional level, which leads to increased representation of important growth pathways, especially those related to auxin responses. Overall, this study details a promising strategy for constructing SynComs based on functional screening, which are capable of enhancing nutrient acquisition and crop yield through the activities of beneficial root-associated microbes.

Cultivable and metagenomic approach to study the combined impact of nanogypsum and Pseudomonas taiwanensis on maize plant health and its rhizospheric microbiome

In the present study we examined the effect of nanogypsum and Pseudomonas taiwanensis strain BCRC 17751on plant and soil health using conventional and metagenomics approaches. Soil physicochemical properties and agronomical parameters of maize plants were reported to be better when applied with nanogypsum and bacterial inoculum together. When compared to control a significant increase in total bacterial counts, nitrogen, phosphorus, potassium (NPK) solubilizing bacterial population and soil enzyme activities (fluorescein diacetate, alkaline phosphatase, dehydrogenase, β-glucosidase, arylesterase and amylase) was reported in treatments. The metagenomics studies revealed dominance of beneficial bacteria such as Proteobacteria, Bacteriodetes, Planctomycetes, Acidobacteria and Nitrospirae in treated soil. On the other hand some novel bacterial diversity was also reported in treated soil which was evident from presence of taxonomically unclassified sequences. Hence, it can be concluded that combined application of nanogypsum and Pseudomonas taiwanensis in maize help in improving the structure and function of soil which affects the plant health without causing any toxic effect. However, in situ validation of the prescribed treatment is required under field conditions on different crops in order to give maximum benefits to the farmers and the environment.

Soil microbial diversity in organic and non-organic pasture systems

Understanding the effects of organic pasture management on the soil microbiome is important for sustainable forage production since soil microbiome diversity contributes to improved nutrient cycling, soil structure, plant growth, and environmental resiliency; however, the soil microbiome response to pasture management is largely unknown. This study assessed the soil microbial diversity, richness, and community structure following 10 years of pasture management (organic or non-organic) of the V4 region of the 16S rRNA using the Illumina MiSeq platform. Soil samples were collected from 0–15 cm in July and August from 2017–2018 and soil nutrient properties (nutrients, carbon, nitrogen, and pH) quantified and correlated with soil microbial diversity. Overall, greater soil bacterial species richness (P ≤ 0.05) occurred in organic relative to non-organic (conventional) systems. Management affected bacterial species richness (Chao1), with greater richness occurring in organic pasture soils and less richness occurring in non-organic systems (P ≤ 0.05). Similarly, management affected bacterial evenness (Simpson’s index), with a more diverse community occurring in organically managed soils relative to non-organic pastures (P ≤ 0.05). Linear discriminant analysis effect size analysis showed statistically significant and biologically consistent differences in bacterial taxa in organic compared with non-organic soils. Therefore, there was a shift in bacterial community structure in organic relative to non-organic soils (P ≤ 0.05). Additionally, soil nutrients (Fe, Mg, Ni, S, Al, K, Cd, and Cu), pH, C, and N were correlated with one or more dominant bacterial phyla (Gemmatimonadetes, Planctomycetes, Firmicutes, Chloroflexi, Actinobacteria, and Acidobacteria). Overall, pasture management affected soil microbial diversity, with greater diversity occurring in organic than non-organic systems, likely owing to applications of organic poultry litter in organic systems compared to non-organic management (use of inorganic-fertilizers and herbicides). Results indicate that when pastures are converted to organic production systems, soil microbial richness and diversity may increase, thereby resulting in enhanced soil microbiome diversity and overall ecosystem services.

Potato plant spheres and to a lesser extent the soil type influence the proportion and diversity of bacterial isolates with in vitro antagonistic activity towards Ralstonia solanacearum

Ralstonia solanacearum biovar2-race3 (Rs r3b2) is an epidemic soil-borne bacterial phytopathogen causing brown rot disease in potato. In this study, we assessed how three soil types stored at the same field site influenced the proportion and diversity of bacterial isolates with in vitro antagonistic activity towards Rs in bulk soil and different potato plant spheres (rhizosphere, endorhiza and endocaulosphere; ecto- and endosphere of seed and yield tubers). In general, the plate counts observed for each sample type were not significantly different. A total of 96 colonies per sample type was picked and screened for in vitro antagonistic activity against Rs. Antagonists were obtained from all bulk soils and plant spheres with the highest proportion obtained from the endorhiza and endocaulosphere of potato plants. BOX-PCR fingerprints of antagonists showed that some were specific for particular plant spheres independent of the soil type, while others originated from different plant spheres of a particular soil type. The majority of antagonists belonged to Pseudomonas. A high proportion of antagonists produced siderophores, and interestingly antagonists from potato tubers frequently carried multiple antibiotic production genes. Our data showed an enrichment of bacteria with genes or traits potentially involved in biocontrol in the rhizosphere and in endophytic compartments. We report that the proportion and diversity of in vitro antagonists towards Rs isolated from bulk soil and different spheres of potato plants grown under field conditions in three different soil types was mainly shaped by the plant sphere and to a lesser extent by the soil type. Bacteria with antagonistic activity towards Ralstonia solanacearum were isolated from all plant spheres and bulk soils but their proportion was highest in endophytic compartments.

Reduced tillage, cover crops and organic amendments affect soil microbiota and improve soil health in Uruguayan vegetable farming systems

Conventional tillage and mineral fertilization (CTMF) jeopardize soil health in conventional vegetable production systems. Using a field experiment established in Uruguay in 2012, we aimed to compare the soil restoration potential of organic fertilization (compost and poultry manure) combined with conventional tillage and cover crop incorporated into the soil (CTOF) or with reduced tillage and the use of cover crop as mulch (RTOF). In 2017, table beet was cultivated under CTMF, CTOF and RTOF, and yields, soil aggregate composition and nutrients, as well as soil and table beet rhizosphere microbiota (here: bacteria and archaea) were evaluated. Microbiota was studied by high-throughput sequencing of 16S rRNA gene fragments amplified from total community DNA. RTOF exhibited higher soil aggregation, soil organic C, nutrient availability and microbial alpha-diversity than CTMF, and became more similar to an adjacent natural undisturbed site. The soil microbiota was strongly shaped by the fertilization source which was conveyed to the rhizosphere and resulted in differentially abundant taxa. However, 229 amplicon sequencing variants were found to form the core table beet rhizosphere microbiota shared among managements. In conclusion, our study shows that after only 5 years of implementation, RTOF improves soil health under intensive vegetable farming systems.

The effect of crop species on DNase-producing bacteria in two soils

Purpose

Extracellular deoxyribonucleases (exDNases) from microbial origin contribute substantially to the restriction of extracellular DNA (exDNA) in the soil. Hence, it is imperative to understand the diversity of bacterial species capable of performing this important soil function and how crop species influence their dynamics in the soil. The present study investigates the occurrence of DNase-producing bacteria (DPB) in leachate samples obtained from soils in which the crop species of alfalfa (Medicago sativa L.), canola (Brassica napus L.), soybean (Glycine max [L.] Merr.) and wheat (Triticum aestivum L.) were raised in a growth room.

Methods

Selective media containing methyl green indicator was used to screen for DPB from leachate samples, whereas the 16S rRNA sequence analysis was employed to identify the isolates.

Results

The proportion of culturable DPB ranged between 5.72 and 40.01%; however, we did observe specific crop effects that shifted throughout the growing period. In general, higher proportions of exDNase producers were observed when the soils had lower nutrient levels. On using the 16S rRNA to classify the DPB isolates, most isolates were found to be members of the Bacillus genera, while other groups included Chryseobacterium, Fictibacillus, Flavobacterium, Microbacterium, Nubsella, Pseudomonas, Psychrobacillus, Rheinheimera, Serratia and Stenotrophomonas. Five candidate exDNase/nuclease-encoding proteins were also identified from Bacillus mycoides genomes using online databases.

Conclusion

Results from this study showed that crop species, growth stage and soil properties were important factors shaping the populations of DPB in leachate samples; however, soil properties seemed to have a greater influence on the trends observed on these bacterial populations. It may be possible to target soil indigenous bacteria that produce exDNases through management to decrease potential unintended effects of transgenes originating from genetically modified organisms (GMOs) or other introduced nucleic acid sequences in the environment.

Spatial and Temporal Distribution of Soil Microbial Properties in Two Shrub Intercrop Systems of the Sahel

The Sahel is an ecologically vulnerable region where increasing populations with a concurrent increase in agricultural intensity has degraded soils. Agroforestry offers an approach to remediate these landscapes. A largely unrecognized agroforestry resource in the Sahel are the native shrubs, Piliostigma reticulatum, and Guiera senegalensis that to varying degrees already coexist with row crops. These shrubs improve soil quality, redistribute water from the deep soil to the surface (hydraulic lift), and can improve crop growth. However, little information is available on whether these shrubs affect spatial and temporal dynamics of microbial communities. Therefore, the objective of this study was to determine microbial composition and activity in the wet and dry seasons of soil in the: shrub rhizosphere (RhizS), inter-root zone (IntrS), and outside the influence of shrub soil (OutS) for both G. senegalensis and P. reticulatum in Senegal. A 3 × 2 factorial field experiment was imposed at two locations (490 and 700 mm annual rainfall with G. senegalensis and P. reticulatum, respectively), that had the soil sampling treatments of three locations (RhizS, IntrS, and OutS) and two seasons (wet and dry). Soils were analyzed for: microbial diversity (DGGE with bacterial 16S or fungal 28S rRNA gene sequences phospholipids fatty acid, PLFA); enzyme activities; microbial biomass carbon (MBC); and nitrogen (N) mineralization potential. For the DGGE profiling, the bacterial community responded more to the rhizosphere effect, whereas, the fungal community was more sensitive to season. PLFA, MBC, enzyme activities and inorganic N were significantly higher in both seasons for the RhizS. The presence of shrubs maintained rhizosphere microbial communities and activity during the dry season. This represents a paradigm shift for semi-arid environments where logically it would be expected to have no microbial activity in the extended dry season. In contrast this study has shown this is not the case that rather the presence of shrub roots maintained the microbial community in the dry season most likely due to hydraulic lift and root exudates. This has implications when these shrubs are in cropped fields in that decomposition and mineralization of nutrients can proceed in the dry season. Thus, enabling accumulation of plant available nutrients during the dry season for uptake by crops in the rainy season.