Bacterial diversity in the rhizosphere of maize and the surrounding carbonate-rich bulk soil

Effects of drought stress and Morchella inoculation on the physicochemical properties, enzymatic activities, and bacterial community of Poa pratensis L. rhizosphere soil

Background

Soil microorganisms are crucial for plant growth, and both plants and their associated rhizosphere microbes are impacted by changes in soil moisture. Inoculation with beneficial fungi can improve bacterial community structure and soil parameters.

Aim

Under drought stress conditions, the effects of inoculation with Morchella on the physicochemical properties, enzyme activity, and bacterial community structure of the rhizosphere soil of Poa pratensis were studied.

Methods

High-throughput sequencing was employed to study rhizosphere soil bacterial communities in both Morchella-inoculated and uninoculated Poa pratensis rhizosphere soil subjected to moderate (50% soil moisture) and severe (30% soil moisture) drought stress, as well as under normal water conditions (70% soil moisture).

Results

Morchella inoculation significantly increased the alkaline nitrogen (AN) and available phosphorus (AP) contents, protease activity (PA), and alkaline phosphatase activity (APA) of Poa pratensis rhizosphere soil. Both Morchella inoculation and drought stress significantly altered the abundance and diversity of the P. pratensis rhizosphere community. The Chao1, Shannon, and Pielou diversity indices decreased with increasing drought stress. The effect of Morchella inoculation was improved under moderate drought stress and unstressed conditions. In addition, Morchella inoculation may help to stabilize the rhizosphere bacterial community under various levels of soil moisture.

Rhizobacterial volatile organic compounds: Implications for agricultural ecosystems' nutrient cycling and soil health

Plant growth-promoting rhizobacteria (PGPR) have emerged as key players in sustainable agriculture due to their ability to enhance plant growth, nutrient uptake, and disease resistance. A significant aspect of PGPR is the emission of volatile organic compounds (VOCs), which serve as signaling molecules that influence various physiological processes in plants. This review article explores the complex interactions between rhizobacterial VOCs and soil health, focusing particularly on their role in nutrient cycling within agricultural ecosystems. By investigating the mechanism of production and release of VOCs by rhizobacteria, along with impacts on soil properties and microbial communities. We aim to highlight the potential of rhizobacterial volatile organic compounds (VOCs) for sustainable agricultural management. Additionally, we discuss the role of rhizobacterial VOCs in promoting root growth, nutrient uptake, and enhancing nutrient cycling processes. By providing insights into these mechanisms, this review offers tailored strategies for exploring the potential of rhizobacterial VOCs to optimize nutrient availability, enhance soil fertility, and address environmental challenges in agriculture. Exploring the potential of rhizobacterial VOCs presents an opportunity to establish sustainable and resilient agricultural systems that significantly enhance global food security and promote environmental stewardship.

Short-term effect of reclaimed water irrigation on soil health, plant growth and the composition of soil microbial communities

The scarcity of freshwater poses significant challenges to agriculture, often necessitating the use of alternative water sources such as reclaimed water. While reclaimed water offers a viable solution by providing water and nutrients to crops, its potential impacts on soil microbial communities remain a subject of investigation. In this investigation, we conducted a field experiment cultivating Maize (Zea mays) and Lavender (Lavandula angustifolia), employing irrigation with reclaimed water originating from domestic wastewater, while control samples were irrigated using freshwater. Utilizing high-throughput sequencing, we assessed the effect of reclaimed water on soil bacteria and fungi. Plant biomass exhibited a significant response to treated wastewater. Alpha diversity metrics of soil microbial communities did not reveal significant changes in soils irrigated with reclaimed water compared to control samples. Reclaimed water, however, demonstrated a selective influence on microorganisms associated with nutrient cycling. Co-occurrence network analysis unveiled that reclaimed water may alter soil microbial community structure and stability. Although our work presents overall positive outcomes, further investigation into the long-term implications of reclaimed water irrigation is warranted.

Exploring Phosphate Solubilizing Bacterial Communities in Rhizospheres of Native and Exotic Forage Grasses in Alkaline-Sodic Soils of the Flooding Pampa

The flooding pampa is one of the most important cattle-raising regions in Argentina. In this region, natural pastures are dominated by low-productivity native grass species, which are the main feed for livestock. In this context, previous studies in the region with the subtropical exotic grass Panicum coloratum highlight it as a promising species to improve pasture productivity. Cultivable phosphate solubilizing bacteria (PSB) communities associated to native (Sporobolus indicus) and exotic (Panicum coloratum) forage grasses adapted to alkaline-sodic soils of the flooding pampa were analyzed. PSB represented 2-14% of cultivable rhizobacteria and Box-PCR fingerprinting revealed a high genetic diversity in both rhizospheres. Taxonomic identification by MALDI-TOF showed that PSB populations of P. coloratum and S. indicus rhizospheres are dominated by the phylum Proteobacteria (92,51% and 96,60% respectively) and to a lesser extent (< 10%), by the phyla Actinobacteria and Firmicutes. At the genus level, both PSB populations were dominated by Enterobacter and Pseudomonas. Siderophore production, nitrogen fixation, and indoleacetic acid production were detected in a variety of PSB genera of both plant species. A higher proportion of siderophore and IAA producers were associated to P. coloratum than S. indicus, probably reflecting a greater dependence of the exotic species on rhizospheric microorganisms to satisfy its nutritional requirements in the soils of the flooding pampa. This work provides a novel knowledge about functional groups of bacteria associated to plants given that there are no previous reports dedicated to the characterization of PSB rhizosphere communities of S indicus and P coloratum. Finally, it should be noted that the collection obtained in this study can be useful for the development of bioinputs that allow reducing the use of chemical fertilizers, providing sustainability to pasture production systems for livestock.

Zonation of bulk and rhizosphere soil bacterial communities and their covariation patterns along the elevation gradient in riparian zones of three Gorges reservoir, China

Zonation is a typical pattern of soil distribution and species assembly across riparian habitats. Microorganisms are essential members of riparian ecosystems and whether soil microbial communities demonstrate similar zonation patterns and how bulk and rhizosphere soil microorganisms interact along the elevation (submergence stress) gradient remain largely unknown. In this study, bulk and rhizosphere (dominant plant) soil samples were collected and investigated across riparian zones where the submergence stress intensity increased as the elevation decreased. Results showed that the richness of bacterial communities in bulk and rhizosphere soil samples was significantly different and presented a zonation pattern along with the submergence stress gradient. Bulk soil at medium elevation that underwent moderate submergence stress had the most abundant bacterial communities, while the species richness of rhizobacteria at low elevation that experienced serious submergence stress was the highest. Additionally, principal coordinate analysis (PCoA) and significance tests showed that bulk and rhizosphere soil samples were distinguished according to the structure of bacterial communities, and so were bulk or rhizosphere soil samples from different elevations. Redundancy analysis (RDA) and Mantel test suggested that bacterial communities of bulk soil mainly relied on the contents of soil organic matter, total carbon (TC), total nitrogen (TN), sodium (Na), calcium (Ca) and magnesium (Mg). Contrastingly, the contents of Na and Mg were the main factors explaining the variation in rhizobacterial community composition. Correlation and microbial source tracking analyses showed thatthe relationship of bulk and rhizosphere soil bacteria became much stronger, and the rhizosphere soil may get more bacterial communities from bulk soil with the increase in submergence severity. Our results suggest that the abiotic and biotic components of the riparian ecosystem are closely covariant along the submergence stress gradient and imply that the bacterial community may be a key node linking soil physiochemical properties and vegetation communities.

Effects of plant growth-promoting rhizobacteria on blueberry growth and rhizosphere soil microenvironment

Background

Plant growth-promoting rhizobacteria (PGPR) have a specific symbiotic relationship with plants and rhizosphere soil. The purpose of this study was to evaluate the effects of PGPR on blueberry plant growth, rhizospheric soil nutrients and the microbial community.

Methods

In this study, nine PGPR strains, belonging to the genera Pseudomonas and Buttiauxella, were selected and added into the soil in which the blueberry cuttings were planted. All the physiological indexes of the cuttings and all rhizospheric soil element contents were determined on day 6 after the quartic root irrigation experiments were completed. The microbial diversity in the soil was determined using high-throughput amplicon sequencing technology. The correlations between phosphorus solubilization, the auxin production of PGPR strains, and the physiological indexes of blueberry plants, and the correlation between rhizospheric microbial diversity and soil element contents were determined using the Pearson's correlation, Kendall's tau correlation and Spearman's rank correlation analysis methods.

Results

The branch number, leaf number, chlorophyllcontentand plant height of the treated blueberry group were significantly higher than those of the control group. The rhizospheric soil element contents also increased after PGPR root irrigation. The rhizospheric microbial community structure changed significantly under the PGPR of root irrigation. The dominant phyla, except Actinomycetota, in the soil samples had the greatest correlation with phosphorus solubilization and the auxin production of PGPR strains. The branch number, leaf number, and chlorophyllcontent had a positive correlation with the phosphorus solubilization and auxin production of PGPR strains and soil element contents. In conclusion, plant growth could be promoted by the root irrigation of PGPR to improve rhizospheric soil nutrients and the microenvironment, with modification of the rhizospheric soil microbial community.

Discussion

Plant growth could be promoted by the root irrigation of PGPR to improve rhizospheric soil nutrients and the microenvironment, with the modification of the rhizospheric soil microbial community. These data may help us to better understand the positive effects of PGPR on blueberry growth and the rhizosphere soil microenvironment, as well as provide a research basis for the subsequent development of a rhizosphere-promoting microbial fertilizer.

Root-associated bacterial microbiome shaped by root selective effects benefits phytostabilization by Athyrium wardii (Hook.)

The root-associated microbiome assembly substantially promotes (hyper)accumulator plant growth and metal accumulation and is influenced by multiple factors, especially host species and environmental stress. Athyrium wardii (Hook.) is a phytostabilizer that grows in lead (Pb)-zinc (Zn) mine tailings and shows high root Pb accumulation. However, there remains little information on the assembly of the root-associated microbiome of A. wardii and its role in phytostabilization. A field study investigated the structural and functional variation in the root-associated bacterial microbiome of Athyrium wardii (Hook.) exposed to different levels of contamination in Pb-Zn mine tailings. The root compartment dominated the variation in the root-associated bacterial microbiome but the levels of contaminants showed less impact. Bacterial co-occurrence was enhanced in the rhizosphere soil and rhizoplane but tended to be much simpler in the endosphere in terms of network complexity and connectivity. This indicates that the microbial community assembly of A. wardii was non-random and shaped by root selective effects. Proteobacteria, Chloroflexi, Actinobacteria, Cyanobacteria, and Acidobacteriota were generally the dominant bacterial phyla. The genera Crossiella and Bradyrhizobium were enriched in the rhizosphere and cyanobacterial genera were enriched in the endosphere, demonstrating substantial advantages to plant survival and adaptation in the harsh mine environment. Functional categories involved in amino acid and carbohydrate metabolism were abundant in the rhizosphere soil, thus contributing to metal solubility and bioavailability in the rhizosphere. Membrane transporters, especially ATP-binding cassette transporters, were enriched in the endosphere, indicating a potential role in metal tolerance and transportation in A. wardii. The study shows substantial variation in the structure and function of microbiomes colonizing different compartments, with the rhizosphere and endophytic microbiota potentially involved in plant metal tolerance and accumulation during phytostabilization.

Agronomic strategies to enhance the early vigor and yield of maize. Part I: the role of seed applied biostimulant, hybrid and starter fertilization on rhizosphere bacteria profile and diversity

The sustainable intensification of maize-based systems may reduce greenhouse-gas emissions and the excessive use of non-renewable inputs. Considering the key role that the microbiological fertility has on crop growth and resilience, it is worth of interest studying the role of cropping system on the rhizosphere bacterial communities, that affect soil health and biological soil fertility. In this work we monitored and characterized the diversity and composition of native rhizosphere bacterial communities during the early growth phases of two maize genotypes of different early vigor, using a nitrogen (N)-phosphorus (P) starter fertilization and a biostimulant seed treatment, in a growth chamber experiment, by polymerase chain reaction-denaturing gradient gel electrophoresis of partial 16S rRNA gene and amplicon sequencing. Cluster analyses showed that the biostimulant treatment affected the rhizosphere bacterial microbiota of the ordinary hybrid more than that of the early vigor, both at plant emergence and at the 5-leaf stage. Moreover, the diversity indices calculated from the community profiles, revealed significant effects of NP fertilization on richness and the estimated effective number of species (H2) in both maize genotypes, while the biostimulant had a positive effect on plant growth promoting community of the ordinary hybrid, both at the plant emergence and at the fifth leaf stage. Our data showed that maize genotype was the major factor shaping rhizosphere bacterial community composition suggesting that the root system of the two maize hybrids recruited a different microbiota. Moreover, for the first time, we identified at the species and genus level the predominant native bacteria associated with two maize hybrids differing for vigor. These results pave the way for further studies to be performed on the effects of cropping system and specific crop practices, considering also the application of biostimulants, on beneficial rhizosphere microorganisms.

Exposure to three herbicide mixtures influenced maize root-associated microbial community structure, function and the network complexity

Herbicide mixtures are a new and effective agricultural strategy for managing suppress weed resistance and have been widely used in controlling weeding growth in maize fields. However, the potential ecotoxicological impact of these mixtures on the microbial community structure and function within various root-associated niches, remains inadequately understood. Here, the effects of nicosulfuron, mesotrione and atrazine on soil enzyme activity and microbial community structure and function were investigated when applied alone and in combination. The findings indicated that herbicide mixtures exhibit a prolonged half-life compared to single herbicides. Ecological niches are the major factor influencing the structure and functions of the microbial community, with the rhizosphere exhibiting a more intensive response to herbicide stress. Herbicides significantly inhibited the activities of soil functional enzymes, including dehydrogenase, urease and sucrose in the short-term. Single herbicide did not drastically influence the alpha or beta diversity of the soil bacterial community, but herbicide mixtures significantly increased the richness of the fungal community. Meanwhile, the key functional microbial populations, such as Pseudomonas and Enterobacteriaceae, were significantly altered by herbicide stress. Both individual and combined use of the three herbicides reduced the complexity and stability of the bacterial network but increased the interspecific cooperations of fungal community in the rhizosphere. Moreover, by quantification of residual herbicide concentrations in the soil, we showed that the degradation period of the herbicide mixture was longer than that of single herbicides. Herbicide mixtures increased the contents of NO3--N and NH4+-N in the soil in the short-term. Overall, our study provided a comprehensive insight into the response of maize root-associated microbial communities to herbicide mixtures and facilitated the assessment of the ecological risks posed by herbicide mixtures to the agricultural environment from an agricultural sustainability perspective.

Urban land uses shape soil microbial abundance and diversity

Soil microbial biodiversity provides many useful services in cities. However, the ecology of microbial communities in urban soils remains poorly documented, and studies are required to better predict the impact of urban land use. We characterized microbial communities (archea/bacteria and fungi) in urban soils in Dijon (Burgundy, France). Three main land uses were considered - public leisure, traffic, and urban agriculture - sub-categorized in sub-land uses according to urban indexes and management practices. Microbial biomass and diversity were determined by quantifying and high-throughput sequencing of soil DNA. Variation partitioning analysis was used to rank soil physicochemical characteristics and land uses according to their relative contribution to the variation of soil microbial communities. Urban soils in Dijon harbored high levels of microbial biomass and diversity that varied according to land uses. Microbial biomass was 1.8 times higher in public leisure and traffic sites than in urban agriculture sites. Fungal richness increased by 25 % in urban agriculture soils, and bacterial richness was lower (by 20 %) in public leisure soils. Partitioning models explained 25.7 %, 46.2 % and 75.6 % of the variance of fungal richness, bacterial richness and microbial biomass, respectively. The organic carbon content and the C/N ratio were the best predictors of microbial biomass, whereas soil bacterial diversity was mainly explained by soil texture and land use. Neither metal trace elements nor polycyclic aromatic hydrocarbons contents explained variations of microbial communities, probably due to their very low concentration in the soils. The microbial composition results highlighted that leisure sites represented a stabilized habitat favoring specialized microbial groups and microbial plant symbionts, as opposed to urban agriculture sites that stimulated opportunistic populations able to face the impact of agricultural practices. Altogether, our results provide evidence that there is scope for urban planners to drive soil microbial diversity through sustainable urban land use and associated management practices.

Screening for Multifarious Plant Growth Promoting and Biocontrol Attributes in Bacillus Strains Isolated from Indo Gangetic Soil for Enhancing Growth of Rice Crops

Multifarious plant growth-promoting Bacillus strains recovered from rhizospheric soils of the Indo Gangetic plains (IGPs) were identified as Bacillus licheniformis MNNITSR2 and Bacillus velezensis MNNITSR18 based on their biochemical characteristics and 16S rDNA gene analysis. Both strains exhibited the ability to produce IAA, siderophores, ammonia, lytic enzymes, HCN production, and phosphate solubilization capability and strongly inhibited the growth of phytopathogens such as Rhizoctonia solani and Fusariun oxysporum in vitro. In addition, these strains are also able to grow at a high temperature of 50 °C and tolerate up to 10-15% NaCl and 25% PEG 6000. The results of the pot experiment showed that individual seed inoculation and the coinoculation of multifarious plant growth promoting (PGP) Bacillus strains (SR2 and SR18) in rice fields significantly enhanced plant height, root length volume, tiller numbers, dry weight, and yield compared to the untreated control. This indicates that these strains are potential candidates for use as PGP inoculants/biofertilizers to increase rice productivity under field conditions for IGPs in Uttar Pradesh, India.

Testing the stress gradient hypothesis in soil bacterial communities associated with vegetation belts in the Andean Atacama Desert

BACKGROUND

Soil microorganisms are in constant interaction with plants, and these interactions shape the composition of soil bacterial communities by modifying their environment. However, little is known about the relationship between microorganisms and native plants present in extreme environments that are not affected by human intervention. Using high-throughput sequencing in combination with random forest and co-occurrence network analyses, we compared soil bacterial communities inhabiting the rhizosphere surrounding soil (RSS) and the corresponding bulk soil (BS) of 21 native plant species organized into three vegetation belts along the altitudinal gradient (2400-4500 m a.s.l.) of the Talabre-Lejía transect (TLT) in the slopes of the Andes in the Atacama Desert. We assessed how each plant community influenced the taxa, potential functions, and ecological interactions of the soil bacterial communities in this extreme natural ecosystem. We tested the ability of the stress gradient hypothesis, which predicts that positive species interactions become increasingly important as stressful conditions increase, to explain the interactions among members of TLT soil microbial communities.

RESULTS

Our comparison of RSS and BS compartments along the TLT provided evidence of plant-specific microbial community composition in the RSS and showed that bacterial communities modify their ecological interactions, in particular, their positive:negative connection ratios in the presence of plant roots at each vegetation belt. We also identified the taxa driving the transition of the BS to the RSS, which appear to be indicators of key host-microbial relationships in the rhizosphere of plants in response to different abiotic conditions. Finally, the potential functions of the bacterial communities also diverge between the BS and the RSS compartments, particularly in the extreme and harshest belts of the TLT.

CONCLUSIONS

In this study, we identified taxa of bacterial communities that establish species-specific relationships with native plants and showed that over a gradient of changing abiotic conditions, these relationships may also be plant community specific. These findings also reveal that the interactions among members of the soil microbial communities do not support the stress gradient hypothesis. However, through the RSS compartment, each plant community appears to moderate the abiotic stress gradient and increase the efficiency of the soil microbial community, suggesting that positive interactions may be context dependent.

Structural diversity of bacterial communities in two divergent sunflower rhizosphere soils

Purpose

Farming practices on farmlands aim to improve nutrients in the fields or crops, soil quality and functions, as well as boost and sustain crop yield; however, the effect of loss of ecological diversity and degradation have impacted ecosystem functions. The beneficial rhizosphere-microorganism network and crop rotation may enhance a stable ecosystem. The use of next-generation sequencing technique will help characterize the entire bacterial species in the sunflower rhizosphere compared with the nearby bulk soils. We investigated the potential of the bacterial community structure of sunflower rhizosphere and bulk soils cultivated under different agricultural practices at two geographical locations in the North West Province of South Africa.

Methods

DNA was extracted from rhizosphere and bulk soils associated with sunflower plants from the crop rotation (rhizosphere soils from Lichtenburg (LTR) and bulk soils from Lichtenburg (LTB) and mono-cropping (rhizosphere soils from Krayburg (KRPR) and bulk soils from Krayburg (KRPB) sites, and sequenced employing 16S amplicon sequencing. Bioinformatics tools were used to analyse the sequenced dataset.

Results

Proteobacteria and Planctomycetes dominated the rhizosphere, while Firmicutes and Actinobacteria were predominant in bulk soils. Significant differences in bacterial structure at phyla and family levels and predicted functional categories between soils (P < 0.05) across the sites were revealed. The effect of physicochemical parameters was observed to influence bacterial dispersal across the sites.

Conclusion

This study provides information on the predominant bacterial community structure in sunflower soils and their predictive functional attributes at the growing stage, which suggests their future study for imminent crop production and management for enhanced agricultural yields.

Deciphering biochar compost co-application impact on microbial communities mediating carbon and nitrogen transformation across different stages of corn development

Under current climatic conditions, developing eco-friendly and climate-smart fertilizers has become increasingly important.The co-application of biochar and compost on agricultural soils has received considerable attention recently.Unfortunately, little is known about its effects on specific microbial taxa involved in carbon and nitrogen transformation in the soil.Herein, we report the efficacy of applying biochar-based amendments on soil physicochemical indices, enzymatic activity, functional genes, bacterial community, and their network patterns in corn rhizosphere at seedling (SS), flowering (FS), and maturity (MS) stages.The applied treatments were: compost alone (COM), biochar alone (BIOC), composted biochar (CMB), fortified compost (CMWB), and the control (no fertilizer (CNTRL).The non-metric multidimensional scaling (NMDS) indicated total nitrogen (TN), pH, NO₃^--N, urease, protease, and microbial biomass C (MBC) as the dominant environmental factors driving soil bacteria in this study.The dominant N mediating genes belonged to nitrate reductase (narG) and nitronate monooxygenase (amo), while beta-galactosidase, catalase, and alpha-amylase were the dominant genes observed relating to C cycling.Interestingly, the abundance of these genes was higher in COM, CMWB, and CMB compared with the CNTRL and BIOC treatments.The bacteria network properties of CWMB and CMB indicated robust niche overlap associated with high cross-feeding between bacterial communities compared to other treatments.Path and stepwise regression analyses revealed norank_Reyranellaceae and Sphingopyxis in CMWB as the major bacterial genera and the major predictive indices mediating soil organic C (SOC), NH₄⁺-N, NO₃^--N, and TN transformation.Overall, biochar with compost amendments improved soil nutrient conditions, regulated the composition of the bacterial community, and benefited C/N cycling in the soil ecosystem.

Microbiomes in agroecosystem: Diversity, function and assembly mechanisms

Soils are a main repository of biodiversity harbouring immense diversity of microbial species that plays a central role in fundamental ecological processes and acts as the seed bank for emergence of the plant microbiome in cropland ecosystems. Crop-associated microbiomes play an important role in shaping plant performance, which includes but not limited to nutrient uptake, disease resistance, and abiotic stress tolerance. Although our understanding of structure and function of soil and plant microbiomes has been rapidly advancing, most of our knowledge comes from ecosystems in natural environment. In this review, we present an overview of the current knowledge of diversity and function of microbial communities along the soil-plant continuum in agroecosystems. To characterize the ecological mechanisms for community assembly of soil and crop microbiomes, we explore how crop host and environmental factors such as plant species and developmental stage, pathogen invasion, and land management shape microbiome structure, microbial co-occurrence patterns, and crop-microbiome interactions. Particularly, the relative importance of deterministic and stochastic processes in microbial community assembly is illustrated under different environmental conditions, and potential sources and keystone taxa of the crop microbiome are described. Finally, we highlight a few important questions and perspectives in future crop microbiome research.

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

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

Poly-γ-glutamic acid promoted maize root development by affecting auxin signaling pathway and the abundance and diversity of rhizosphere microbial community

BACKGROUND

The root systems of higher plants play an important role in plant growth and development. In our present study, it was found that poly-γ-glutamic acid (γ-PGA), an environmentally friendly biomacromolecule, significantly improved root development in maize.

RESULTS

After treatment with γ-PGA for 7 days, the fresh weight of maize roots was significantly increased and the differences between γ-PGA treated group and control group were mainly caused by the number (higher by 71.87% compared to the control) and length of lateral roots. RNAseq and RT-PCR analyses showed that γ-PGA treatment upregulated the expression of genes related to the synthesis of auxins and auxin signal in maize roots. In addition, γ-PGA promoted the accumulation of plant growth-promoting bacteria, such as Azospirillum, Azohydromonas, Ramlibacter, and Sphingobium (Proteobacteria), Streptomyces (Actinobacteria), Parasegetibacter (Bacteroidetes), and Gemmatimonas (Gemmatimonadetes) in rhizosphere soil and the secretion of auxins. The results of this study deepened our understanding of the effects and mechanism of γ-PGA on maize root development, and as well as highlighted the possibility of using γ-PGA to improve crop growth and soil environment.

CONCLUSIONS

γ-PGA promotes early growth and development of maize roots by inducing the secretion and accumulation of auxin in roots and in rhizosphere soil, and increasing the abundance of plant growth promoting bacteria.

Effects of Insect-Resistant Maize HGK60 on Community Diversity of Bacteria and Fungi in Rhizosphere Soil

The influence of biotech crops on microbial communities in rhizosphere soil is an important issue in biosafety assessments. The transgenic maize HGK60 harboring the Bt cry1Ah gene enhanced the resistance to lepidopteran pests, while the ecological risk of HGK60 maize on rhizosphere microorganisms is unclear. In this study, we comprehensively analyzed the diversity and composition of bacterial and fungal communities in the rhizosphere soil around Bt maize HGK60 and the near-isogenic non-Bt maize ZD958 at four growth stages via a high-throughput sequencing technique. The results showed that HGK60 maize unleashed temporary effects on the bacterial and fungal diversity and richness during the study plant's development, which would be restored after one cycle of plant cultivation due to the application of the same agricultural management. The differences of bacterial and fungal communities were marked by seasonality, while the different growth stage was the important factor as opposed to the cultivar contributing to the shifts in the bacterial and fungal communities' structure. This study will provide useful information regarding the impact of Bt transgenic maize on the soil microbiome and a theoretical basis for the development of a safety assessment approach for Bt maize in China.

Comparison of bacterial diversity, root exudates and soil enzymatic activities in the rhizosphere of AVP1-transgenic and non-transgenic wheat (Triticum aestivum L.)

AIMS

Soil microbial communities are among the most diverse communities that might be affected due to transgenic crops. Therefore, risk assessment studies on transgenes are essentially required as any adverse effects may depend not only on the specific gene and crop involved but also on soil conditions.

METHODS AND RESULTS

The present study deals with the comparison of bacterial populations, root exudates, and activities of soil enzymes in non-transgenic and AVP1-transgenic wheat rhizosphere, overexpressing vacuolar H+pyrophosphatase for salinity and drought stress tolerance. Amounts of organic acids and sugars produced as root exudates and activities of dehydrogenase, phosphatase, and protease enzymes in soil solution showed no significant differences in AVP1-transgenic and non-transgenic wheat rhizosphere, except for urease and phenol oxidase activities. The higher copy number of nifH gene showed the abundance of nitrogen-fixing bacteria in the rhizosphere of AVP1-transgenic wheat compared with non-transgenic wheat. nifH gene sequence analysis indicated the common diazotrophic genera Azospirillum, Bradyrhizobium, Rhizobium, and Pseudomonas in AVP1-transgenic and non-transgenic wheat except for Zoogloea detected only in non-transgenic wheat. Using 454-pyrosequencing of 16S rRNA gene from soil DNA, a total of 156, 282 sequences of 18 phyla were obtained, which represented bacterial (128,006), Archeal (7,928), and unclassified (21,568) sequences. Proteobacteria, Crenarchaeota, and Firmicutes were the most abundant phyla in transgenic and non-transgenic wheat rhizosphere. Further comparison of different taxonomic units at the genus level showed similar distribution in transgenic and non-transgenic wheat rhizosphere.

CONCLUSION

We conclude that AVP1 gene in transgenic wheat has no apparent adverse effects on the soil environment and different bacterial communities. However, bacterial community depends on several other factors not only genetic composition of the host plants.

SIGNIFICANCE OF THE STUDY

The present research supports introduction and cultivation of transgenic plants in agricultural systems without any adverse effects on indigenous bacterial communities and soil ecosystem.

Nutrients in the rhizosphere: A meta-analysis of content, availability, and influencing factors

Nutrient deficiency in most terrestrial ecosystems constrains global primary productivity. Rhizosphere nutrient availability directly regulates plant growth and is influenced by many factors, including soil properties, plant characteristics and climate. A quantitatively comprehensive understanding of the role of these factors in modulating rhizosphere nutrient availability remains largely unknown. We reviewed 123 studies to assess nutrient availability in the rhizosphere compared to bulk soil depending on various factors. The increase in microbial nitrogen (N) content and N-cycling related enzyme activities in the rhizosphere led to a 10% increase in available N relative to bulk soil. The available phosphorus (P) in the rhizosphere decreased by 12% with a corresponding increase in phosphatase activities, indicating extreme demand and competition between plants and microorganisms for P. Greater organic carbon (C) content around taproots (+17%) confirmed their stronger ability to store more organic compounds than the fibrous roots. This corresponds to higher bacterial and fungal contents and slightly higher available nutrients in the rhizosphere of taproots. The maximal rhizosphere nutrient accumulation was common for low-fertile soils, which is confirmed by the negative correlation between most soil chemical properties and the effect sizes of available nutrients. Increases in rhizosphere bacterial and fungal population densities (205-254%) were much higher than microbial biomass increases (indicated as microbial C: +19%). Consequently, despite the higher microbial population densities in the rhizosphere, the biomass of individual microbial cells decreased, pointing on their younger age and faster turnover. This meta-analysis shows that, contrary to the common view, most nutrients are more available in the rhizosphere than in bulk soil because of higher microbial activities around roots.

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.

Influence of Maize Residues in Shaping Soil Microbiota and Fusarium spp. Communities

Fusarium head blight (FHB) is a devastating fungal disease of small grain cereals including wheat. Causal fungal agents colonize various components of the field during their life cycle including previous crop residues, soil, and grains. Although soil and residues constitute the main inoculum source, these components have received much less attention than grains. This study aimed at disentangling the role of previous crop residues in shaping soil microbiota, including Fusarium spp. communities, in fields under wheat-maize rotation. Such knowledge may contribute to better understand the complex interactions between Fusarium spp. and soil microbiota. Dynamics of bacterial and fungal communities, with a special focus on Fusarium spp., were monitored in soils at 3 time points: during wheat cultivation (April 2015 and 2017) and after maize harvest (November 2016) and in maize residues taken from fields after harvest. Shifts in microbiota were also evaluated under mesocosm experiments using soils amended with maize residues. Fusarium graminearum and F. avenaceum were predominant on maize residues but did not remain in soils during wheat cultivation. Differences in soil bacterial diversity and compositions among years were much lower than variation between fields, suggesting that bacterial communities are field-specific and more conserved over time. In contrast, soil fungal diversity and compositions were more influenced by sampling time. Maize residues, left after harvest, led to a soil enrichment with several fungal genera, including Epicoccum, Fusarium, Vishniacozyma, Papiliotrema, Sarocladium, Xenobotryosphaeria, Ramularia, Cladosporium, Cryptococcus, and Bullera, but not with bacterial genera. Likewise, under mesocosm conditions, the addition of maize residues had a stronger influence on fungal communities than on bacterial communities. In particular, addition of maize significantly increased soil fungal richness, while bacteria were much less prone to changes. Based on co-occurrence networks, OTUs negatively correlated to Fusarium spp. were identified, such as those assigned to Epicoccum and Vishniacozyma. Altogether, our results allowed to gain a deeper insight into the complex microbiota interactions in soils, with bacteria and fungi responding differently to environmental disturbances.

Investigation of bacterial diversity using 16S rRNA sequencing and prediction of its functionalities in Moroccan phosphate mine ecosystem

Native plants in extreme environments may harbor some unique microbial communities with particular functions to sustain their growth and tolerance to harsh conditions. The aim of this study was to investigate the bacterial communities profiles in some native plants and samples of the Moroccan phosphate mine ecosystem by assessing the percentages of taxonomic identification using six hypervariable regions of the 16S rRNA. The rhizosphere of the three wild plants in the Moroccan phosphate mine is characterized by interesting bacterial diversity including Proteobacteria (62.24%, 71.15% and 65.61%), Actinobacteria (22.53%, 15.24%, 22.30%), Bacteroidetes (7.57%; 4.23%; 7.63%), and Firmicutes (5.82%; 1.17%; 2.83%). The bulk phosphate mine samples were dominated by Actinobacteria with average relative abundance of 97.73% that are different from those inferred in the rhizosphere samples of the native plants. The regions V3, V4 and V67 performed better in the taxonomic profiling at different taxonomic levels. Results indicated that both plant genotype and mainly soil conditions may be involved in the shaping of bacterial diversity. Such indication was also confirmed by the prediction of functional profiles that showed enrichment of many functions related to biological nitrogen fixation in the rhizosphere of native plants and the stress related functions in the bulk phosphate mine in comparison with the wheat rhizosphere samples.

Poly-γ-glutamic acid enhanced the drought resistance of maize by improving photosynthesis and affecting the rhizosphere microbial community

BACKGROUND

Compared with other abiotic stresses, drought stress causes serious crop yield reductions. Poly-γ-glutamic acid (γ-PGA), as an environmentally friendly biomacromolecule, plays an important role in plant growth and regulation.

RESULTS

In this project, the effect of exogenous application of γ-PGA on drought tolerance of maize (Zea mays. L) and its mechanism were studied. Drought dramatically inhibited the growth and development of maize, but the exogenous application of γ-PGA significantly increased the dry weight of maize, the contents of ABA, soluble sugar, proline, and chlorophyll, and the photosynthetic rate under severe drought stress. RNA-seq data showed that γ-PGA may enhance drought resistance in maize by affecting the expression of ABA biosynthesis, signal transduction, and photosynthesis-related genes and other stress-responsive genes, which was also confirmed by RT-PCR and promoter motif analysis. In addition, diversity and structure analysis of the rhizosphere soil bacterial community demonstrated that γ-PGA enriched plant growth promoting bacteria such as Actinobacteria, Chloroflexi, Firmicutes, Alphaproteobacteria and Deltaproteobacteria. Moreover, γ-PGA significantly improved root development, urease activity and the ABA contents of maize rhizospheric soil under drought stress. This study emphasized the possibility of using γ-PGA to improve crop drought resistance and the soil environment under drought conditions and revealed its preliminary mechanism.

CONCLUSIONS

Exogenous application of poly-γ-glutamic acid could significantly enhance the drought resistance of maize by improving photosynthesis, and root development and affecting the rhizosphere microbial community.

Isolation and characterization of plant growth promoting rhizobacteria isolated from organically grown high yielding pole type native pea (Pisum sativum L.) variety Dentami of Sikkim, India

•

The present research showcases the significant findings pertaining to the assessment and report of the first ever study on the isolation and identification of plant growth promoting rhizobacterial diversity of organic farming pea variety (Dentami) of Sikkim. Proteobacteria dominated the rhizospheric soil whereas the bulk soil was governed by Actinobacteria. Bacillus cereus P8 (66.5 µg ml⁻¹) and Bacillus mycoides PP1 (45.1 µg ml⁻¹) were the highest IAA producer and also showed other plant growth promoting and biocontrol traits, such as phosphorous and potassium solubilization, nitrogen-fixing activity and siderophore production. As, Sikkim is the first state in India to practice organic agriculture farming, hence, such study on the soil microbiology is of immense significance. In these rhizospheric soil, it was dominated by the Proteobacteria and similar bacterial isolates, suggesting that these soil flora might be playing significant roles to enhancing the crop production and soil fertility.

•

Culture-dependent technique was used to assess plant growth promoting rhizobacterial diversity of pole type pea variety (Dentami) of Sikkim.

•

The dominant phylum was Proteobacteria (56%) from rhizosphere soil and Actinobacteria (58%) from bulk soil.

•

PCA analysis showed that Firmicutes (bulk soil) were positively correlated to SOC, and available K, whereas, Proteobacteria (rhizosphere soil) exhibited a high correlation to pH, and available P.

•

Bacillus cereus P8, Arthrobacter woluwensis DP2, Paenarthrobacter nitroguajacolicus UP1, and Bacillus mycoides PP1 showed plant growth promotion and bio-control traits.

•

Bacillus cereus P8 (66.5 µg mL⁻¹) and Bacillus mycoides PP1 (45.1 µg mL⁻¹) was thehighest IAA producer.

•

Pot experiment confirmed that these isolates can be potential plant growth promoter under the agro-climatic conditions of Sikkim, India.

Organic farming is an eco-friendly and sustainable farming practice that enhances soil fertility and helps in improving soil quality. But with the commencement of more sophisticated advances in agricultural techniques, organic farming has gradually become limited in the world. Culture-dependent plant growth-promoting bacterial isolates were isolated from the bulk and rhizospheric soil, of the native high yielding pole type organic pea (Pisum sativum L.) cultivar Dentami of Dentam, West Sikkim, India. Based on the 16S rRNA gene sequencing identification of these isolates, it was found that from the bulk soil, Actinobacteria (58%) was the dominant phyla followed by Firmicutes (28%), and Proteobacteria (14%). In the rhizospheric soil it was dominated by Proteobacteria (56%), followed by Firmicutes (33%), and Bacteriodetes (11%). A total of 40 bacterial isolates were initially screened for the plant growth-promoting (PGP) activity and out of them only four bacterial isolates i.e., Bacillus cereus P8, Arthrobacter woluwensis DP2, Paenarthrobacter nitroguajacolicus PP3, and Bacillus mycoides PP10 with accession numbers MN589697, MN559516, MN519462 and MN589696 respectively were found to possess higher PGP activity (i.e. phosphorous, potassium solubilization and nitrogen-fixing activity) as compared to the other bacteria present in the soil. Based on the indole-3-acetic acid (IAA) quantitative assay and siderophore production assay, it was found that Bacillus cereus (MN589697) produced the highest IAA (65.5 µg mL⁻¹) and siderophore (71%) when compared with the other isolates. The statistical correlation suggests that pH and available phosphorus were the strongest influencing factors for the distribution of Proteobacteria in the rhizospheric soil. The results indicate that these isolates can be potential plant growth promoter under the agro-climatic conditions of Sikkim, India. To the best of our knowledge the present study is the first report of its kind and showcases significant findings pertaining to the assessment of diversity, isolation and identification of plant growth-promoting rhizobacteria of organic pea grown in Sikkim.

Tomato Endophytic Bacteria Composition and Mechanism of Suppressiveness of Wilt Disease (Fusarium oxysporum)

Tomato wilt disease, caused by the Fusarium oxysporum is an ever-increasing threat for agricultural production, and unreasonable fertilization and pesticide abuse caused environmental challenge. Increasing evidence suggested that microbiomes or those associated with crops, played key roles on plant health. Plant disease dynamics were affected by multiple biotic and abiotic factors including phytopathogen population density, the genetic type of the pathogen and the host, in particular, the composition and assembly of the host-associated microbiome. However, it was unclear how pathogen invasion interaction and correlate with endophytic bacterial communities in natural field conditions. To study this, we sampled temporally the tomato plants that were exposed to F. oxysporum invasions over one crop season. High-throughput sequencing were performed to explore the correlation between agricultural practice, pathogen invasion, and endophytic microbiota communities. Results showed that pathogen invasion had clear effect on the endophytic and a strong link between increased pathogen densities and reduced abundance of Bacillus sp., which are crucial taxonomy for suppressiveness to F. oxysporum in vitro and in greenhouse condition. In summary, monitoring the dynamics of endophytic bacteria communities and densities of pathogen could thus open new avenue for more accurate disease diagnostics and high-efficiency screening antagonisms methods in the future, and our results will broaden the agricultural view of beneficial microbiota as biological control agents against plant pathogen.

The Perception of Rhizosphere Bacterial Communication Signals Leads to Transcriptome Reprogramming in Lysobacter capsici AZ78, a Plant Beneficial Bacterium

The rhizosphere is a dynamic region governed by complex microbial interactions where diffusible communication signals produced by bacteria continuously shape the gene expression patterns of individual species and regulate fundamental traits for adaptation to the rhizosphere environment. Lysobacter spp. are common bacterial inhabitants of the rhizosphere and have been frequently associated with soil disease suppressiveness. However, little is known about their ecology and how diffusible communication signals might affect their behavior in the rhizosphere. To shed light on the aspects determining rhizosphere competence and functioning of Lysobacter spp., we carried out a functional and transcriptome analysis on the plant beneficial bacterium Lysobacter capsici AZ78 (AZ78) grown in the presence of the most common diffusible communication signals released by rhizosphere bacteria. Mining the genome of AZ78 and other Lysobacter spp. showed that Lysobacter spp. share genes involved in the production and perception of diffusible signal factors, indole, diffusible factors, and N-acyl-homoserine lactones. Most of the tested diffusible communication signals (i.e., indole and glyoxylic acid) influenced the ability of AZ78 to inhibit the growth of the phytopathogenic oomycete Pythium ultimum and the Gram-positive bacterium Rhodococcus fascians. Moreover, RNA-Seq analysis revealed that nearly 21% of all genes in AZ78 genome were modulated by diffusible communication signals. 13-Methyltetradecanoic acid, glyoxylic acid, and 2,3-butanedione positively influenced the expression of genes related to type IV pilus, which might enable AZ78 to rapidly colonize the rhizosphere. Moreover, glyoxylic acid and 2,3-butanedione downregulated tRNA genes, possibly as a result of the elicitation of biological stress responses. On its behalf, indole downregulated genes related to type IV pilus and the heat-stable antifungal factor, which might result in impairment of twitching motility and antibiotic production in AZ78. These results show that diffusible communication signals may affect the ecology of Lysobacter spp. in the rhizosphere and suggest that diffusible communication signals might be used to foster rhizosphere colonization and functioning of plant beneficial bacteria belonging to the genus Lysobacter.

Comparative Effect of Fertilization Practices on Soil Microbial Diversity and Activity: An Overview

Continuously increasing human population demands increased food production, which needs greater fertilizer's input in agricultural lands to enhance crop yield. In this respect, different fertilization practices gained acceptance among farmers. We reviewed effect of three main fertilization practices (Conventional-, Organic-, and Bio-fertilization) on soil microbial diversity, activity, and community composition. Studies reported that over application of inorganic fertilizers decline soil pH, change soil osmolarity, cause soil degradation, disturb taxonomic diversity and metabolism of soil microbes and cause accumulation of extra nutrients into the soil such as phosphorous (P) accumulation. On the contrary, organic fertilizers increase organic carbon (OC) input in the soil, which strongly encourage growth of heterotrophic microbes. Organic fertilizer vermicompost application provides readily available nutrients to both plants as well as microbes and encourage overall microbial number in the soil. Most recently, role of beneficial bacteria in long-term sustainable agriculture attracted attention of scientists towards their use as biofertilizer in the soil. Studies documented favorable effect of biofertilization on microbial Shannon, Chao and ACE diversity indices in the soil. It is concluded from intensive review of literature that all the three fertilization practices have their own way to benefit the soil with nutrients, but biofertilization provides long-term sustainability to crop lands. When it is used in integration with organic fertilizers, it makes the soil best for microbial growth and activity and increase microbial diversity, providing nutrients to soil for a longer time, thus improving crop productivity.

The influence of maize genotype on the rhizosphere eukaryotic community

The microbiota colonizing the rhizosphere contributes to plant growth, productivity, carbon sequestration and phytoremediation. Several studies address plant-associated bacteria; however, few studies analyze the effect of plant genotype on the eukaryotic community. Here, we analyzed the eukaryotic composition of maize rhizosphere from three different plant landraces and one inbred line grown in the same soil (common garden approach). This experimental design, coupled with 18S rDNA gene amplicon sequencing, allowed us to test the influence of maize and its genotype on the rhizosphere's eukaryotic community. We found that plant growth modified the eukaryotic community in soil, as diversity comparisons between maize rhizosphere and unplanted soil revealed significantly different eukaryotic composition. Various genera of nematodes and fungi, predominantly bacterial feeding nematodes and mycorrhizal fungi among other taxa, were increased in the rhizosphere samples. We also observed that maize genotype differentially shaped the relative abundance of the following fungal families in the rhizosphere: Acaulosporaceae, Aspergillaceae, Chaetomiaceae, Claroideoglomeraceae, Corticiaceae, Mortierellaceae, Trichocomaceae and Trichomeriaceae. Thus, plant genotype has a selective influence on establishing fungal communities in the rhizosphere. This study emphasizes the importance of an integrated consideration of plant genetics for future agricultural applications of microbes to crops.

Composted biochar affects structural dynamics, function and co-occurrence network patterns of fungi community

A few researchers have reported enhancing soil physicochemical properties and reducing greenhouse gas emission using biochar-compost mixture as an alternative method to address soil fertility, soil degradation and climate change. However, information about its effects on soil microbiome has rarely been studied. This investigation was on the impact of a combined biochar-compost application on soil physicochemical variables, fungal community composition, function and network patterns in maize at seedling stage (SS), reproductive stage (RS), and maturity stage (MS). The experimental design consists of five treatments: control (CNT), compost (CMP), composted biochar (CMB), compost fortified with biochar (CFWB), biochar (BCH). The results showed that CFWB, CMB, and CMP increased fungal diversity indices (Shannon, Sobs, and Chao) at the RS and MS stages respectively, compared to BCH and CNT. Distance-based redundancy analysis (db-RDA) at genus level indicated that the pH, available nitrogen, and soil organic matter at SS; available phosphorus at RS; Mg, Mn, Fe, and Zn at MS significantly and positively affected the fungi community. Based on the Linear discriminant analysis (LDA) and effect size (LEfSe) analysis, the results revealed that only Cystofilobasidiaceae and Guehomyces were the MS biomarkers; and significantly enriched in CFWB. FUNGuild analysis indicated that organic amendments (CFWB, CMB, CMP, and BCH) suppressed the abundance of plant pathogenic fungi (Edenia and Waitea) compared to CNT. Network analysis showed that CFWB and CMB had a high niche overlap and cross-feeding in their networks compared to other treatments. However, CMP network had more positive links with Saprotroph, Pathotroph-Saprotroph-Symbiotroph, Pathotroph and Pathotroph-Symbiotroph compared with other treatments. This study showed that applying biochar, compost and a mixture of both, positively affected soil fungal communities plus co-occurrence network pattern in a single cropping season. Thus, their application as soil amendments may improve the soil fungi ecosystem, soil health and quality and mitigate climate change.

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.

Plant Growth-Promoting Bacteria as an Emerging Tool to Manage Bacterial Rice Pathogens

As a major food crop, rice (Oryza sativa) is produced and consumed by nearly 90% of the population in Asia with less than 9% produced outside Asia. Hence, reports on large scale grain losses were alarming and resulted in a heightened awareness on the importance of rice plants' health and increased interest against phytopathogens in rice. To serve this interest, this review will provide a summary on bacterial rice pathogens, which can potentially be controlled by plant growth-promoting bacteria (PGPB). Additionally, this review highlights PGPB-mediated functional traits, including biocontrol of bacterial rice pathogens and enhancement of rice plant's growth. Currently, a plethora of recent studies address the use of PGPB to combat bacterial rice pathogens in an attempt to replace existing methods of chemical fertilizers and pesticides that often lead to environmental pollutions. As a tool to combat bacterial rice pathogens, PGPB presented itself as a promising alternative in improving rice plants' health and simultaneously controlling bacterial rice pathogens in vitro and in the field/greenhouse studies. PGPB, such as Bacillus, Pseudomonas, Enterobacter, Streptomyces, are now very well-known. Applications of PGPB as bioformulations are found to be effective in improving rice productivity and provide an eco-friendly alternative to agroecosystems.

Synthetic community with six Pseudomonas strains screened from garlic rhizosphere microbiome promotes plant growth

The rhizosphere microbiome plays an important role in the growth and health of many plants, particularly for plant growth-promoting rhizobacteria (PGPR). Although the use of PGPR could improve plant production, real-world applications are still held back by low-efficiency methods of finding and using PGPR. In this study, the structure of bacterial and fungal rhizosphere communities of Jinxiang garlic under different growth periods (resume growth, bolting and maturation), soil types (loam, sandy loam and sandy soil) and agricultural practices (with and without microbial products) were explored by using amplicon sequencing. High-efficiency top-down approaches based on high-throughput technology and synthetic community (SynCom) approaches were used to find PGPR in garlic rhizosphere and improve plant production. Our findings indicated that Pseudomonas was a key PGPR in the rhizosphere of garlic. Furthermore, SynCom with six Pseudomonas strains isolated from the garlic rhizosphere were constructed, which showed that they have the ability to promote plant growth.

Bioactive diterpenoids impact the composition of the root-associated microbiome in maize (Zea mays)

Plants deploy both primary and species-specific, specialized metabolites to communicate with other organisms and adapt to environmental challenges, including interactions with soil-dwelling microbial communities. However, the role of specialized metabolites in modulating plant-microbiome interactions often remains elusive. In this study, we report that maize (Zea mays) diterpenoid metabolites with known antifungal bioactivities also influence rhizosphere bacterial communities. Metabolite profiling showed that dolabralexins, antibiotic diterpenoids that are highly abundant in roots of some maize varieties, can be exuded from the roots. Comparative 16S rRNA gene sequencing determined the bacterial community composition of the maize mutant Zman2 (anther ear 2), which is deficient in dolabralexins and closely related bioactive kauralexin diterpenoids. The Zman2 rhizosphere microbiome differed significantly from the wild-type sibling with the most significant changes observed for Alphaproteobacteria of the order Sphingomonadales. Metabolomics analyses support that these differences are attributed to the diterpenoid deficiency of the Zman2 mutant, rather than other large-scale metabolome alterations. Together, these findings support physiological functions of maize diterpenoids beyond known chemical defenses, including the assembly of the rhizosphere microbiome.

Tomato Cultivars With Variable Tolerances to Water Deficit Differentially Modulate the Composition and Interaction Patterns of Their Rhizosphere Microbial Communities

Since drought is the leading environmental factor limiting crop productivity, and plants have a significant impact in defining the assembly of plant-specific microbial communities associated with roots, we aimed to determine the effect of thoroughly selected water deficit tolerant and susceptible Solanum lycopersicum cultivars on their rhizosphere microbiome and compared their response with plant-free soil microbial communities. We identified a total of 4,248 bacterial and 276 fungal different operational taxonomic units (OTUs) in soils by massive sequencing. We observed that tomato cultivars significantly affected the alpha and beta diversity of their bacterial rhizosphere communities but not their fungal communities compared with bulk soils (BSs), showing a plant effect exclusively on the bacterial soil community. Also, an increase in alpha diversity in response to water deficit of both bacteria and fungi was observed in the susceptible rhizosphere (SRz) but not in the tolerant rhizosphere (TRz) cultivar, implying a buffering effect of the tolerant cultivar on its rhizosphere microbial communities. Even though water deficit did not affect the microbial diversity of the tolerant cultivar, the interaction network analysis revealed that the TRz microbiota displayed the smallest and least complex soil network in response to water deficit with the least number of connected components, nodes, and edges. This reduction of the TRz network also correlated with a more efficient community, reflected in increased cooperation within kingdoms. Furthermore, we identified some specific bacteria and fungi in the TRz in response to water deficit, which, given that they belong to taxa with known beneficial characteristics for plants, could be contributing to the tolerant phenotype, highlighting the metabolic bidirectionality of the holobiont system. Future assays involving characterization of root exudates and exchange of rhizospheres between drought-tolerant and susceptible cultivars could determine the effect of specific metabolites on the microbiome community and may elucidate their functional contribution to the tolerance of plants to water deficit.

Elucidating the Diversity and Potential Function of Nonribosomal Peptide and Polyketide Biosynthetic Gene Clusters in the Root Microbiome

Polyketides (PKs) and nonribosomal peptides (NRPs) are two microbial secondary metabolite (SM) families known for their variety of functions, including antimicrobials, siderophores, and others. Despite their involvement in bacterium-bacterium and bacterium-plant interactions, root-associated SMs are largely unexplored due to the limited cultivability of bacteria. Here, we analyzed the diversity and expression of SM-encoding biosynthetic gene clusters (BGCs) in root microbiomes by culture-independent amplicon sequencing, shotgun metagenomics, and metatranscriptomics. Roots (tomato and lettuce) harbored distinct compositions of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) relative to the adjacent bulk soil, and specific BGC markers were both enriched and highly expressed in the root microbiomes. While several of the highly abundant and expressed sequences were remotely associated with known BGCs, the low similarity to characterized genes suggests their potential novelty. Low-similarity genes were screened against a large set of soil-derived cosmid libraries, from which five whole BGCs of unknown function were retrieved. Three clusters were taxonomically affiliated with Actinobacteria, while the remaining were not associated with known bacteria. One Streptomyces-derived BGC was predicted to encode a polyene with potential antifungal activity, while the others were too novel to predict chemical structure. Screening against a suite of metagenomic data sets revealed higher abundances of retrieved clusters in roots and soil samples. In contrast, they were almost completely absent in aquatic and gut environments, supporting the notion that they might play an important role in root ecosystems. Overall, our results indicate that root microbiomes harbor a specific assemblage of undiscovered SMs.IMPORTANCE We identified distinct secondary-metabolite-encoding genes that are enriched (relative to adjacent bulk soil) and expressed in root ecosystems yet almost completely absent in human gut and aquatic environments. Several of the genes were distantly related to genes encoding antimicrobials and siderophores, and their high sequence variability relative to known sequences suggests that they may encode novel metabolites and may have unique ecological functions. This study demonstrates that plant roots harbor a diverse array of unique secondary-metabolite-encoding genes that are highly enriched and expressed in the root ecosystem. The secondary metabolites encoded by these genes might assist the bacteria that produce them in colonization and persistence in the root environment. To explore this hypothesis, future investigations should assess their potential role in interbacterial and bacterium-plant interactions.

Impact of Inoculation with Pseudomonas aestus CMAA 1215T on the Non-target Resident Bacterial Community in a Saline Rhizosphere Soil

Plant growth reduction caused by osmotic stress, pathogens, and nutrient scarcity can be overcome by inoculation with plant growth-promoting rhizobacteria (PGPR). Knowing the effects of PGPR on the microbial community beyond those on plant growth can bring new options of soil microbiota management. The present study aimed to investigate the effect of inoculation with the newly described Pseudomonas aestus CMAA 1215^T [a 1-aminocyclopropane-1-carboxylate (ACC) deaminase and glycine-betaine producer] on the rhizosphere bacterial community of Zea mays in natural (non-salinized) and saline soil. The bacterial community structure was assessed by sequencing the V6-V7 16S ribosomal RNA using the Ion Personal Genome Machine^™. The non-metric multidimensional scaling (NMDS) of the OTU profile (ANOSIM P < 0.01) distinguishes all the treatments (with and without inoculation under saline and natural soils). Inoculated samples shared 1234 OTUs with non-inoculated soil. The most abundant classes in all samples were Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Acidobacteriia, Bacteroidia, Thermoleophilia, Verrucomicrobiae, Ktenodobacteria, and Bacilli. The inoculation, on the other hand, caused an increase in the abundance of the genera Bacillus, Bryobacter, Bradyrhizobium, "Candidatus Xiphinematobacter", and "Candidatus Udaeobacter" independent of soil salinization. "Candidatus Udaeobacter" has the largest Mean Decrease in Gini Values with higher abundance on inoculated salted soil. In addition, Pseudomonas inoculation reduced the abundance of Gammaproteobacteria and Phycisphaerae. Understanding how inoculation modifies the bacterial community is essential to manage the rhizospheric microbiome to create a multi-inoculant approach and to understand its effects on ecological function.

Exploring the Microbiota of East African Indigenous Leafy Greens for Plant Growth, Health, and Resilience

Indigenous leafy green vegetable crops provide a promising nutritious alternative for East African agriculture under a changing climate; they are better able to cope with biotic and abiotic stresses than cosmopolitan vegetable crops. To verify our hypothesis that the associated microbiome is involved, we studied archaeal and bacterial communities of four locally popular leafy green crops in Uganda (Bidens pilosa, Solanum scabrum, Abelmoschus esculentus, and Gynandropsis gynandra) and of four plant microhabitats (phyllosphere, root endosphere, rhizosphere, and soil) by complementary analyses of amplicon and isolate libraries. All plants shared an unusually large core microbiome, comprising 18 procaryotic families but primarily consisting of Bacillus, Sphingobium, Comamonadaceae, Pseudomonas, and one archaeon from the soil crenarchaeotic group. Microbiome composition did not differ significantly for plant species but differed for microhabitats. The diversity was, in general, higher for bacteria (27,697 ASVs/H = 6.91) than for archaea (2,995 ASVs/H = 4.91); both groups form a robust network of copiotrophic bacteria and oligotrophic archaea. Screening of selected isolates for stress and plant health protecting traits showed that strains of Bacillus and Sphingomonas spp. div. constituted a substantial portion (15-31%) of the prokaryotic plant-associated communities. Across plant species, microbiota were characterized by a high proportion of potential copiotrophic and plant-beneficial species, which was not specific by plant species. The use of identified plant-beneficial isolates could provide the basis for the development of consortia of isolates for both abiotic and biotic stress protection to improve plant and ecosystem health, ensuring food security in East Africa.

Effectsof growth-promoting rhizobacteria on maize growth and rhizosphere microbial community under conservation tillage in Northeast China

Conservation tillage in conjunction with straw mulching is a sustainable agricultural approach. However, straw mulching reduces the soil temperature, inhibits early maize growth and reduces grain yield in cold regions. To address this problem, we investigated the effects of inoculation of plant growth‐promoting rhizobacteria (PGPR) on maize growth and rhizosphere microbial communities under conservation tillage in Northeast China. The PGPR strains Sinorhizobium sp. A15, Bacillus sp. A28, Sphingomonas sp. A55 and Enterobacter sp. P24 were isolated from the maize rhizosphere in the same area and inoculated separately. Inoculation of these strains significantly enhanced maize growth, and the strains A15, A28 and A55 significantly increased grain yield by as much as 22%–29%. Real‐time quantitative PCR and high‐throughput sequencing showed that separate inoculation with the four strains increased the abundance and species richness of bacteria in the maize rhizosphere. Notably, the relative abundance of Acidobacteria_Subgroup_6, Chloroflexi_KD4‐96, and Verrucomicrobiae at the class level and Mucilaginibacter at the genus level were positively correlated with maize biomass and yield. Inoculation with PGPR shows potential for improvement of maize production under conservation tillage in cold regions by regulating the rhizosphere bacterial community structure and by direct stimulation of plant growth.

Functional characterization of asnC family transcriptional regulator in Pseudomonas aeruginosa PGPR2 during root colonization

Transcriptional regulators in bacteria are the crucial players in mediating communication between environmental cues and DNA transcription through a complex network process. Pseudomonas aeruginosa PGPR2 is an efficient root colonizer and a biocontrol strain. Previously, we identified that the transcriptional regulator, asnC, negatively regulates the corn root colonization of P. aeruginosa PGPR2. In a transposon insertion sequencing (INSeq) screen, the asnC insertion mutant was positively selected during root colonization, meaning the disruption of asnC improves the fitness of the P. aeruginosa PGPR2 strain for the root colonization. In this study, we constructed isogenic mutant of asnC family transcriptional regulator encoded by PGPR2_17510 by allele exchange mutagenesis. The ΔasnC mutant was able to efficiently colonize corn roots with a twofold increase in population when compared to the wild-type strain. Similarly, the mutant strain outcompeted the wild-type strain in a competition assay, where the mutant strain represented 90% of the total population recovered from the root. We compared the whole transcriptome of the wild-type and the ΔasnC mutant of P. aeruginosa PGPR2 when exposed to the corn root exudates. The RNA-Seq revealed that a total of 360 genes were differentially expressed in the ΔasnC strain of P. aeruginosa PGPR2. Inactivation of asnC transcriptional regulator resulted in the up-regulation of several genetic factors implicated in metabolism, uptake of nutrients, motility, stress response, and signal transduction, which could play crucial roles in root colonization. This notion was further validated by phenotypic characterization and quantification of transcription pattern of selected genes associated with metabolism, motility, and carbon catabolite repression between wild type and mutant strain, which was in agreement with transcriptome data. Similarly, ΔasnC strain formed increased biofilm on abiotic surface validating our RNA-seq analysis, where transcript levels of several genes associated with biofilm formation were up-regulated in the mutant strain. We report that the inactivation of an asnC family transcriptional regulator encoded by PGPR2_17510 enhances the root colonization and biofilm-forming ability of P. aeruginosa PGPR2. Together, our results provide evidence for the molecular adaptations that enable ΔasnC mutant strain to colonize on the corn roots and to form a biofilm.

Insights on Engineered Microbes in Sustainable Agriculture: Biotechnological Developments and Future Prospects

Background

Enhanced agricultural production is essential for increasing demand of the growing world population. At the same time, to combat the adverse effects caused by conventional agriculture practices to the environment along with the impact on human health and food security, a sustainable and healthy agricultural production needs to be practiced using beneficial microorganisms for enhanced yield. It is quite challenging because these microorganisms have rich biosynthetic repositories to produce biomolecules of interest; however, the intensive research in allied sectors and emerging genetic tools for improved microbial consortia are accepting new approaches that are helpful to farmers and agriculturists to meet the ever-increasing demand of sustainable food production. An important advancement is improved strain development via genetically engineered microbial systems (GEMS) as well as genetically modified microorganisms (GMOs) possessing known and upgraded functional characteristics to promote sustainable agriculture and food security. With the development of novel technologies such as DNA automated synthesis, sequencing and influential computational tools, molecular biology has entered the systems biology and synthetic biology era. More recently, CRISPR/Cas has been engineered to be an important tool in genetic engineering for various applications in the agri sector. The research in sustainable agriculture is progressing tremendously through GMOs/GEMS for their potential use in biofertilizers and as biopesticides.

Conclusion

In this review, we discuss the beneficial effects of engineered microorganisms through integrated sustainable agriculture production practices to improve the soil microbial health in order to increase crop productivity.

Bacterial microbiome associated with the rhizosphere and root interior of crops in Saskatchewan, Canada

Rhizosphere and root associated bacteria are key components of plant microbiomes and influence crop production. In sustainable agriculture, it is important to investigate bacteria diversity in various plant species and how edaphic factors influence the bacterial microbiome. In this study, we used high-throughput sequencing to assess bacterial communities associated with the rhizosphere and root interior of canola, wheat, field pea, and lentil grown at four locations in Saskatchewan, Canada. Rhizosphere bacteria communities exhibited distinct profiles among crops and sampling locations. However, each crop was associated with distinct root endophytic bacterial communities, suggesting that crop species may influence the selection of root bacterial microbiome. Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla in the root interior, whereas Gemmatimonadetes, Firmicutes, and Acidobacteria were prevalent in the rhizosphere soil. Pseudomonas and Stenotrophomonas were predominant in the rhizosphere and root interior, whereas Acinetobacter, Arthrobacter, Rhizobium, Streptomyces, Variovorax, and Xanthomonas were dominant in the root interior of all crops. The relative abundance of specific bacterial groups in the rhizosphere correlated with soil pH and silt and organic matter contents; however, there was no correlation between root endophytes and analyzed soil properties. These results suggest that the root microbiome may be modulated by plant factors rather than soil characteristics.

Effect of Re-acidification on Buffalo Grass Rhizosphere and Bulk Microbial Communities During Phytostabilization of Metalliferous Mine Tailings

Phytostabilized highly acidic, pyritic mine tailings are susceptible to re-acidification over time despite initial addition of neutralizing amendments. Studies examining plant-associated microbial dynamics during re-acidification of phytostabilized regions are sparse. To address this, we characterized the rhizosphere and bulk bacterial communities of buffalo grass used in the phytostabilization of metalliferous, pyritic mine tailings undergoing re-acidification at the Iron King Mine and Humboldt Smelter Superfund Site in Dewey-Humboldt, AZ. Plant-associated substrates representing a broad pH range (2.35-7.76) were sampled to (1) compare the microbial diversity and community composition of rhizosphere and bulk compartments across a pH gradient, and (2) characterize how re-acidification affects the abundance and activity of the most abundant plant growth-promoting bacteria (PGPB; including N2-fixing) versus acid-generating bacteria (AGB; including Fe-cycling/S-oxidizing). Results indicated that a shift in microbial diversity and community composition occurred at around pH 4. At higher pH (>4) the species richness and community composition of the rhizosphere and bulk compartments were similar, and PGPB, such as Pseudomonas, Arthrobacter, Devosia, Phyllobacterium, Sinorhizobium, and Hyphomicrobium, were present and active in both compartments with minimal presence of AGB. In comparison, at lower pH (<4) the rhizosphere had a significantly higher number of species than the bulk (p < 0.05) and the compartments had significantly different community composition (unweighted UniFrac; PERMANOVA, p < 0.05). Whereas some PGPB persisted in the rhizosphere at lower pH, including Arthrobacter and Devosia, they were absent from the bulk. Meanwhile, AGB dominated in both compartments; the most abundant were the Fe-oxidizer Leptospirillum and Fe-reducers Acidibacter and Acidiphilium, and the most active was the Fe-reducer Aciditerrimonas. This predominance of AGB at lower pH, and even their minimal presence at higher pH, contributes to acidifying conditions and poses a significant threat to sustainable plant establishment. These findings have implications for phytostabilization field site management and suggest re-application of compost or an alternate buffering material may be required in regions susceptible to re-acidification to maintain a beneficial bacterial community conducive to long-term plant establishment.

Consistent bacterial selection by date palm root system across heterogeneous desert oasis agroecosystems

Highly productive conventional agroecosystems are spatially embedded in resource-homogeneous systems and count on generally nutrient-rich soils. On the contrary, desert oases are isolated, the soil is relatively poor, but yet productivity is similar to conventional agroecosystems. Soil dominates over plant as the main factor shaping root-associated microbiomes in conventional agroecosystems. We hypothesize that in desert oasis, the environmental discontinuity, the resource paucity and limited microbial diversity of the soil make the plant a prevailing factor. We have examined the bacterial communities in the root system of date palm (Phoenix dactylifera), the iconic keystone species of the oases, grown in heterogeneous soils across a broad geographic range (22,200 km² surface area) of the Sahara Desert in Tunisia. We showed that, regardless of the edaphic conditions and geographic location, the plant invariably selects similar Gammaproteobacteria- and Alphaproteobacteria-dominated bacterial communities. The phylogeny, networking properties and predicted functionalities of the bacterial communities indicate that these two phyla are performing the ecological services of biopromotion and biofertilization. We conclude that in a desert agroecosystem, regardless of the soil microbial diversity baseline, the plant, rather than soil type, is responsible of the bacterial community assembly in its root systems, reversing the pattern observed in conventional agroecosystem.

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

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

Genome variations between rhizosphere and bulk soil ecotypes of a Pseudomonas koreensis population

Bulk soil and rhizosphere are soil compartments selecting different microbial communities. However, it is unknown whether this selection also can change the genome content of specific bacterial taxa, splitting a population in distinct ecotypes. To answer this question we compared the genome sequences of 53 isolates obtained from sugarcane rhizosphere (28) and bulk soil (25). These isolates were previously classified in the Pseudomonas koreensis subgroup of the P. fluorescens complex. Phylogenomics showed a trend of separation between bulk soil and rhizosphere isolates. Discriminant analysis of principal components (DAPC) identified differences in the accessory genome of rhizosphere and bulk soil sub-populations. We found significant changes in gene frequencies distinguishing rhizosphere from bulk soil ecotypes, for example, enrichment of phosphatases and xylose utilization (xut) genes, respectively. Phenotypic assays and deletion of xutA gene indicated that accumulation of xut genes in the bulk soil sub-population provided a higher growth capacity in a d-xylose medium, supporting the corresponding genomic differences. Despite the clear differences distinguishing the two ecotypes, all 53 isolates were classified in a single 16S rRNA gene OTU. Collectively, our results revealed that the gene pool and ecological behavior of a bacterial population can be different for ecotypes living in neighbouring soil habitats.

Rhizobacterial communities of five co-occurring desert halophytes

BACKGROUND

Recently, researches have begun to investigate the microbial communities associated with halophytes. Both rhizobacterial community composition and the environmental drivers of community assembly have been addressed. However, few studies have explored the structure of rhizobacterial communities associated with halophytic plants that are co-occurring in arid, salinized areas.

METHODS

Five halophytes were selected for study: these co-occurred in saline soils in the Ebinur Lake Nature Reserve, located at the western margin of the Gurbantunggut Desert of Northwestern China. Halophyte-associated bacterial communities were sampled, and the bacterial 16S rDNA V3-V4 region amplified and sequenced using the Illumina Miseq platform. The bacterial community diversity and structure were compared between the rhizosphere and bulk soils, as well as among the rhizosphere samples. The effects of plant species identity and soil properties on the bacterial communities were also analyzed.

RESULTS

Significant differences were observed between the rhizosphere and bulk soil bacterial communities. Diversity was higher in the rhizosphere than in the bulk soils. Abundant taxonomic groups (from phylum to genus) in the rhizosphere were much more diverse than in bulk soils. Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Planctomycetes were the most abundant phyla in the rhizosphere, while Proteobacteria and Firmicutes were common in bulk soils. Overall, the bacterial community composition were not significantly differentiated between the bulk soils of the five plants, but community diversity and structure differed significantly in the rhizosphere. The diversity of Halostachys caspica, Halocnemum strobilaceum and Kalidium foliatum associated bacterial communities was lower than that of Limonium gmelinii and Lycium ruthenicum communities. Furthermore, the composition of the bacterial communities of Halostachys caspica and Halocnemum strobilaceum was very different from those of Limonium gmelinii and Lycium ruthenicum. The diversity and community structure were influenced by soil EC, pH and nutrient content (TOC, SOM, TON and AP); of these, the effects of EC on bacterial community composition were less important than those of soil nutrients.

DISCUSSION

Halophytic plant species played an important role in shaping associated rhizosphere bacterial communities. When salinity levels were constant, soil nutrients emerged as key factors structuring bacterial communities, while EC played only a minor role. Pairwise differences among the rhizobacterial communities associated with different plant species were not significant, despite some evidence of differentiation. Further studies involving more halophyte species, and individuals per species, are necessary to elucidate plant species identity effects on the rhizosphere for co-occurring halophytes.

Metatranscriptome Analysis Deciphers Multifunctional Genes and Enzymes Linked With the Degradation of Aromatic Compounds and Pesticides in the Wheat Rhizosphere

Agricultural soils are becoming contaminated with synthetic chemicals like polyaromatic compounds, petroleum hydrocarbons, polychlorinated biphenyls (PCBs), phenols, herbicides, insecticides and fungicides due to excessive dependency of crop production systems on the chemical inputs. Microbial degradation of organic pollutants in the agricultural soils is a continuous process due to the metabolic multifunctionalities and enzymatic capabilities of the soil associated communities. The plant rhizosphere with its complex microbial inhabitants and their multiple functions, is amongst the most live and dynamic component of agricultural soils. We analyzed the metatranscriptome data of 20 wheat rhizosphere samples to decipher the taxonomic microbial communities and their multifunctionalities linked with the degradation of organic soil contaminants. The analysis revealed a total of 21 different metabolic pathways for the degradation of aromatic compounds and 06 for the xenobiotics degradation. Taxonomic annotation of wheat rhizosphere revealed bacteria, especially the Proteobacteria, actinobacteria, firmicutes, bacteroidetes, and cyanobacteria, which are shown to be linked with the degradation of aromatic compounds as the dominant communities. Abundance of the transcripts related to the degradation of aromatic amin compounds, carbazoles, benzoates, naphthalene, ketoadipate pathway, phenols, biphenyls and xenobiotics indicated abundant degradation capabilities in the soils. The results highlighted a potentially dominant role of crop rhizosphere associated microbial communities in the remediation of contaminant aromatic compounds.