Sphingomonas sp. Cra20 Increases Plant Growth Rate and Alters Rhizosphere Microbial Community Structure of Arabidopsis thaliana Under Drought Stress

The Impacts of Field Management on Soil and Tea Root Microbiomes

Due to the importance of microbes in soil health and crop production, manipulation of microbiomes provides a new strategy for improving crop growth and agricultural ecosystems. Current understanding is limited regarding the responses of soil and crop endophytic microbiomes to field management and microbiome programming. In this study, we investigated soil and tea root bacterial communities under conventional and organic cropping systems using 16S rRNA gene sequencing. A significant difference in soil and root bacterial community structure was observed under different field managements, leading to 43% and 35% variance, respectively. We also identified field management-sensitive species both in soils and tea roots that have great potential as bioindicators for bacterial microbiome manipulation. Moreover, through functional profile predictions of microbiomes, xenobiotics degradation in soil bacterial communities is enriched in organic farms, suggesting that biodegradation capabilities are enhanced under organic cropping systems. Our results demonstrate the effects of field management on both soil and tea root bacterial microbiomes and provide new insights into the reprogramming of microbial structures.

Clover Root Exudates Favor Novosphingobium sp. HR1a Establishment in the Rhizosphere and Promote Phenanthrene Rhizoremediation

Rhizoremediation is based on the ability of microorganisms to metabolize nutrients from plant root exudates and, thereby, to cometabolize or even mineralize toxic environmental contaminants. Novosphingobium sp. HR1a is a bacterial strain able to degrade a wide variety of polycyclic aromatic hydrocarbons (PAHs). Here, we have demonstrated that the number of CFU in microcosms vegetated with clover was almost 2 orders of magnitude higher than that in nonvegetated microcosms or microcosms vegetated with rye-grass or grass. Strain HR1a was able to eliminate 92% of the phenanthrene in the microcosms with clover after 9 days. We have studied the molecular basis of the interaction between strain HR1a and clover by phenomic, metabolomic, and transcriptomic analyses. By measuring the relative concentrations of several metabolites exudated by clover both in the presence and in the absence of the bacteria, we identified some compounds that were probably consumed in the rhizosphere; the transcriptomic analyses confirmed the expression of genes involved in the catabolism of these compounds. By using a transcriptional fusion of the green fluorescent protein (GFP) to the promoter of the gene encoding the dioxygenase involved in the degradation of PAHs, we have demonstrated that this gene is induced at higher levels in clover microcosms than in nonvegetated microcosms. Therefore, the positive interaction between clover and Novosphingobium sp. HR1a during rhizoremediation is a result of the bacterial utilization of different carbon and nitrogen sources released during seedling development and the capacity of clover exudates to induce the PAH degradation pathway. IMPORTANCE The success of an eco-friendly and cost-effective strategy for soil decontamination is conditioned by the understanding of the ecology of plant-microorganism interactions. Although many studies have been published about the bacterial metabolic capacities in the rhizosphere and about rhizoremediation of contaminants, there are fewer studies dealing with the integration of bacterial metabolic capacities in the rhizosphere during PAH bioremediation, and some aspects still remain controversial. Some authors have postulated that the presence of easily metabolizable carbon sources in root exudates might repress the expression of genes required for contaminant degradation, while others found that specific rhizosphere compounds can induce such genes. Novosphingobium sp. HR1a, which is our model organism, has two characteristics desirable in bacteria for use in remediation: its ubiquity and the capacity to degrade a wide variety of contaminants. We have demonstrated that this bacterium consumes several rhizospheric compounds without repression of the genes required for the mineralization of PAHs. In fact, some compounds even induced their expression.

Phyllosphere Community Assembly and Response to Drought Stress on Common Tropical and Temperate Forage Grasses

Grasslands represent a critical ecosystem important for global food production, soil carbon storage, and water regulation. Current intensification and expansion practices add to the degradation of grasslands and dramatically increase greenhouse gas emissions and pollution. Thus, new ways to sustain and improve their productivity are needed. Research efforts focus on the plant-leaf microbiome, or phyllosphere, because its microbial members impact ecosystem function by influencing pathogen resistance, plant hormone production, and nutrient availability through processes including nitrogen fixation. However, little is known about grassland phyllospheres and their response to environmental stress. In this study, globally dominant temperate and tropical forage grass species were grown in a greenhouse under current climate conditions and drought conditions that mimic future climate predictions to understand if (i) plant host taxa influence microbial community assembly, (ii) microbial communities respond to drought stress, and (iii) phyllosphere community changes correlate to changes in plant host traits and stress-response strategies. Community analysis using high-resolution sequencing revealed Gammaproteobacteria as the dominant bacterial class, which increased under severe drought stress on both temperate and tropical grasses while overall bacterial community diversity declined. Bacterial community diversity, structure, and response to drought were significantly different between grass species. This community dependence on plant host species correlated with differences in grass species traits, which became more defined under drought stress conditions, suggesting symbiotic evolutionary relationships between plant hosts and their associated microbial community. Further understanding these strategies and the functions microbes provide to plants will help us utilize microbes to promote agricultural and ecosystem productivity in the future. IMPORTANCE Globally important grassland ecosystems are at risk of degradation due to poor management practices compounded by predicted increases in severity and duration of drought over the next century. Finding new ways to support grassland productivity is critical to maintaining their ecological and agricultural benefits. Discerning how grassland microbial communities change in response to climate stress will help us understand how plant-microbe relationships may be useful to sustainably support grasslands in the future. In this study, phyllosphere community diversity and composition were significantly altered under drought conditions. The significance of our research is demonstrating how severe climate stress reduces bacterial community diversity, which previously was directly associated with decreased plant productivity. These findings guide future questions about functional plant-microbe interactions under stress conditions, greatly enhancing our understanding of how bacteria can increase food security by promoting grassland growth and resilience.

The Diversity of Culture-Dependent Gram-Negative Rhizobacteria Associated with Manihot esculenta Crantz Plants Subjected to Water-Deficit Stress

There is a lack of studies on the root-associated bacterial microbiome of cassava plants. The identification and characterization of rhizobacteria can contribute to understanding the adaptation of the agriculturally important crop plants to abiotic stress. Rhizobacteria play a significant role in plants, as they can alleviate the drought stress by various mechanisms that enhance the plant growth under these stressor conditions. In this study, Gram-negative bacterial strains from the plant rhizosphere of cassava Manihot esculenta Crantz CIAT MCOL1734 variety subjected to water deprivation were isolated, characterized according to their morphological properties, and then identified by VITEK® 2. An increase in the diversity, abundance, and species richness of Gram-negative rhizobacterial community was found in cassava plants subjected to water-deficit stress. In total, 58 rhizobacterial strains were isolated from cassava plants. The identification process found that the bacteria belonged to 12 genera: Achromobacter, Acinetobacter, Aeromonas, Buttiauxella, Cronobacter, Klebsiella, Ochrobactrum, Pluralibacter, Pseudomonas, Rhizobium, Serratia, and Sphingomonas. Interestingly, Pseudomonas luteola and Ocrhobactrum anthropi were rhizobacteria isolated exclusively from plants submitted to drought conditions. The cassava roots constitute a great reservoir of Gram-negative bacteria with a remarkable potential for biotechnological application to improve the drought tolerance of plant crops under water-deficit conditions.

Insights into the plant responses to drought and decoding the potential of root associated microbiome for inducing drought tolerance

Global increase in water scarcity is a serious problem for sustaining crop productivity. The lack of water causes the degeneration of the photosynthetic apparatus, an imbalance in key metabolic pathways, an increase in free radical generation as well as weakens the root architecture of plants. Drought is one of the major stresses that directly interferes with the osmotic status of plant cells. Abscisic acid (ABA) is known to be a key player in the modulation of drought responses in plants and involvement of both ABA-dependent and ABA-independent pathways have been observed during drought. Concomitantly, other phytohormones such as auxins, ethylene, gibberellins, cytokinins, jasmonic acid also confer drought tolerance and a crosstalk between different phytohormones and transcription factors at the molecular level exists. A number of drought-responsive genes and transcription factors have been utilized for producing transgenic plants for improved drought tolerance. Despite relentless efforts, biotechnological advances have failed to design completely stress tolerant plants until now. The root microbiome is the hidden treasure that possesses immense potential to revolutionize the strategies for inducing drought resistance in plants. Root microbiota consist of plant growth-promoting rhizobacteria, endophytes and mycorrhizas that form a consortium with the roots. Rhizospheric microbes are proliferous producers of phytohormones, mainly auxins, cytokinin, and ethylene as well as enzymes like the 1-aminocyclopropane-1-carboxylate deaminase (ACC deaminase) and metabolites like exopolysaccharides that help to induce systemic tolerance against drought. This review, therefore focuses on the major mechanisms of plant-microbe interactions under drought-stressed conditions and emphasizes the importance of drought-tolerant microbes for sustaining and improving the productivity of crop plants under stress.

Tomato roots secrete tomatine to modulate the bacterial assemblage of the rhizosphere

Saponins are the group of plant specialized metabolites which are widely distributed in angiosperm plants and have various biological activities. The present study focused on α-tomatine, a major saponin present in tissues of tomato (Solanum lycopersicum) plants. α-Tomatine is responsible for defense against plant pathogens and herbivores, but its biological function in the rhizosphere remains unknown. Secretion of tomatine was higher at the early growth than the green-fruit stage in hydroponically grown plants, and the concentration of tomatine in the rhizosphere of field-grown plants was higher than that of the bulk soil at all growth stages. The effects of tomatine and its aglycone tomatidine on the bacterial communities in the soil were evaluated in vitro, revealing that both compounds influenced the microbiome in a concentration-dependent manner. Numerous bacterial families were influenced in tomatine/tomatidine-treated soil as well as in the tomato rhizosphere. Sphingomonadaceae species, which are commonly observed and enriched in tomato rhizospheres in the fields, were also enriched in tomatine- and tomatidine-treated soils. Moreover, a jasmonate-responsive ETHYLENE RESPONSE FACTOR 4 mutant associated with low tomatine production caused the root-associated bacterial communities to change with a reduced abundance of Sphingomonadaceae. Taken together, our results highlight the role of tomatine in shaping the bacterial communities of the rhizosphere and suggest additional functions of tomatine in belowground biological communication.

Bacterial Endophytes of Spring Wheat Grains and the Potential to Acquire Fe, Cu, and Zn under Their Low Soil Bioavailability

Simple Summary

Unmasking the overall endophytic bacteria communities from wheat grains may help to identify and describe the microbial colonization of bread and emmer varieties, their link to the bioactive compounds produced, and their possible role in mineral nutrition. The possibility of using microorganisms to improve the microelemental composition of grain is an important food security concern, as approximately one-third of the human population experiences latent starvation caused by Fe (anemia), Zn, or Cu deficiency. Four wheat varieties from T. aestivum L. and T. turgidum subsp. dicoccum were grown in field conditions with low bioavailability of microelements in the soil. Varietal differences in the yield, yield characteristics, and the grain micronutrient concentrations were compared with the endophytic bacteria isolated from the grains. Twelve different bacterial isolates were obtained that represented the genera Staphylococcus, Pantoea, Sphingobium, Bacillus, Kosakonia, and Micrococcus. All studied strains were able to synthesize indole-related compounds (IRCs) with phytohormonal activity. IRCs produced by the bacterial genera Pantoea spp. and Bacillus spp. isolated from high-yielding Oksamyt myronivs’kyi and Holikovs’ka grains may be considered as one of the determinants of the yield of wheat and its nutritional characteristics.

Abstract

Wheat grains are usually low in essential micronutrients. In resolving the problem of grain micronutritional quality, microbe-based technologies, including bacterial endophytes, seem to be promising. Thus, we aimed to (1) isolate and identify grain endophytic bacteria from selected spring wheat varieties (bread Oksamyt myronivs’kyi, Struna myronivs’ka, Dubravka, and emmer Holikovs’ka), which were all grown in field conditions with low bioavailability of microelements, and (2) evaluate the relationship between endophytes’ abilities to synthesize auxins and the concentration of Fe, Zn, and Cu in grains. The calculated biological accumulation factor (BAF) allowed for comparing the varietal ability to uptake and transport micronutrients to the grains. For the first time, bacterial endophytes were isolated from grains of emmer wheat T. turgidum subsp. dicoccum. Generally, the 12 different isolates identified in the four varieties belonged to the genera Staphylococcus, Pantoea, Sphingobium, Bacillus, Kosakonia, and Micrococcus (NCBI accession numbers: MT302194—MT302204, MT312840). All the studied strains were able to synthesize the indole-related compounds (IRCs; max: 16.57 µg∙mL⁻¹) detected using the Salkowski reagent. The IRCs produced by the bacterial genera Pantoea spp. and Bacillus spp. isolated from high-yielding Oksamyt myronivs’kyi and Holikovs’ka grains may be considered as one of the determinants of the yield of wheat and its nutritional characteristics.

Alkaline soil pH affects bulk soil, rhizosphere and root endosphere microbiomes of plants growing in a Sandhills ecosystem

Soil pH is a major factor shaping bulk soil microbial communities. However, it is unclear whether the belowground microbial habitats shaped by plants (e.g. rhizosphere and root endosphere) are also affected by soil pH. We investigated this question by comparing the microbial communities associated with plants growing in neutral and strongly alkaline soils in the Sandhills, which is the largest sand dune complex in the northern hemisphere. Bulk soil, rhizosphere and root endosphere DNA were extracted from multiple plant species and analyzed using 16S rRNA amplicon sequencing. Results showed that rhizosphere, root endosphere and bulk soil microbiomes were different in the contrasting soil pH ranges. The strongest impact of plant species on the belowground microbiomes was in alkaline soils, suggesting a greater selective effect under alkali stress. Evaluation of soil chemical components showed that in addition to soil pH, cation exchange capacity also had a strong impact on shaping bulk soil microbial communities. This study extends our knowledge regarding the importance of pH to microbial ecology showing that root endosphere and rhizosphere microbial communities were also influenced by this soil component, and highlights the important role that plants play particularly in shaping the belowground microbiomes in alkaline soils.

A Degeneration Gradient of Poplar Trees Contributes to the Taxonomic, Functional, and Resistome Diversity of Bacterial Communities in Rhizosphere Soils

Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient of poplar, with a focus on plant growth promoting bacteria (PGPB) and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG (antibiotics resistance genes) annotation revealed that available potassium (AK) was correlated with microbial diversity and function. We proposed several microbes, Bradyrhizobium, Sphingomonas, Mesorhizobium, Nocardioides, Variovorax, Gemmatimonadetes, Rhizobacter, Pedosphaera, Candidatus Solibacter, Acidobacterium, and Phenylobacterium, as candidates to reflect the soil fertility and the plant health. The highest abundance of multidrug resistance genes and the four mainly microbial resistance mechanisms (antibiotic efflux, antibiotic target protection, antibiotic target alteration, and antibiotic target replacement) in healthy poplar rhizosphere, corroborated the relationship between soil fertility and microbial activity. This result suggested that healthy rhizosphere soil harbored microbes with a higher capacity and had more complex microbial interaction network to promote plant growing and reduce intracellular levels of antibiotics. Our findings suggested a correlation between the plant degeneration gradient and bacterial communities, and provided insight into the role of high-turnover microbial communities as well as potential PGPB as real-time indicators of forestry soil quality, and demonstrated the inner interaction contributed by the bacterial communities.

Bacillus circulans GN03 Alters the Microbiota, Promotes Cotton Seedling Growth and Disease Resistance, and Increases the Expression of Phytohormone Synthesis and Disease Resistance-Related Genes

Plant growth-promoting bacteria (PGPB) are components of the plant rhizosphere that promote plant growth and/or inhibit pathogen activity. To explore the cotton seedlings response to Bacillus circulans GN03 with high efficiency of plant growth promotion and disease resistance, a pot experiment was carried out, in which inoculations levels of GN03 were set at 10⁴ and 10⁸ cfu^⋅mL^-1. The results showed that GN03 inoculation remarkably enhanced growth promotion as well as disease resistance of cotton seedlings. GN03 inoculation altered the microbiota in and around the plant roots, led to a significant accumulation of growth-related hormones (indole acetic acid, gibberellic acid, and brassinosteroid) and disease resistance-related hormones (salicylic acid and jasmonic acid) in cotton seedlings, as determined with ELISA, up-regulated the expression of phytohormone synthesis-related genes (EDS1, AOC1, BES1, and GA20ox), auxin transporter gene (Aux1), and disease-resistance genes (NPR1 and PR1). Comparative genomic analyses was performed between GN03 and four similar species, with regards to phenotype, biochemical characteristics, and gene function. This study provides valuable information for applying the PGPB alternative, GN03, as a plant growth and disease-resistance promoting fertilizer.

Microbe to Microbiome: A Paradigm Shift in the Application of Microorganisms for Sustainable Agriculture

Light, water and healthy soil are three essential natural resources required for agricultural productivity. Industrialization of agriculture has resulted in intensification of cropping practices using enormous amounts of chemical pesticides and fertilizers that damage these natural resources. Therefore, there is a need to embrace agriculture practices that do not depend on greater use of fertilizers and water to meet the growing demand of global food requirements. Plants and soil harbor millions of microorganisms, which collectively form a microbial community known as the microbiome. An effective microbiome can offer benefits to its host, including plant growth promotion, nutrient use efficiency, and control of pests and phytopathogens. Therefore, there is an immediate need to bring functional potential of plant-associated microbiome and its innovation into crop production. In addition to that, new scientific methodologies that can track the nutrient flux through the plant, its resident microbiome and surrounding soil, will offer new opportunities for the design of more efficient microbial consortia design. It is now increasingly acknowledged that the diversity of a microbial inoculum is as important as its plant growth promoting ability. Not surprisingly, outcomes from such plant and soil microbiome studies have resulted in a paradigm shift away from single, specific soil microbes to a more holistic microbiome approach for enhancing crop productivity and the restoration of soil health. Herein, we have reviewed this paradigm shift and discussed various aspects of benign microbiome-based approaches for sustainable agriculture.

Stress tolerance in flax plants inoculated with Bacillus and Azotobacter species under deficit irrigation

Drought stress affects not only crop growth but also its morpho-physiological and biochemical traits to reduce crop productivity. The study reported in this article was designed and implemented to determine the effects of deficit irrigation and bacterial inoculation on flax plants. For this purpose, seeds were inoculated with Bacillus amyloliquefaciens (B₁ ), Bacillus sp. Strain1 (B₂ ), and Azotobacter chroococcum (A) as plant growth promoting rhizobacteria (PGPR). The individual inoculated plants were then grown under field conditions in 2015, while individually and in combination in pots in 2016. The irrigation regimes in either experiments included 50, 75 and 100% crop water requirement. Bacterial cultures were observed to produce ammonia (except B₂ ), indole acetic acid and siderophores. Results showed that the PGPRs significantly mitigated the effects of water deficit. Compared with the control plants, the bacterially-inoculated plants had an enhanced relative water content, plant height, water-soluble carbohydrate and proline contents and antioxidant enzyme activities, but a decreased malondialdehyde content. B₁ exhibited greater effects on most of the traits investigated under the field conditions rather than those with moderate and severe drought stress, while application of the triple bacteria in pots had greater effects on relative water content, carbohydrate and proline contents as well as malondialdehyde. The significant differences in abiotic stress indicators in PGPR-treated plants suggest that these bacteria could be used as biofertilizers to assist plant growth and to reduce the adverse effects of deficit irrigation.

High-throughput sequencing-based analysis of the composition and diversity of endophytic bacterial community in seeds of upland rice

Upland rice is an ecotype crop resulting from the long-term domestication and evolution of rice in dry land without a water layer. Generally, the stems and leaves are thick and luxuriant, while the leaves also typically broad and light. The root system is developed with abundant root hair, and the osmotic pressure of the root and cell juice concentration in the leaves is high, while this plant is drought-resistant, heat-resistant, and water absorbent. This study aims to reveal the "core flora" of the endophytes in upland rice seeds by examining their diversity and community structures. It further intends to reveal the impact of the soil environment on the formation of endophyte community structures in upland rice seeds by comparing the environmental soil microorganisms in upland rice habitats. In this study, high-throughput sequencing technology based on the Illumina Hiseq 2500 platform was used to investigate the structure and diversity of endophytic bacterial communities using upland rice varieties collected from different locations and soil samples from unified planting sites as materials. Here, 42 endophytic OTUs were found to coexist in the 14 samples. At the phylum level, the first dominant phyla in all the samples were Proteobacteria (93.81-99.99%). At the genus level, Pantoea (8.77-87.77%), Pseudomonas (1.15-61.58%), Methylobacterium (0.40-4.64%), Sphingomonas (0.26-3.85%), Microbacterium (0.01-4.67%) and Aurantimonas (0.04-4.34%), which represent the core microflora in upland rice seeds, served as the dominant genera that coexisted in all the upland rice seeds tested. This study significant for the isolation, screening, functional evaluation, and re-action of various functional microorganisms in upland rice to improve its agronomic traits. It also provides a specific reference for the interaction between microorganisms and plants.

Bacterial community dynamics with rhizosphere of Calotropis procera and Senna alexandrina desert plants in Saudi Arabia

It is of interest to study the rhizobacteria associated with two different desert wild plants, e.g., Calotropis procera and Senna alexandrina compared with bulk soil sample in order to identify signatures of microbes in rhizospheres of the two plants and detect influence of soil microbiome in drawing soil architecture. Analysis of deep sequencing microbial dataset indicated occurrence of 296,642 sequence tags assigned 5,210 OTUs (operational taxonomic units). Species richness in control sample was higher than those of either plant's rhizosphere, while microbial abundance was lower. Principal coordinate analysis (PCoA) plot indicated complete separation of microbiome diversity among groups. Abundances of Pseudomonas stutzeri and Virgibacillus koreensis increased in the rhizosphere of C. procera compared with that of S. alexandrina, while those of Streptococcus sobrinus, Veillonella parvula and unassigned species of Sphingomonas genus increased in rhizosphere of S. alexandrina. Unassigned species of genera Marinobacter, Porticoccus and Alcanivorax only exist in rhizosphere microbiome of C. procera, while unassigned species of genus Pseudomonas only exists in rhizosphere microbiome of Senna alexandrina. High abundances of the two microbes Pseudomonas stutzeri and Virgibacillus koreensis in rhizosphere of C. procera allow the plant to grow well under both normal and saline condition. Also, Marinobacter, Porticoccus and Alcanivorax genera only exist in rhizosphere microbiome of C. procera. These microbes produce siderophores that protect plant from pathogens. Data shows that C. procera might be more protected from microbial pathogens compared with S. alexandrina. The differential abundances or exclusive presence of soil microbes reflect the ability of plant species to survive under biotic and abiotic stresses. Results imply that rhizospheric microbes can be used as biomarkers of plant growth rate and the ability to survive under harsh conditions.

Water management and phenology influence the root-associated rice field microbiota

Microbial communities associated with plants are greatly influenced by water availability in soil. In flooded crops, such as rice, the impact of water management on microbial dynamics is not fully understood. Here, we present a comprehensive study of the rice microbiota investigated in an experimental field located in one of the most productive areas of northern Italy. The microbiota associated with paddy soil and root was investigated using 454 pyrosequencing of 16S, ITS and 18S rRNA gene amplicons under two different water managements, upland (non-flooded, aerobic) and lowland (traditional flooding, anaerobic), at three plant development stages. Results highlighted a major role of the soil water status in shaping microbial communities, while phenological stage had low impacts. Compositional shifts in prokaryotic and fungal communities upon water management consisted in significant abundance changes of Firmicutes, Methanobacteria, Chloroflexi, Sordariomycetes, Dothideomycetes and Glomeromycotina. A vicariance in plant beneficial microbes and between saprotrophs and pathotrophs was observed between lowland and upland. Moreover, through network analysis, we demonstrated different co-abundance dynamics between lowland and upland conditions with a major impact on microbial hubs (strongly interconnected microbes) that fully shifted to aerobic microbes in the absence of flooding.

Rhizosphere Soil Microbial Properties on Tetraena mongolica in the Arid and Semi-Arid Regions, China

Tetraena mongolica is a rare and endangered species unique to China. The total number and density of Tetraena mongolica shrubs in desertification areas have experienced a sharp decrease with increases in coal mining activities. However, available information on the T. mongolica rhizosphere soil quality and microbial properties is scarce. Here, we investigated the effect of coal mining on the soil bacterial community and its response to the soil environment in the T. mongolica region. The results showed that the closer to the coal mining area, the lower the vegetation coverage and species diversity. The electrical conductivity (EC) in the contaminated area increased, while the total nitrogen (TN), available phosphorus (AP), available potassium (AK), and soil organic carbon (SOC) decreased. The activity of NAG, sucrose, β-glucosidase, and alkaline phosphatase further decreased. In addition, the mining area could alter the soil’s bacterial abundance and diversity. The organic pollutant degradation bacteria such as Sphingomonas, Gemmatimonas, Nocardioides, and Gaiella were enriched in the soil, and the carbon-nitrogen cycle was changed. Canonical correspondence analysis (CCA) and Pearson’s correlation coefficients showed that the change in the bacterial community structure was mainly caused by environmental factors such as water content (SWC) and EC. Taken together, these results suggested that open pit mining led to the salinization of the soil, reduction the soil nutrient content and enzyme activity, shifting the rhizosphere soil microbial community structure, and altering the carbon-nitrogen cycle, and the soil quality declined and the growth of T. mongolica was affected in the end. Therefore, the development of green coal mining technology is of great significance to protect the growth of T. mongolica.

Streptomyces lydicus M01 Regulates Soil Microbial Community and Alleviates Foliar Disease Caused by Alternaria alternata on Cucumbers

Due to the adverse effect on the environment caused by excessive use of chemical fertilizers, the development of sustainable agriculture attracts a growing demand of biological based fertilizers composed of living microorganisms. In this study, an Actinobacteria Streptomyces lydicus M01 was isolated from the rhizosphere soil of Pyrus calleryana. This strain effectively promoted the plant growth and suppressed a foliar disease caused by Alternaria alternata on cucumbers. S. lydicus M01 exhibited growth promoting characteristics such as phosphate solubilization, IAA secretion, siderophore and ACC deaminase production. Through Illumina sequencing of the 16S rRNA gene and ITS gene of the soil microbes, we found that the application of S. lydicus M01 altered the composition of the microbial community by promoting beneficial groups, including bacteria genera Pseudarthrobacter, Sphingomonas, Rhodanobacter, and Pseudomonas, fungi genera Fusicolla, Humicola, Solicoccozyma, and Paraphaeosphaeria. Most of these bacteria and eukaryotes exhibit positive effects on growth promotion, such as nutrient accumulation, auxin secretion, abiotic stress alleviation, biological control, or bioremediation. Furthermore, studies on the reactive oxygen species (ROS) level and antioxidants of cucumber leaves revealed that S. lydicus M01 treatment reduced the ROS accumulation and increased the activities of antioxidases related with ROS scavenging, which indicated an enhanced disease resistance of cucumbers under biotic stress. Thus, our results suggest that the application of S. lydicus M01 can systemically affect plant microbiome interactions and represent a promising sustainable solution to improve agricultural production instead of chemical fertilizers.

Fungal and Bacterial Microbiome Associated with the Rhizosphere of Native Plants from the Atacama Desert

The rhizosphere microbiome is key in survival, development, and stress tolerance in plants. Salinity, drought, and extreme temperatures are frequent events in the Atacama Desert, considered the driest in the world. However, little information of the rhizosphere microbiome and its possible contribution to the adaptation and tolerance of plants that inhabit the desert is available. We used a high-throughput Illumina MiSeq sequencing approach to explore the composition, diversity, and functions of fungal and bacterial communities of the rhizosphere of Baccharis scandens and Solanum chilense native plants from the Atacama Desert. Our results showed that the fungal phyla Ascomycota and Basidiomycota and the bacterial phyla Actinobacteria and Proteobacteria were the dominant taxa in the rhizosphere of both plants. The linear discriminant analysis (LDA) effect size (LefSe) of the rhizosphere communities associated with B. scandens showed the genera Penicillium and Arthrobacter were the preferential taxa, whereas the genera Oidiodendron and Nitrospirae was the preferential taxa in S. chilense. Both plant showed similar diversity, richness, and abundance according to Shannon index, observed OTUs, and evenness. Our results indicate that there are no significant differences (p = 0.1) between the fungal and bacterial communities of both plants, however through LefSe, we find taxa associated with each plant species and the PCoA shows a separation between the samples of each species. This study provides knowledge to relate the assembly of the microbiome to the adaptability to drought stress in desert plants.

Sphingomonas: from diversity and genomics to functional role in environmental remediation and plant growth

The species belonging to the Sphingomonas genus possess multifaceted functions ranging from remediation of environmental contaminations to producing highly beneficial phytohormones, such as sphingan and gellan gum. Recent studies have shown an intriguing role of Sphingomonas species in the degradation of organometallic compounds. However, the actual biotechnological potential of this genus requires further assessment. Some of the species from the genus have also been noted to improve plant-growth during stress conditions such as drought, salinity, and heavy metals in agricultural soil. This role has been attributed to their potential to produce plant growth hormones e.g. gibberellins and indole acetic acid. However, the current literature is scattered, and some of the important areas, such as taxonomy, phylogenetics, genome mapping, and cellular transport systems, are still being overlooked in terms of elucidation of the mechanisms behind stress-tolerance and bioremediation. In this review, we elucidated the prospective role and function of this genus for improved utilization during environmental biotechnology.