Desert plant bacteria reveal host influence and beneficial plant growth properties

From trade-off to synergy: microbial insights into enhancing plant growth and immunity

The reduction in crop yield caused by pathogens and pests presents a significant challenge to global food security. Genetic engineering, which aims to bolster plant defence mechanisms, emerges as a cost-effective solution for disease control. However, this approach often incurs a growth penalty, known as the growth-defence trade-off. The precise molecular mechanisms governing this phenomenon are still not completely understood, but they generally fall under two main hypotheses: a "passive" redistribution of metabolic resources, or an "active" regulatory choice to optimize plant fitness. Despite the knowledge gaps, considerable practical endeavours are in the process of disentangling growth from defence. The plant microbiome, encompassing both above- and below-ground components, plays a pivotal role in fostering plant growth and resilience to stresses. There is increasing evidence which indicates that plants maintain intimate associations with diverse, specifically selected microbial communities. Meta-analyses have unveiled well-coordinated, two-way communications between plant shoots and roots, showcasing the capacity of plants to actively manage their microbiota for balancing growth with immunity, especially in response to pathogen incursions. This review centers on successes in making use of specific root-associated microbes to mitigate the growth-defence trade-off, emphasizing pivotal advancements in unravelling the mechanisms behind plant growth and defence. These findings illuminate promising avenues for future research and practical applications.

Plant-parasitic nematode research in the arid desert landscape: a systematic review of challenges and bridging interventions

Plant-parasitic nematode research in the Middle East and North Africa (MENA) region faces significant challenges rooted in a need for proper assembly, diversity, and a unified and purpose-driven framework. This led to exacerbating their detrimental effects on crop production. This systematic review addresses the current situation and challenges that require targeted interventions to sustainably manage plant-parasitic nematodes and reduce their detrimental impact on agriculture production in the MENA region. We analyzed the nematode-related research conducted within the region over the past three decades to assess available resources and promote diverse research approaches beyond basic morphology-focused surveys. We show that crops are attacked by a diverse spectrum of plant-parasitic nematodes that exceed the global economic threshold limits. In particular, Meloidogyne species exceed the threshold limit by 8 - 14-fold, with a 100% frequency of occurrence in the collected soil samples, posing a catastrophic threat to crop production and the economy. We highlight detrimental agriculture practices in the MENA region, such as transferring soil from established fields to barren land, which enhances the dissemination of plant-parasitic nematodes, disrupting soil ecology and causing significant agricultural challenges in newly cultivated areas. Looking into the behavior of farmers, raising awareness must be accompanied by available solutions, as more practical alternatives are needed to gain the confidence of the farmers. We propose integrating microbial-based products and soil development practices in hygienic farming as resilient and sustainable solutions for nematode management. Increased emphasis is required to diversify the nematode-related research areas to bridge the gaps and facilitate the transition from fundamental knowledge to practical solutions. A cohesive network of nematologists and collaboration with national and international entities is crucial for exchanging knowledge related to legislation against invasive species.

Unveiling the influence of salinity on bacterial microbiome assembly of halophytes and crops

BACKGROUND

Climate change and anthropogenic activities intensify salinity stress impacting significantly on plant productivity and biodiversity in agroecosystems. There are naturally salt-tolerant plants (halophytes) that can grow and withstand such harsh conditions. Halophytes have evolved along with their associated microbiota to adapt to hypersaline environments. Identifying shared microbial taxa between halophyte species has rarely been investigated. We performed a comprehensive meta-analysis using the published bacterial 16S rRNA gene sequence datasets to untangle the rhizosphere microbiota structure of two halophyte groups and non-halophytes. We aimed for the identification of marker taxa of plants being adapted to a high salinity using three independent approaches.

RESULTS

Fifteen studies met the selection criteria for downstream analysis, consisting of 40 plants representing diverse halophyte and non-halophyte species. Microbiome structural analysis revealed distinct compositions for halophytes that face high salt concentrations in their rhizosphere compared to halophytes grown at low salt concentrations or from non-halophytes. For halophytes grown at high salt concentrations, we discovered three bacterial genera that were independently detected through the analysis of the core microbiome, key hub taxa by network analysis and random forest analysis. These genera were Thalassospira, Erythrobacter, and Marinobacter.

CONCLUSIONS

Our meta-analysis revealed that salinity level is a critical factor in affecting the rhizosphere microbiome assembly of plants. Detecting marker taxa across high-halophytes may help to select Bacteria that might improve the salt tolerance of non-halophytic plants.

Current Advances in the Functional Diversity and Mechanisms Underlying Endophyte-Plant Interactions

Plant phenotype is a complex entity largely controlled by the genotype and various environmental factors. Importantly, co-evolution has allowed plants to coexist with the biotic factors in their surroundings. Recently, plant endophytes as an external plant phenotype, forming part of the complex plethora of the plant microbial assemblage, have gained immense attention from plant scientists. Functionally, endophytes impact the plant in many ways, including increasing nutrient availability, enhancing the ability of plants to cope with both abiotic and biotic stress, and enhancing the accumulation of important plant secondary metabolites. The current state of research has been devoted to evaluating the phenotypic impacts of endophytes on host plants, including their direct influence on plant metabolite accumulation and stress response. However, there is a knowledge gap in how genetic factors influence the interaction of endophytes with host plants, pathogens, and other plant microbial communities, eventually controlling the extended microbial plant phenotype. This review will summarize how host genetic factors can impact the abundance and functional diversity of the endophytic microbial community, how endophytes influence host gene expression, and the host-endophyte-pathogen disease triangle. This information will provide novel insights into how breeders could specifically target the plant-endophyte extended phenotype for crop improvement.

Harnessing rhizospheric core microbiomes from arid regions for enhancing date palm resilience to climate change effects

Date palm cultivation has thrived in the Gulf Cooperation Council region since ancient times, where it represents a vital sector in agricultural and socio-economic development. However, climate change conditions prevailing for decades in this area, next to rarefication of rain, hot temperatures, intense evapotranspiration, rise of sea level, salinization of groundwater, and intensification of cultivation, contributed to increase salinity in the soil as well as in irrigation water and to seriously threaten date palm cultivation sustainability. There are also growing concerns about soil erosion and its repercussions on date palm oases. While several reviews have reported on solutions to sustain date productivity, including genetic selection of suitable cultivars for the local harsh environmental conditions and the implementation of efficient management practices, no systematic review of the desertic plants' below-ground microbial communities and their potential contributions to date palm adaptation to climate change has been reported yet. Indeed, desert microorganisms are expected to address critical agricultural challenges and economic issues. Therefore, the primary objectives of the present critical review are to (1) analyze and synthesize current knowledge and scientific advances on desert plant-associated microorganisms, (2) review and summarize the impacts of their application on date palm, and (3) identify possible gaps and suggest relevant guidance for desert plant microbes' inoculation approach to sustain date palm cultivation within the Gulf Cooperation Council in general and in Qatar in particular.

High-throughput sequencing reveals the structure and metabolic resilience of desert microbiome confronting climate change

Introduction

Desert ecosystems harbor a unique microbial diversity that is crucial for ecological stability and biogeochemical cycles. An in-depth understanding of the biodiversity, compositions, and functions of these microbial communities is imperative to navigate global changes and confront potential threats and opportunities applicable to agricultural ecosystems amid climate change.

Methods

This study explores microbial communities in the rhizosphere and endosphere of desert plants native to the Arabian Peninsula using next-generation sequencing of the 16S rRNA gene (V3-V4 hypervariable region).

Results

Our results reveal that each microbial community has a diverse and unique microbial composition. Based on alpha and beta diversity indices, the rhizosphere microbiome is significantly diverse and richer in microbial taxa compared to the endosphere. The data reveals a shift towards fast-growing microbes with active metabolism, involvement in nutrient cycling, nitrogen fixation, and defense pathways. Our data reveals the presence of habitat-specific microbial communities in the desert, highlighting their remarkable resilience and adaptability to extreme environmental conditions. Notably, we observed the existence of radiation-resistant microbes such as Deinococcus radiotolerans, Kocuria sp., and Rubrobacter radiotolerans which can tolerate high levels of ionizing radiation. Additionally, examples of microbes exhibiting tolerance to challenging conditions include Nocardioides halotolerans, thriving in high-salinity environments, and hyperthermophilic microbes such as Quasibacillus thermotolerans. Moreover, functional analysis reveals enrichment in chaperon biosynthesis pathways associated with correct protein folding under heat stress conditions.

Discussion

Our research sheds light on the unique diversity of desert microbes and underscores their potential applications to increase the resilience of agriculture ecosystems, offering a promising strategy to fortify crops against the challenges posed by climate change, ultimately supporting sustainable food production for our ever-expanding global population.

Horizon scanning the application of probiotics for wildlife

The provision of probiotics benefits the health of a wide range of organisms, from humans to animals and plants. Probiotics can enhance stress resilience of endangered organisms, many of which are critically threatened by anthropogenic impacts. The use of so-called 'probiotics for wildlife' is a nascent application, and the field needs to reflect on standards for its development, testing, validation, risk assessment, and deployment. Here, we identify the main challenges of this emerging intervention and provide a roadmap to validate the effectiveness of wildlife probiotics. We cover the essential use of inert negative controls in trials and the investigation of the probiotic mechanisms of action. We also suggest alternative microbial therapies that could be tested in parallel with the probiotic application. Our recommendations align approaches used for humans, aquaculture, and plants to the emerging concept and use of probiotics for wildlife.

A plant's perception of growth-promoting bacteria and their metabolites

Many recent studies have highlighted the importance of plant growth-promoting (rhizo)bacteria (PGPR) in supporting plant's development, particularly under biotic and abiotic stress. Most focus on the plant growth-promoting traits of selected strains and the latter's effect on plant biomass, root architecture, leaf area, and specific metabolite accumulation. Regarding energy balance, plant growth is the outcome of an input (photosynthesis) and several outputs (i.e., respiration, exudation, shedding, and herbivory), frequently neglected in classical studies on PGPR-plant interaction. Here, we discuss the primary evidence underlying the modifications triggered by PGPR and their metabolites on the plant ecophysiology. We propose to detect PGPR-induced variations in the photosynthetic activity using leaf gas exchange and recommend setting up the correct timing for monitoring plant responses according to the specific objectives of the experiment. This research identifies the challenges and tries to provide future directions to scientists working on PGPR-plant interactions to exploit the potential of microorganisms' application in improving plant value.

Enhancing climate change resilience in agricultural crops

Climate change threatens global food and nutritional security through negative effects on crop growth and agricultural productivity. Many countries have adopted ambitious climate change mitigation and adaptation targets that will exacerbate the problem, as they require significant changes in current agri-food systems. In this review, we provide a roadmap for improved crop production that encompasses the effective transfer of current knowledge into plant breeding and crop management strategies that will underpin sustainable agriculture intensification and climate resilience. We identify the main problem areas and highlight outstanding questions and potential solutions that can be applied to mitigate the impacts of climate change on crop growth and productivity. Although translation of scientific advances into crop production lags far behind current scientific knowledge and technology, we consider that a holistic approach, combining disciplines in collaborative efforts, can drive better connections between research, policy, and the needs of society.

The Composition and Diversity of the Rhizosphere Bacterial Community of Ammodendron bifolium Growing in the Takeermohuer Desert Are Different from Those in the Nonrhizosphere

Soil microorganisms play important roles in vegetation establishment and soil biogeochemical cycling. Ammodendron bifolium is a dominant sand-fixing (i.e., stabilizing sand dunes) and endangered plant in the Takeermohuer Desert, and the bacterial community associated with this plant rhizosphere is still unclear. In this study, we investigated the composition and diversity of the bacterial community from the A. bifolium rhizosphere and bulk soil at different soil depths (i.e., 0-40 cm, 40-80 cm, 80-120 cm) using culture and high-throughput sequencing methods. We preliminarily analyzed the edaphic factors influencing the structure of bacterial communities. The results showed that the high-salinity Takeermohuer Desert has an oligotrophic environment, while the A. bifolium rhizosphere exhibited a relatively nutrient-rich environment due to higher contents of soil organic matter (SOM) and soil alkaline nitrogen (SAN) than bulk soil. The dominant bacterial groups in the desert were Actinobacteria (39.8%), Proteobacteria (17.4%), Acidobacteria (10.2%), Bacteroidetes (6.3%), Firmicutes (6.3%), Chloroflexi (5.6%), and Planctomycetes (5.0%) at the phylum level. However, the relative abundances of Proteobacteria (20.2%) and Planctomycetes (6.1%) were higher in the rhizosphere, and those of Firmicutes (9.8%) and Chloroflexi (6.9%) were relatively higher in barren bulk soil. A large number of Actinobacteria were detected in all soil samples, of which the most abundant genera were Streptomyces (5.4%) and Actinomadura (8.2%) in the bulk soil and rhizosphere, respectively. The Chao1 and PD_whole_tree indices in the rhizosphere soil were significantly higher than those in the bulk soil at the same soil depth and tended to decrease with increasing soil depth. Co-occurrence network analyses showed that the keystone species in the Takeermohuer Desert were the phyla Actinobacteria, Acidobacteria, Proteobacteria, and Chloroflexi. Furthermore, the major edaphic factors affecting the rhizosphere bacterial community were electrical conductivity (EC), SOM, soil total nitrogen (STN), SAN, and soil available potassium (SAK), while the major edaphic factors affecting the bacterial community in bulk soil were distance and ratio of carbon to nitrogen (C/N). We concluded that the A. bifolium rhizosphere bacterial community is different from that of the nonrhizosphere in composition, structure, diversity, and driving factors, which may improve our understanding of the relationship between plant and bacterial communities and lay a theoretical foundation for A. bifolium species conservation in desert ecosystems.

Response of total belowground soil biota in Alhagi sparsifolia monoculture at different soil vertical profiles in desert ecosystem

The soil organisms are extremely important for the land-based ecosystem. There is a growing interest in studying the variety and composition of the entire underground soil organism community at a large ecological scale. Soil organisms show different patterns in relation to soil physiochemical properties (SPPs) in various ecosystems. However, there is limited knowledge regarding their response to soil vertical profiles (SVPs) in monoculture of Alhagi sparsifolia, which is the primary shrub in the deserts of China, and is well-known for its contributions to sand dune stabilization, traditional Chinese medicine, and forage. Here, we investigated the population dynamics of soil bacteria, fungi, archaea, protists and metazoa across six different SVPs ranging from 0 to 100 cm in monoculture of A. sparsifolia, in its natural desert ecosystem. Our findings indicate that the soil biota communities displayed a declining pattern in the alpha diversity of bacteria, protists, and metazoa with an increase in soil depth. However, the opposite trend was observed for fungi and archaea. The beta diversity of soil biota was significantly affected by SVPs, particularly for metazoa, fungi and protists as revealed by Non-Metric Dimensional Scaling. The most prevalent soil bacterial, fungal, archaeal, protist, and metazoa classes were Actinobacteria, Sordariomycetes, Nitrososphaeria, Filosa-Sarcomonadea, and Nematoda, respectively. The correlation among vertical distribution of the most abundant biotic communities and variations in SPPs exhibited that the variations in total carbon (TC) and total nitrogen (TN) had the most significant influence on bacterial changes, while available potassium (AK) had an impact on fungi. Archaea were affected by TC and pH, protists by the C/N-Ratio and TP, and metazoa by TN, AK, and soil water capacity (SWC). Collectively, our findings provide a new perspective on the vertical distribution and distinct response patterns of soil biota in A. sparsifolia monoculture under natural desert ecosystem of China.

Composition and Distribution Characteristics of Rhizosphere Bacterial Community of Ammodendron bifolium Growing in Takeermohuer Desert Are Different from Those in Non-rhizosphere

Soil microorganisms play important roles in vegetation establishment and soil biogeochemical cycling. Ammodendron bifolium is a dominant sand-fixing and endangered plant in Takeermohuer Desert, and bacterial community associated with this plant rhizosphere is still unclear. In this study, we studied the composition and diversity of bacterial community from A. bifolium rhizosphere and bulk soil at different soil depths (i.e., 0-40 cm, 40-80 cm, 80-120 cm) using traditional bacterial isolation and high-throughput sequencing approaches, and preliminarily analyzed the edaphic factors influencing the structure of bacterial communities. Results showed that Takeermohuer Desert with high salinity has been an oligotrophic environment, while the rhizosphere exhibited eutrophication resulting from high content SOM (soil organic matter) and SAN (soil alkaline nitrogen) compared with bulk soil. The dominant bacterial groups in the desert were Actinobacteria (39.8%), Proteobacteria (17.4%), Acidobacteria (10.2%), Bacteroidetes (6.3%), Firmicutes (6.3%), Chloroflexi (5.6%), and Planctomycetes (5.0%) at the phyla level. However, the relative abundances of Proteobacteria (20.2%) and Planctomycetes (6.1%) were higher in eutrophic rhizosphere, and Firmicutes (9.8%) and Chloroflexi (6.9%) relatively higher in barren bulk soil. A large number of Actinobacteria were detected in all soil samples, of which the most abundant genus was Streptomyces (5.4%) and Actinomadura (8.2%) in the bulk soil and rhizosphere, respectively. The Chao1 and PD indexes in rhizosphere were significantly higher than those in bulk soil at the same soil depth, and tended to decrease with increasing soil depth. Co-occurrence network analyses showed that the keystone species in Takeermohuer Desert were Actinobacteria, Acidobacteria, Proteobacteria, and Chlorofexi. Furthermore, the major environmental factors affecting rhizosphere bacterial community were EC (electrical conductivity), SOM, STN (soil total nitrogen), SAN, and SAK (soil available potassium), while bulk soil were distance and C/N (STC/STN). We concluded that A. bifolium rhizosphere bacterial community is different from non-rhizosphere in composition, distribution, and environmental influencing factors, which will have important significances for understanding their ecological functions and maintaining biodiversity.

Engineering the Maize Root Microbiome: A Rapid MoClo Toolkit and Identification of Potential Bacterial Chassis for Studying Plant-Microbe Interactions

Sustainably enhancing crop production is a global necessity to meet the escalating demand for staple crops while sustainably managing their associated carbon/nitrogen inputs. Leveraging plant-associated microbiomes is a promising avenue for addressing this demand. However, studying these communities and engineering them for sustainable enhancement of crop production have remained a challenge due to limited genetic tools and methods. In this work, we detail the development of the Maize Root Microbiome ToolKit (MRMTK), a rapid Modular Cloning (MoClo) toolkit that only takes 2.5 h to generate desired constructs (5400 potential plasmids) that replicate and express heterologous genes in Enterobacter ludwigii strain AA4 (Elu), Pseudomonas putida strain AA7 (Ppu), Herbaspirillum robiniae strain AA6 (Hro), Stenotrophomonas maltophilia strain AA1 (Sma), and Brucella pituitosa strain AA2 (Bpi), which comprise a model maize root synthetic community (SynCom). In addition to these genetic tools, we describe a highly efficient transformation protocol (107-109 transformants/μg of DNA) 1 for each of these strains. Utilizing this highly efficient transformation protocol, we identified endogenous Expression Sequences (ES; promoter and ribosomal binding sites) for each strain via genomic promoter trapping. Overall, MRMTK is a scalable and adaptable platform that expands the genetic engineering toolbox while providing a standardized, high-efficiency transformation method across a diverse group of root commensals. These results unlock the ability to elucidate and engineer plant-microbe interactions promoting plant growth for each of the 5 bacterial strains in this study.

Complete genome sequence analysis of plant growth-promoting bacterium, Isoptericola sp. AK164 isolated from the rhizosphere of Avicennia marina growing at the Red Sea coast

Isoptericola sp. AK164 is a Gram-positive, aerobic bacterial genus from the family Promicromonosporaceae, isolated from the root rhizosphere of Avicennia marina. AK164 significantly enhanced the growth of the Arabidopsis thaliana plant under normal and saline conditions. These bacteria can produce ACC deaminase and several enzymes playing a role in carbohydrate hydrolyses, such as cellulose, hemicellulose, and chitin degradation, which may contribute to plant growth, salt tolerance, and stress elevation. The genome sequence AK164 has a single circular chromosome of approximately 3.57 Mbp with a GC content of 73.53%. A whole genome sequence comparison of AK164 with type strains from the same genus, using digital DNA-DNA hybridization and average nucleotide identity calculations, revealed that AK164 might potentially belong to a new species of Isoptericola. Genome data and biochemical analyses indicate that AK164 could be a potential biostimulant for improving agriculture in submerged saline land.

The Role of Plant Growth-Promoting Microorganisms (PGPMs) and Their Feasibility in Hydroponics and Vertical Farming

There are many reasons for the increase in hydroponics/soil-free systems in agriculture, and these systems have now advanced to the form of vertical farming. The sustainable use of space, the reduction in water use compared to soil-based agriculture, the lack of pesticides, the ability to control nutrient inputs, and the implementation of user-friendly technology for environmental control and harvesting are all factors that have made the global market for vertical farming predicted to reach more than USD 10.02 billion by 2027. By comparison, soil-based agriculture consumes 20 times more water, and some agricultural practices promote soil deterioration and cause environmental pollution. Plant growth-promoting microorganisms (PGPMs) have been used extensively in traditional agriculture to enhance plant growth, environmental stress tolerance, and the efficacy of phytoremediation in soil-based farming. Due to the controlled atmosphere in hydroponics and vertical farms, there is strong potential to maximize the use of PGPMs. Here, we review the leveraging of plant growth-promoting microorganism mechanisms in hydroponics and vertical farming. We recommend a synchronized PGPM treatment using a biostimulant extract added to the hydroponic medium while also pre-treating seeds or seedlings with a microbial suspension for aquaponic and aeroponic systems.

Microbiome of Citrullus colocynthis (L.) Schrad. Reveals a Potential Association with Non-Photosynthetic Cyanobacteria

Citrullus colocynthis grows in the sandy desert soil of the Arabian Peninsula with limited access to water, aside from occasional precipitation or dew. Understanding its ability to produce water-filled fruit and nutrient-rich seeds despite the harsh environment, can be useful for agricultural applications. However, information regarding the microbiome of C. colocynthis is lacking. We hypothesized that C. colocynthis associates with bacteria that aid its survival, like what has been observed in other desert plants. Here, we used 16S rRNA gene data to gain insight into the microbiome of C. colocynthis to identify its associated bacteria. In total, 9818 and 6983 OTUs were generated from root, soil, and leaf samples combined. Overall, bulk soils had the highest alpha diversity, followed by rhizosphere and root zone soils. Furthermore, C. colocynthis is associated with known plant-growth-promoting bacteria (including Acidobacteria, Bacterioidetes, and Actinobacteria), and interestingly a class of non-photosynthetic Cyanobacteria (Melainabacteria) that is more abundant on the inside and outside of the root surface than control samples, suggesting its involvement in the rhizophagy process. This study will provide a foundation for functional studies to further understand how C. colocynthis-microbes interactions help them grow in the desert, paving the path for possible agricultural applications.

Polyketides with IDH1 R132h and PTP1B inhibitory activities from the desert-plant-derived fungus Alternaria sp. HM 134

Five new polyketides named alternafurones A (1) and B (2), alternapyrones M-O (3–5), together with fourteen known ones (6–19), were isolated from the desert-plant-derived fungus Alternaria sp. HM 134. The structures of the new compounds were elucidated from spectroscopic data and ECD spectroscopic analyses. Alternafurones A and B represent polyketides with an unprecedented 6/5/6 skeleton core. Compounds 1, 2 and 4 showed definite inhibitory activities against isocitrate dehydrogenase 1 gene (IDH1 R132h) with IC₅₀ values of 29.38, 19.41 and 14.14 μg/ml, respectively. Seven compounds (6, 7, 9–12, 14) showed potent protein tyrosine phosphatase 1B (PTP1B) inhibitory activity with IC₅₀ values ranging from 0.97 μg/ml to 89.80 μg/ml.

Synthetic bacterial community derived from a desert rhizosphere confers salt stress resilience to tomato in the presence of a soil microbiome

The root bacterial microbiome is important for the general health of the plant. Additionally, it can enhance tolerance to abiotic stresses, exemplified by plant species found in extreme ecological niches like deserts. These complex microbe-plant interactions can be simplified by constructing synthetic bacterial communities or SynComs from the root microbiome. Furthermore, SynComs can be applied as biocontrol agents to protect crops against abiotic stresses such as high salinity. However, there is little knowledge on the design of a SynCom that offers a consistent protection against salt stress for plants growing in a natural and, therefore, non-sterile soil which is more realistic to an agricultural setting. Here we show that a SynCom of five bacterial strains, originating from the root of the desert plant Indigofera argentea, protected tomato plants growing in a non-sterile substrate against a high salt stress. This phenotype correlated with the differential expression of salt stress related genes and ion accumulation in tomato. Quantification of the SynCom strains indicated a low penetrance into the natural soil used as the non-sterile substrate. Our results demonstrate how a desert microbiome could be engineered into a simplified SynCom that protected tomato plants growing in a natural soil against an abiotic stress.

Microbial Metabolites Beneficial to Plant Hosts Across Ecosystems

Plants are intimately connected with their associated microorganisms. Chemical interactions via natural products between plants and their microbial symbionts form an important aspect in host health and development, both in aquatic and terrestrial ecosystems. These interactions range from negative to beneficial for microbial symbionts as well as their hosts. Symbiotic microbes synchronize their metabolism with their hosts, thus suggesting a possible coevolution among them. Metabolites, synthesized from plants and microbes due to their association and coaction, supplement the already present metabolites, thus promoting plant growth, maintaining physiological status, and countering various biotic and abiotic stress factors. However, environmental changes, such as pollution and temperature variations, as well as anthropogenic-induced monoculture settings, have a significant influence on plant-associated microbial community and its interaction with the host. In this review, we put the prominent microbial metabolites participating in plant-microbe interactions in the natural terrestrial and aquatic ecosystems in a single perspective and have discussed commonalities and differences in these interactions for adaptation to surrounding environment and how environmental changes can alter the same. We also present the status and further possibilities of employing chemical interactions for environment remediation. Our review thus underlines the importance of ecosystem-driven functional adaptations of plant-microbe interactions in natural and anthropogenically influenced ecosystems and their possible applications.

Rhizosphere Microbial Community Diversity and Function Analysis of Cut Chrysanthemum During Continuous Monocropping

As an ornamental flower crop, the long-term continuous monocropping of cut chrysanthemum causes frequent occurrence of diseases, seriously affecting the quality of cut chrysanthemum. The rhizosphere microbial community plays an important role in maintaining the healthy growth of plants, whereas the composition and dynamics of rhizosphere microbial community under continuous monocropping of cut chrysanthemum have not been fully revealed. In this study, the Illumina MiSeq high-throughput sequencing platform was used to monitor the dynamic changes of rhizosphere microbial communities in four varieties of cut chrysanthemum during 0–3 years of monocropping, and the soil physicochemical properties were also determined. Results showed that continuous monocropping significantly increased the fungal community richness and altered the profiles of the bacterial and fungal communities, leading to variation of community beta-diversity. With the increase of continuous cropping time, biocontrol bacteria decreased, while some plant pathogenic fungi were enriched in the rhizosphere of cut chrysanthemum. FAPROTAX-based functional prediction showed that the abundance of gene related to nitrogen and sulfur metabolism and chitin lysis was reduced in the rhizosphere of cut chrysanthemum. FUNGuild-based fungal function prediction showed that plant pathogenic fungal taxa were increasing in the rhizosphere of cut chrysanthemum, mainly Acremonium, Plectosphaerellaceae, Fusarium, and Cladosporium. Continuous cropping also reduced the content of ammonium nitrogen and increased soil salinity, resulting in deterioration of soil physical and chemical properties, which, together with the transformation of rhizosphere microbial community, became part of the reasons for the continuous cropping obstacle of cut chrysanthemum.

Succession of soil bacterial community along a 46-year choronsequence artificial revegetation in an arid oasis-desert ecotone

How the bacterial community structure and potential metabolic functions will change after revegetation in arid desert ecosystems is still unknown. We used high-throughput pyrosequencing to explore changes in soil bacterial diversity, structure and metabolic pathways, and the key driving factors along a chronosequence of 46-year Haloxylon ammodendron revegetation in an oasis-desert ecotone in the northwestern China. Our results indicated that establishment of H. ammodendron on shifting sand dunes significantly changed the structure of bacterial communities and increased their diversity and richness. The main dominant phyla were Actinobacteria (32.1-41.3%) and Proteobacteria (19.2-27.0%); in that, α-Proteobacteria (16.4-20.7%) were the most abundant Proteobacteria. Kocuria coexisted at different succession stage after year 0, and their relative abundance ranged from 3.8-9.0%. Principal coordinates analysis (PCoA) showed that bacterial community from the same revegetation site grouped together and generally separated from each other, indicating that significant shifts in bacterial community structure occurred after revegetation. LEfSe analysis identified unique biomarkers in the soil samples from seven sites. Moreover, PICRUSt analysis indicated similar overall patterns of metabolic pathways in different succession stage. Redundancy analysis (RDA) showed that total carbon, pH and total phosphorus were major abiotic factors driving the structure of bacterial communities, which explained 57.5% of the variation in bacterial communities. Our findings advance the current understanding of plant-soil interactions in the processes of ecological restoration and desertification reversal.

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.

Endophytic Bacteria Colonizing the Petiole of the Desert Plant Zygophyllum dumosum Boiss: Possible Role in Mitigating Stress

Zygophyllum dumosum is a dominant shrub in the Negev Desert whose survival is accomplished by multiple mechanisms including abscission of leaflets to reduce whole plant transpiration while leaving the fleshy, wax-covered petioles alive but dormant during the dry season. Petioles that can survive for two full growing seasons maintain cell component integrity and resume metabolic activity at the beginning of the winter. This remarkable survival prompted us to investigate endophytic bacteria colonizing the internal tissues of the petiole and assess their role in stress tolerance. Twenty-one distinct endophytes were isolated by culturing from surface-sterile petioles and identified by sequencing of the 16S rDNA. Sequence alignments and the phylogenetic tree clustered the isolated endophytes into two phyla, Firmicutes and Actinobacteria. Most isolated endophytes displayed a relatively slow growth on nutrient agar, which was accelerated by adding petiole extracts. Metabolic analysis of selected endophytes showed several common metabolites whose level is affected by petiole extract in a species-dependent manner including phosphoric acid, pyroglutamic acid, and glutamic acid. Other metabolites appear to be endophyte-specific metabolites, such as proline and trehalose, which were implicated in stress tolerance. These results demonstrate the existence of multiple endophytic bacteria colonizing Z. dumosum petioles with the potential role in maintaining cell integrity and functionality via synthesis of multiple beneficial metabolites that mitigate stress and contribute to stress tolerance.

Shared features and reciprocal complementation of the Chlamydomonas and Arabidopsis microbiota

Microscopic algae release organic compounds to the region immediately surrounding their cells, known as the phycosphere, constituting a niche for colonization by heterotrophic bacteria. These bacteria take up algal photoassimilates and provide beneficial functions to their host, in a process that resembles the establishment of microbial communities associated with the roots and rhizospheres of land plants. Here, we characterize the microbiota of the model alga Chlamydomonas reinhardtii and reveal extensive taxonomic and functional overlap with the root microbiota of land plants. Using synthetic communities derived from C. reinhardtii and Arabidopsis thaliana, we show that phycosphere and root bacteria assemble into taxonomically similar communities on either host. We show that provision of diffusible metabolites is not sufficient for phycosphere community establishment, which additionally requires physical proximity to the host. Our data suggest the existence of shared ecological principles driving the assembly of the A. thaliana root and C. reinhardtii phycosphere microbiota, despite the vast evolutionary distance between these two photosynthetic organisms.

Coordinated bacterial and plant sulfur metabolism in Enterobacter sp. SA187-induced plant salt stress tolerance

Although plant growth–promoting bacteria (PGPB) enhance the performance of plants, only a few mechanisms have been identified so far. We show that the sulfur metabolisms in both PGPB Enterobacter sp. SA187 and Arabidopsis plants play a key role in plant salt stress tolerance. Salt stress induces a sulfur starvation response in plants that is attenuated by SA187. Arabidopsis sulfur metabolic mutants are hypersensitive to salt stress but can be rescued by SA187. Most plant sulfur metabolism occurs in chloroplasts and is linked to stress-induced accumulation of reactive oxygen species that is suppressed by SA187. This work reveals that plant salt stress tolerance requires the coordinated regulation of the sulfur metabolic pathways in both beneficial microbe and host plant.

Enterobacter sp. SA187 is a root endophytic bacterium that maintains growth and yield of plants under abiotic stress conditions. In this work, we compared the metabolic wirings of Arabidopsis and SA187 in the free-living and endophytic interaction states. The interaction of SA187 with Arabidopsis induced massive changes in bacterial gene expression for chemotaxis, flagellar biosynthesis, quorum sensing, and biofilm formation. Besides modification of the bacterial carbon and energy metabolism, various nutrient and metabolite transporters and the entire sulfur pathway were up-regulated. Under salt stress, Arabidopsis resembled plants under sulfate starvation but not when colonized by SA187, which reprogramed the sulfur regulon of Arabidopsis. In accordance, salt hypersensitivity of multiple Arabidopsis sulfur metabolism mutants was partially or completely rescued by SA187 as much as by the addition of sulfate, L-cysteine, or L-methionine. Many components of the sulfur metabolism that are localized in the chloroplast were partially rescued by SA187. Finally, salt-induced accumulation of reactive oxygen species as well as the hypersensitivity of LSU mutants were suppressed by SA187. LSUs encode a central regulator linking sulfur metabolism to chloroplast superoxide dismutase activity. The coordinated regulation of the sulfur metabolic pathways in both the beneficial microorganism and the host plant is required for salt stress tolerance in Arabidopsis and might be a common mechanism utilized by different beneficial microbes to mitigate the harmful effects of different abiotic stresses on plants.

Co-occurrence and patterns of phosphate solubilizing, salt and metal tolerant and antibiotic-resistant bacteria in diverse soils

Soil is a treasure chest for beneficial bacteria with applications in diverse fields, which include agriculture, rhizoremediation, and medicine. Metagenomic analysis of four soil samples identified Proteobacteria as the dominant phylum (32-52%) followed by the phylum Acidobacteria (11-21% in three out of four soils). Bacteria that were prevalent at the highest level belong to the genus Kaistobacter (8-19%). PICRUSt analysis predicted KEGG functional pathways associated with the metagenomes of the four soils. The identified pathways could be attributed to metal tolerance, antibiotic resistance and plant growth promotion. The prevalence of phosphate solubilizing bacteria (PSB) was investigated in four soil samples, ranging from 26 to 59% of the total culturable bacteria. The abundance of salt-tolerant and metal-tolerant bacteria showed considerable variation ranging from 1 to 62% and 4-69%, respectively. In comparison, the soil with the maximum prevalence of temperature-tolerant and antibiotic-resistant bacteria was close 30%. In this study, the common pattern observed was that PSB were the most abundant in all types of soils compared to other traits. Conversely, most of the isolates, which are salt-tolerant, copper-tolerant, and ampicillin-resistant, showed phosphate solubilization activity. The sequencing of the partial 16S-rRNA gene revealed that PSB belonged to Bacillus genera.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02904-7.

Rooting in the Desert: A Developmental Overview on Desert Plants

Plants, as sessile organisms, have evolved a remarkable developmental plasticity to cope with their changing environment. When growing in hostile desert conditions, plants have to grow and thrive in heat and drought. This review discusses how desert plants have adapted their root system architecture (RSA) to cope with scarce water availability and poor nutrient availability in the desert soil. First, we describe how some species can survive by developing deep tap roots to access the groundwater while others produce shallow roots to exploit the short rain seasons and unpredictable rainfalls. Then, we discuss how desert plants have evolved unique developmental programs like having determinate meristems in the case of cacti while forming a branched and compact root system that allows efficient water uptake during wet periods. The remote germination mechanism in date palms is another example of developmental adaptation to survive in the dry and hot desert surface. Date palms have also designed non-gravitropic secondary roots, termed pneumatophores, to maximize water and nutrient uptake. Next, we highlight the distinct anatomical features developed by desert species in response to drought like narrow vessels, high tissue suberization, and air spaces within the root cortex tissue. Finally, we discuss the beneficial impact of the microbiome in promoting root growth in desert conditions and how these characteristics can be exploited to engineer resilient crops with a greater ability to deal with salinity induced by irrigation and with the increasing drought caused by global warming.

Endophytic Bacteria from the Sahara Desert Protect Tomato Plants Against Botrytis cinerea Under Different Experimental Conditions

Bacteria endophytes are living microorganisms that live inside plant tissues without visible harmful symptoms, providing a mutualistic interaction. In this study, different bacterial endophytic strains were isolated from different plants primed to live in an arid area, namely, the Sahara Desert. Up to 27 of these strains were selected based on their ability to inhibit Botrytis cinerea growth in dual-culture assay and by bacterial volatiles. The results presented in this study show the capacity of most of the bacterial strains to protect Solanum lycopersicum against the pathogenic fungus B. cinerea, under different experimental conditions. Five of these strains induced susceptibility in tomato plants and no callose accumulation upon fungal infection, pointing to callose deposition as a protective mechanism mediated by endophytic bacteria. Moreover, there was a significant correlation between the bacterial strains inducing callose and the level of protection against B. cinerea. On the other hand, hormone production by bacteria does not explain the relationship between protection and the differences between the phenotypic results obtained in vitro and those obtained in plant experiments. Induced resistance is highly specific in the inducer-plant-stress interaction.

Complete Genome Sequence of Cellulomonas sp. JZ18, a Root Endophytic Bacterium Isolated from the Perennial Desert Tussock-Grass Panicum turgidum

Cellulomonas sp. JZ18 is a gram-positive, rod shaped bacterium that was previously isolated from the root endosphere of the perennial desert tussock-grass Panicum turgidum. Genome coverage of PacBio sequencing was approximately 199X. Genome assembly generated a single chromosome of 7,421,843 base pairs with a guanine-cytosine (GC) content of 75.60% with 3240 protein coding sequences, 361 pseudo genes, three ribosomal RNA operons, three non-coding RNAs and 45 transfer RNAs. Comparison of JZ18's genome with type strains from the same genus, using digital DNA-DNA hybridization and average nucleotide identity calculations, revealed that JZ18 might potentially belong to a new species. Functional analysis revealed the presence of genes that may complement previously observed biochemical and plant phenotypes. Furthermore, the presence of a number of enzymes could be of potential use in industrial processes as biocatalysts. Genome sequencing and analysis, coupled with comparative genomics, of endophytic bacteria for their potential plant growth promoting activities under different soil conditions will accelerate the knowledge and applications of biostimulants in sustainable agriculture.

Root endophyte induced plant thermotolerance by constitutive chromatin modification at heat stress memory gene loci

Global warming has become a critical challenge to food security, causing severe yield losses of major crops worldwide. Conventional and transgenic breeding strategies to enhance plant thermotolerance are laborious and expensive. Therefore, the use of beneficial microbes could be an alternative approach. Here, we report that the root endophyte Enterobacter sp. SA187 induces thermotolerance in wheat in the laboratory as well as in open-field agriculture. To unravel the molecular mechanisms, we used Arabidopsis thaliana as model plant. SA187 reprogramed the Arabidopsis transcriptome via HSFA2-dependent enhancement of H3K4me3 levels at heat stress memory gene loci. Unlike thermopriming, SA187-induced thermotolerance is mediated by ethylene signaling via the transcription factor EIN3. In contrast to the transient chromatin modification by thermopriming, SA187 induces constitutive H3K4me3 modification of heat stress memory genes, generating robust thermotolerance in plants. Importantly, microbial community composition of wheat plants in open-field agriculture is not influenced by SA187, indicating that beneficial microbes can be a powerful tool to enhance thermotolerance of crops in a sustainable manner.

Endophytic actinobacteria of a halophytic desert plant Pteropyrum olivieri: promising growth enhancers of sunflower

In the present study, 40 actinobacterial isolates were obtained from the roots of a desert plant, Pteropyrum olivieri and tested for extracellular hydrolytic enzyme activities, hydrogen cyanide, and siderophore production. Based on these activities, three isolates designated UTMC 2482, UTMC 2483, and UTMC 3136 were selected with an aim of developing bio-fertilizing agent to improve the growth of sunflower plants under normal conditions. The selected isolates showed 98.2, 98.4, and 100% similarities in the 16S rRNA gene sequences to Streptomyces chromofuscus, Streptomyces ambofaciens, and Streptomyces gardneri, respectively. These isolates exhibited indole acetic acid production while UTMC 2483 was found to produce 1-aminocyclopropane-1-carboxylate deaminase, as well. Sunflower seeds soaked in the bacterial spore suspensions increased the tolerance of sunflower seedlings to the stresses of salinity and water deficiency up to 270 mM of NaCl and - 2Mpa of PEG6000, respectively. Under normal conditions, inoculation with individual isolates and their consortia enhanced the yield (plant length, weight, and flower diameter) and biochemical contents (i.e. chlorophyll, protein, and oil) up to 5.3, 1.7, and 2.4 times higher than that of un-inoculated plants, significantly (p < 0.05) in greenhouse and field experiments. This is the first study demonstrating that endophytic actinobacteria from the desert plant, P. olivieri, have profound bio-fertilizing effects on the growth of sunflower.

Opposing effects of bacterial endophytes on biomass allocation of a wild donor and agricultural recipient

Root endophytes are a promising tool for increasing plant growth, but it is unclear whether they perform consistently across plant hosts. We characterized the blue grama (Bouteloua gracilis) root microbiome using two sequencing methods, quantified the effects of root endophytes in the original host (blue grama) and an agricultural recipient, corn (Zea mays), under drought and well-watered conditions and examined in vitro mechanisms for plant growth promotion. 16S rRNA amplicon sequencing revealed that the blue grama root microbiome was similar across an elevation gradient, with the exception of four genera. Culturing and Sanger sequencing revealed eight unique endophytes belonging to the genera Bacillus, Lysinibacillus and Pseudomonas. All eight endophytes colonized corn roots, but had opposing effects on aboveground and belowground biomass in each plant species: they increased blue grama shoot mass by 45% (19) (mean +/- SE) while decreasing corn shoot mass by 10% (19), and increased corn root:shoot by 44% (7), while decreasing blue grama root:shoot by 17% (7). Furthermore, contrary to our expectations, endophytes had stronger effects on plant growth under well-watered conditions rather than drought conditions. Collectively, these results suggest that ecological features, including host identity, bacterial traits, climate conditions and morphological outcomes, should be carefully considered in the design and implementation of agricultural inocula.

Pseudomonas stutzeri MJL19, a rhizosphere-colonizing bacterium that promotes plant growth under saline stress

AIMS

The aim of this study was to find and use rhizobacteria able to confer plants advantages to deal with saline conditions.

METHODS AND RESULTS

We isolated 24 different bacterial species from the rhizosphere of halophyte plants growing in Santiago del Estero, Argentina salt flat. Four strains were selected upon their ability to grow in salinity and their biochemical traits associated with plant growth promotion. Next, we tested the adhesion on soybean seeds surface and root colonization with the four selected isolates. Isolate 19 stood out from the rest and was selected for further experiments. This strain showed positive chemotaxis towards soybean root exudates and a remarkable ability to form biofilm both in vitro conditions and on soybean roots. Interestingly, this trait was enhanced in high saline conditions, indicating the extremely adapted nature of the bacterium to high salinity. In addition, this strain positively impacted on seed germination, plant growth and general plant health status also under saline stress.

CONCLUSIONS

A bacterium isolate with outstanding ability to promote seed germination and plant growth under saline conditions was found.

SIGNIFICANCE AND IMPACT OF THE STUDY

The experimental approach allowed us to find a suitable bacterial candidate for a biofertilizer intended to alleviate saline stress on crops. This would allow the use of soil now considered inadequate for agriculture and thus prevent further advancement of agriculture frontiers into areas of environmental value.

Nitrifying Microbes in the Rhizosphere of Perennial Grasses are Modified by Biological Nitrification Inhibition

Soil nitrification (microbial oxidation of ammonium to nitrate) can lead to nitrogen leaching and environmental pollution. A number of plant species are able to suppress soil nitrifiers by exuding inhibitors from roots, a process called biological nitrification inhibition (BNI). However, the BNI activity of perennial grasses in the nutrient-poor soils of Australia and the effects of BNI activity on nitrifying microbes in the rhizosphere microbiome have not been well studied. Here we evaluated the BNI capacity of bermudagrass (Cynodon dactylon L.), St. Augustinegrass (Stenotaphrum secundatum (Walt.) Kuntze), saltwater couch (Sporobolus virginicus), seashore paspalum (Paspalum vaginatum Swartz.), and kikuyu grass (Pennisetum clandestinum) compared with the known positive control, koronivia grass (Brachiaria humidicola). The microbial communities were analysed by sequencing 16S rRNA genes. St. Augustinegrass and bermudagrass showed high BNI activity, about 80 to 90% of koronivia grass. All the three grasses with stronger BNI capacities suppressed the populations of Nitrospira in the rhizosphere, a bacteria genus with a nitrite-oxidizing function, but not all of the potential ammonia-oxidizing archaea. The rhizosphere of saltwater couch and seashore paspalum exerted a weak recruitment effect on the soil microbiome. Our results demonstrate that BNI activity of perennial grasses played a vital role in modulating nitrification-associated microbial populations.

Screening of Bacterial Endophytes Able to Promote Plant Growth and Increase Salinity Tolerance

Bacterial endophytes can colonize plant tissues without harming the plant. Instead, they are often able to increase plant growth and tolerance to environmental stresses. In this work, new strains of bacterial endophytes were isolated from three economically important crop plants (sorghum, cucumber and tomato) grown in three different regions in soils with different management. All bacterial strains were identified by 16S rRNA sequencing and characterized for plant beneficial traits. Based on physiological activities, we selected eight strains that were further tested for their antibiotic resistance profile and for the ability to efficiently colonize the interior of sorghum plants. According to the results of the re-inoculation test, five strains were used to inoculate sorghum seeds. Then, plant growth promotion activity was assessed on sorghum plants exposed to salinity stress. Only two bacterial endophytes increased plant biomass, but three of them delayed or reduced plant salinity stress symptoms. These five strains were then characterized for the ability to produce the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase, which is involved in the increase of stress tolerance. Pseudomonas brassicacearum SVB6R1 was the only strain that was able to produce this enzyme, suggesting that ACC deaminase is not the only physiological trait involved in conferring plant tolerance to salt stress in these bacterial strains.

Climatic Aridity Gradient Modulates the Diversity of the Rhizosphere and Endosphere Bacterial Microbiomes of Opuntia ficus-indica

Recent microbiome research has shown that soil fertility, plant-associated microbiome, and crop production can be affected by abiotic environmental parameters. The effect of aridity gradient on rhizosphere-soil (rhizosphere) and endosphere-root (endosphere) prokaryotic structure and diversity associated with cacti remain poorly investigated and understood. In the current study, next-generation sequencing approaches were used to characterize the diversity and composition of bacteria and archaea associated with the rhizosphere and endosphere of Opuntia ficus-indica spineless cacti in four bioclimatic zones (humid, semi-arid, upper-arid, and lower-arid) in Tunisia. Our findings showed that bacterial and archaeal cactus microbiomes changed in inside and outside roots and along the aridity gradient. Plant compartment and aridity gradient were the influencing factors on the differentiation of microbial communities in rhizosphere and endosphere samples. The co-occurrence correlations between increased and decreased OTUs in rhizosphere and endosphere samples and soil parameters were determined according to the aridity gradient. Blastococcus, Geodermatophilus, Pseudonocardia, Promicromonospora, and Sphingomonas were identified as prevailing hubs and were considered as specific biomarkers taxa, which could play a crucial role on the aridity stress. Overall, our findings highlighted the prominence of the climatic aridity gradient on the equilibrium and diversity of microbial community composition in the rhizosphere and endosphere of cactus.

Desert Microbes for Boosting Sustainable Agriculture in Extreme Environments

A large portion of the earth's surface consists of arid, semi-arid and hyper-arid lands. Life in these regions is profoundly challenged by harsh environmental conditions of water limitation, high levels of solar radiation and temperature fluctuations, along with soil salinity and nutrient deficiency, which have serious consequences on plant growth and survival. In recent years, plants that grow in such extreme environments and their naturally associated beneficial microbes have attracted increased interest. The rhizosphere, rhizosheath, endosphere, and phyllosphere of desert plants display a perfect niche for isolating novel microbes. They are well adapted to extreme environments and offer an unexploited reservoir for bio-fertilizers and bio-control agents against a wide range of abiotic and biotic stresses that endanger diverse agricultural ecosystems. Their properties can be used to improve soil fertility, increase plant tolerance to various environmental stresses and crop productivity as well as benefit human health and provide enough food for a growing human population in an environment-friendly manner. Several initiatives were launched to discover the possibility of using beneficial microbes. In this review, we will be describing the efforts to explore the bacterial diversity associated with desert plants in the arid, semi-arid, and hyper-arid regions, highlighting the latest discoveries and applications of plant growth promoting bacteria from the most studied deserts around the world.

Emerging Technologies to Enable Sustainable Controlled Environment Agriculture in the Extreme Environments of Middle East-North Africa Coastal Regions

Despite global shifts in attitudes toward sustainability and increasing awareness of human impact on the environment, projected population growth and climate change require technological adaptations to ensure food and resource security at a global scale. Although desert areas have long been proposed as ideal sites for solar electricity generation, only recently have efforts shifted toward development of specialized and regionally focused agriculture in these extreme environments. In coastal regions of the Middle East and North Africa (MENA), the most abundant resources are consistent intense sunlight and saline sea water. MENA coastal regions hold incredible untapped potential for agriculture driven by the combination of key emerging technologies in future greenhouse concepts: transparent infrared collecting solar panels and low energy salt water cooling. These technologies can be combined to create greenhouses that drive regionally relevant agriculture in this extreme environment, especially when the target crops are salt-tolerant plants and algal biomass. Future controlled environment agriculture concepts will not compete for municipal fresh water and can be readily integrated into local human/livestock/fisheries food chains. With strategic technological implementation, marginal lands in these environments could participate in production of biomass, sustainable energy generation, and the circular carbon economy. The goal of this perspective is to reframe the idea of these environments as extreme, to having incredible untapped development potential.

Microbial Diversity of Some Sabkha and Desert Sites in Saudi Arabia

Several studies isolated fungal and bacterial species from extreme environments, such as Sabkha and hot deserts, as their natural habitat, some of which are of medicinal importance. Current research aimed investigating the microbial (fungi and bacteria) diversity and abundance in Sabkha and desert areas in Saudi Arabia. Soil samples from nine different geographical areas (Al-Aushazia lake, AlQasab, AlKasar, Tabuk, Al-Kharj, Al-Madina, Jubail, Taif and Abqaiq) were collected and cultured for microbial isolation. Isolated fungi and bacteria were identified by molecular techniques (PCR and sequencing). Based on 18S rDNA sequencing, 203 fungal species belonging to 33 genera were identified. The most common fungal genera were Fusarium, Alternaria, Chaetomium, Aspergillus Cochliobolus and Pencillium, while the most common species were Chaetomium globosum and Fusarium oxysporum. By 16S rDNA sequencing 22 bacterial species belonging to only two genera, Bacillus and Lactobacillus, were identified. The most commonly isolated bacterial species were Bacillus subtilis and Lactobacillus murinus. Some fungal species were confined to specific locations, such as Actinomyces elegans, Fusarium proliferatum, Gymnoascus reesii and Myzostoma spp. that were only isolated from Al-Aushazia soil. AlQasab soil had the highest microbial diversity among other areas with abundances of 23.5% and 4.4% of total fungi, and bacteria, respectively. Findings of this study show a higher degree of fungal diversity than that of bacteria in all studied areas. Further studies needed to investigate the connection between some isolated species and their habitat ecology, as well as to identify those of medicinal importance.

Tailoring plant-associated microbial inoculants in agriculture: a roadmap for successful application

Plants are now recognized as metaorganisms which are composed of a host plant associated with a multitude of microbes that provide the host plant with a variety of essential functions to adapt to the local environment. Recent research showed the remarkable importance and range of microbial partners for enhancing the growth and health of plants. However, plant-microbe holobionts are influenced by many different factors, generating complex interactive systems. In this review, we summarize insights from this emerging field, highlighting the factors that contribute to the recruitment, selection, enrichment, and dynamic interactions of plant-associated microbiota. We then propose a roadmap for synthetic community application with the aim of establishing sustainable agricultural systems that use microbial communities to enhance the productivity and health of plants independently of chemical fertilizers and pesticides. Considering global warming and climate change, we suggest that desert plants can serve as a suitable pool of potentially beneficial microbes to maintain plant growth under abiotic stress conditions. Finally, we propose a framework for advancing the application of microbial inoculants in agriculture.

Complete genome sequence of the endophytic bacterium Cellulosimicrobium sp. JZ28 isolated from the root endosphere of the perennial desert tussock grass Panicum turgidum

Cellulosimicrobium sp. JZ28, a root endophytic bacterium from the desert plant Panicum turgidum, was previously identified as a plant growth-promoting bacterium. The genome of JZ28 consists of a 4378,193 bp circular chromosome and contains 3930 CDSs with an average GC content of 74.5%. Whole-genome sequencing analysis revealed that JZ28 was closely related to C. aquatile 3 bp. The genome harbors genes responsible for protection against oxidative, osmotic and salinity stresses, such as the production of osmoprotectants. It also contains genes with a role in the production of volatiles, such as hydrogen sulfide, which promote biotic and abiotic stress tolerance in plants. The presence of three copies of chitinase genes indicates a possible role of JZ28 as biocontrol agent against fungal pathogens, while a number of genes for the degradation of plant biopolymers indicates potential application in industrial processes. Genome sequencing and mining of culture-dependent collections of bacterial endophytes from desert plants provide new opportunities for biotechnological applications.

Genome Insights of the Plant-Growth Promoting Bacterium Cronobacter muytjensii JZ38 With Volatile-Mediated Antagonistic Activity Against Phytophthora infestans

Salinity stress is a major challenge to agricultural productivity and global food security in light of a dramatic increase of human population and climate change. Plant growth promoting bacteria can be used as an additional solution to traditional crop breeding and genetic engineering. In the present work, the induction of plant salt tolerance by the desert plant endophyte Cronobacter sp. JZ38 was examined on the model plant Arabidopsis thaliana using different inoculation methods. JZ38 promoted plant growth under salinity stress via contact and emission of volatile compounds. Based on the 16S rRNA and whole genome phylogenetic analysis, fatty acid analysis and phenotypic identification, JZ38 was identified as Cronobacter muytjensii and clearly separated and differentiated from the pathogenic C. sakazakii. Full genome sequencing showed that JZ38 is composed of one chromosome and two plasmids. Bioinformatic analysis and bioassays revealed that JZ38 can grow under a range of abiotic stresses. JZ38 interaction with plants is correlated with an extensive set of genes involved in chemotaxis and motility. The presence of genes for plant nutrient acquisition and phytohormone production could explain the ability of JZ38 to colonize plants and sustain plant growth under stress conditions. Gas chromatography-mass spectrometry analysis of volatiles produced by JZ38 revealed the emission of indole and different sulfur volatile compounds that may play a role in contactless plant growth promotion and antagonistic activity against pathogenic microbes. Indeed, JZ38 was able to inhibit the growth of two strains of the phytopathogenic oomycete Phytophthora infestans via volatile emission. Genetic, transcriptomic and metabolomics analyses, combined with more in vitro assays will provide a better understanding the highlighted genes' involvement in JZ38's functional potential and its interaction with plants. Nevertheless, these results provide insight into the bioactivity of C. muytjensii JZ38 as a multi-stress tolerance promoting bacterium with a potential use in agriculture.

Characterization of plant growth-promoting alkalotolerant Alcaligenes and Bacillus strains for mitigating the alkaline stress in Zea mays

Intensification of sodic soil due to increasing pH is an emerging environmental issue. The present study aimed to isolate and characterise alkaline stress-tolerant and plant growth-promoting bacterial strains from moderately alkaline soil (pH 8-9), strongly alkaline soil (pH 9-10), and very strongly alkaline soil (> 10). Total 68 bacteria were isolated, and screened for multiple plant growth promoting (PGP) attributes. Out of total, 42 isolates demonstrating at least three plant growth promoting PGP traits selected for further assays. Then out of 42, 15 bacterial isolates were selected based on enhanced maize plant growth under greenhouse experiment, and 16S rRNA gene sequencing revealed Bacillus spp. as a dominant genus. Furthermore, based on improved seed germination percentage and biomass of maize (Zea mays L.) under alkaline stress conditions Alcaligenes sp. NBRI NB2.5, Bacillus sp. NBRI YE1.3, and Bacillus sp. NBRI YN4.4 bacterial strains were selected, and evaluated for growth-promotion and alkaline stress amelioration under greenhouse condition. Amongst the selected 3 plant growth promoting rhizobacterial (PGPR) strains, Bacillus sp. NBRI YN4.4 significantly improved the photosynthetic pigments and soluble sugar content, and decreased proline level in inoculated maize plants as compared to uninoculated control under stress conditions. Moreover, significantly enhanced soil enzymes such as dehydrogenase, alkaline phosphatase and betaglucosidase due to inoculation of Bacillus sp. NBRI YN4.4 in maize plants grown in alkaline soil attributes to its role in improving the soil health. Therefore, alkaline stress-tolerant PGPR NBRI YN4.4 can be useful for developing strategies for the reclamation of saline/sodic soils and improving the plant growth and soil health in sustainable manner.

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

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

Divulging diazotrophic bacterial community structure in Kuwait desert ecosystems and their N2-fixation potential

Kuwait is a semi-arid region with soils that are relatively nitrogen-poor. Thus, biological nitrogen fixation is an important natural process in which N₂-fixing bacteria (diazotrophs) convert atmospheric nitrogen into plant-usable forms such as ammonium and nitrate. Currently, there is limited information on free-living and root-associated nitrogen-fixing bacteria and their potential to fix nitrogen and aid natural plant communities in the Kuwait desert. In this study, free living N₂-fixing diazotrophs were enriched and isolated from the rhizosphere soil associated with three native keystone plant species; Rhanterium epapposum, Farsetia aegyptia, and Haloxylon salicornicum. Root-associated bacteria were isolated from the root nodules of Vachellia pachyceras. The result showed that the strains were clustered in five groups represented by class: γ-proteobacteria, and α-proteobacteria; phyla: Actinobacteria being the most dominant, followed by phyla: Firmicutes, and class: β-proteobacteria. This study initially identified 50 nitrogen-fixers by16S rRNA gene sequencing, of which 78% were confirmed to be nitrogen-fixers using the acetylene reduction assay. Among the nitrogen fixers identified, the genus Rhizobium was predominant in the rhizosphere soil of R. epapposum and H. salicornicum, whereas Pseudomonas was predominant in the rhizosphere soil of F. aegyptia, The species Agrobacterium tumefaciens was mainly found to be dominant among the root nodules of V. pachyceras and followed by Cellulomonas, Bacillus, and Pseudomonas genera as root-associated bacteria. The variety of diazotrophs revealed in this study, signifying the enormous importance of free-living and root-associated bacteria in extreme conditions and suggesting potential ecological importance of diazotrophs in arid ecosystem. To our knowledge, this study is the first to use culture-based isolation, molecular identification, and evaluation of N₂-fixing ability to detail diazotroph diversity in Kuwaiti desert soils.

Bioprospecting desert plant Bacillus endophytic strains for their potential to enhance plant stress tolerance

Plant growth-promoting bacteria (PGPB) are known to increase plant tolerance to several abiotic stresses, specifically those from dry and salty environments. In this study, we examined the endophyte bacterial community of five plant species growing in the Thar desert of Pakistan. Among a total of 368 culturable isolates, 58 Bacillus strains were identified from which the 16 most divergent strains were characterized for salt and heat stress resilience as well as antimicrobial and plant growth-promoting (PGP) activities. When the 16 Bacillus strains were tested on the non-host plant Arabidopsis thaliana, B. cereus PK6-15, B. subtilis PK5-26 and B. circulans PK3-109 significantly enhanced plant growth under salt stress conditions, doubling fresh weight levels when compared to uninoculated plants. B. circulans PK3-15 and PK3-109 did not promote plant growth under normal conditions, but increased plant fresh weight by more than 50% when compared to uninoculated plants under salt stress conditions, suggesting that these salt tolerant Bacillus strains exhibit PGP traits only in the presence of salt. Our data indicate that the collection of 58 plant endophytic Bacillus strains represents an important genomic resource to decipher plant growth promotion at the molecular level.

Variable Influences of Water Availability and Rhizobacteria on the Growth of Schizachyrium scoparium (Little Bluestem) at Different Ages

There is significant interest in understanding the role of plant growth-promoting rhizobacteria (PGPR) in alleviating different types of plant stress. Schizachyrium scoparium (little bluestem) is a moderately drought tolerant, perennial bunchgrass native to North America. The goal of this experiment was to evaluate whether the addition of a bacterial root isolate in the Pseudomonas genus promoted the growth of S. scoparium with changes in water availability. Pseudomonas are common rhizobacteria and have been shown to improve plant growth. It was hypothesized that plants inoculated with the PGPR strain would have greater growth and health, and would be less affected by shifts in water availability. Pseudomonas strains were isolated from the roots of native S. scoparium plants. After germination, S. scoparium seedlings were subjected to four treatment groups: low water; high water; low water with PGPR; and high water with PGPR. The experiment was run three times with plants at different starting ages; 14-, 28-, and 70-day-old plants. The effects of the water and PGPR treatments were variable between the experimental trials. There were no significant effects of the water treatments on plant growth in Trial 1 (14-day-old plants) or Trial 2 (28-day-old plants), however, there was a significant negative effect of the high watering treatment on the shoot length and biomass in Trial 3. High water availability was significantly associated with greater plant health in Trial 1, but appeared to reduce plant health in Trials 2 and 3. The PGPR treatment appeared to promote root growth and biomass in Trial 2, and was associated with greater plant health in all three trials, especially when paired with the low water treatment. Results from a permutational MANOVA indicate that plant growth was significantly different between the trials due to differences in the starting age of the plants and the duration of the experiments. Thus, methodological choices, such as plant life history stage and experiment duration, may affect the response of plants to PGPR in the rhizosphere. This research provides an insight into the interactions between PGPR and water availability on the growth and health of native plants.