Oxalotrophy refers to the ability of bacteria to utilize oxalate as a carbon and energy source. This is a critical process, with significant implications for the global carbon cycle. Oxalate-degrading bacteria play a key role in carbon sequestration through the oxalate-carbonate pathway, contributing to stable inorganic carbon pools. In this study, we identified and catalogued 19 enzymes and a transporter associated with various facets of oxalate metabolism to characterize the oxalotrophic potential of bacteria. Within this group, sets of enzymes were grouped into two functional categories in the context of carbon sequestration: a biomineralization toolkit for converting oxalate to inorganic carbon and an assimilation toolkit for incorporating oxalate into metabolic pathways such as amino acid biosynthesis and energy production. Using bioinformatic approaches, we analysed a collection of 536 bacterial genomes from desert and dryland strains spanning 81 genera to identify oxalotrophs. To validate our findings, we tested several bacterial strains for growth on media supplemented with exogenous oxalate. Notably, while multiple bacterial strains grew on oxalate media, two Pseudomonas species, namely JZ043 and JZ097, failed to grow despite genomic predictions suggesting otherwise. Further investigation of these strains revealed several non-conservative amino acid substitutions in the glyoxylate carboligase enzyme (EC 4.1.1.47), a key player in oxalate metabolism, suggesting a potential link between these mutations and their inability to metabolize oxalate. Our findings highlight the significance of our approach for identifying oxalotrophic bacteria and offer valuable insights into the molecular basis of oxalate metabolism.

Microbial communities associated with desert plants play a pivotal role in enhancing host survival under extreme environmental stressors, including drought, salinity, and nutrient limitation. The Desert Plant Endophyte Microbial Collection is one of the largest curated repositories of 2500 cultivable endophytic bacteria isolated from 23 native desert plant species across Saudi Arabia, Jordan, and Pakistan. Representing a broad spectrum of arid microhabitats from inland deserts and mountain wadis to coastal mangroves and date palm oases, the collection supports integrative studies on microbial ecology and plant-microbe interactions in water-limited ecosystems. A central component of this initiative is the Desert Plant Endophyte Genome Database, which currently hosts whole-genome sequences of 534 endophytic bacterial isolates annotated with extensive ecological metadata, assembly statistics, functional traits, and host associations. The database interface provides tools for genome exploration, metadata filtering, and functional gene mining, enabling users to identify taxa and traits of agronomic interest, particularly for applications in sustainable agriculture and sustainable desert revegetation. By combining genomic, ecological, and functional data, the Desert Plant Endophyte Genome Database serves as a foundational platform for the development of targeted microbial inoculants and fosters data-driven research into desert microbiomes and plant resilience mechanisms.

Plants associate with diverse microbial communities that influence growth and health. Although plant immune regulatory networks are known to balance defense activation and microbial accommodation during pathogen attack, how they coordinate beneficial plant-microbe interactions across complex microbial contexts remains unclear. Here, we systematically screened 39 immune-pathway mutants using individual plant growth-promoting bacteria (PGPBs), binary combinations, and synthetic and natural communities. We identified the bik1-1 mutant as exhibiting a broad defect in growth promotion across multiple beneficial microbial systems. Extensive genetic analyses using independent BIK1 CRISPR and T-DNA insertion alleles, as well as overexpression lines, demonstrated that the growth promotion defect observed in the bik1-1 line is not caused by loss of BIK1 function but is instead associated with a chromosomal fragment duplication. Although induced systemic resistance (ISR) and beneficial bacteria-mediated pathogen protection remain intact in bik1-1, immune activation is elevated during beneficial interactions. Microbiome profiling revealed reduced diversity and altered community structure, and microbiome transfer experiments indicated that host immune status influences selection of microbial taxa associated with growth promotion. These findings indicate that balanced immune signaling is a key determinant of plant-microbiome compatibility across diverse microbial contexts.

Frequent drought and variable rainfall limit tree establishment in drylands. Over a 4-month field trial, we examined how early acacia seedling transplantation and irrigation pulses shape desert soil microbiomes, and whether irrigation primarily stabilizes transplant-associated trajectories rather than driving them. Moisture formed the dominant environmental gradient across treatments, while early transplantation shifted bulk-soil stoichiometric ratios, with water and vegetation lowering C/N and altering nutrient context. Using 16S rRNA gene and ITS2 region amplicon sequencing together with time-series generalized Lotka-Volterra modeling, we assessed changes in community composition and inferred interaction signs at phylum and genus resolution. Seedling transplantation exerted a stronger influence on microbial diversity and genus-level composition, whereas irrigation mainly modified the magnitude and stability of inferred interaction patterns. Phylum-level responses were comparatively stable, but genus-level trajectories diverged across vegetation × irrigation combinations. Model-based growth tendencies and inferred interaction signs were consistent with resilience in non-watered bare soil, opportunistic responses under irrigation in bare soil, and a shift toward more negative inferred associations in vegetated non-watered soil, whereas irrigated vegetated soil showed higher connectivity and a higher proportion of positive inferred links. Together, these results frame early transplantation as a discrete window of microbiome assembly in desert soils and support a testable hypothesis for nursery-to-field workflows. Irrigation may primarily function as a stabilizing input to a seedling-associated microbiome state, while establishment outcomes and functional mechanisms require direct validation.

Transposon mutagenesis is a powerful tool for investigating gene function in bacteria, particularly in newly discovered species. In this study, we applied the hyperactive EZ-Tn5 transposase system to Pseudomonas argentinensis SA190, an endophytic bacterium known for enhancing plant resilience under drought stress. By leveraging the random amplification of transposon ends (RATE)-PCR method, we successfully mapped the insertion sites of the transposon within the SA190 genome. This approach enabled the precise identification of disrupted genes, offering insights into their roles in bacterial function and interaction with host plants. Our comprehensive protocol, including competent cell preparation, transformation, and insertion site mapping, provides a reliable framework for future studies aiming to explore gene function through mutagenesis. Key features • The use of the hyperactive EZ-Tn5 transposase system ensures efficient and detectable random mutagenesis across the Pseudomonas argentinensis SA190 genome, facilitating comprehensive gene disruption studies. • The technique is employed to identify and map the transposon insertion sites, allowing for precise determination of gene function and its impact on bacterial phenotypes. • This method enables the exploration of a broad range of gene functions within SA190, particularly those involved in plant growth promotion and stress tolerance. • This method can be readily adapted to generate mutant libraries in other bacterial species, emphasizing its transferability.

Global climate change increasingly challenges agriculture with flooding and salinity. Among strategies to enhance crop resilience to these stresses, we tested several endophytic bacterial strains from mangroves, which are permanently exposed to flooding and high salinity. We show several strains that can enhance flooding and salinity tolerance in Arabidopsis and rice plants. Two strains and their combination massively enhanced the growth and yield of Oryza sativa cv. Nipponbare under both soil and hydroponic growth conditions with and without salt treatment. The bacteria-induced transcriptome changes in O. sativa roots, particularly related to ABA-signaling and lignin and suberin deposition in root tissues, explain the altered responses of colonized rice plants to hypoxic and saline stress conditions. Importantly, bacterially colonized rice plants exhibited enhanced yield and improved grain quality. These results show that microbes can be a powerful tool for enhancing the yield and resilience of rice to hypoxic and saline stress conditions.

Pseudomonas argentinensis SA190 is a desert-adapted, plant-associated bacterium with demonstrated potential to enhance plant growth under abiotic stress. In this study, we conducted a comprehensive genomic and functional characterization of SA190 to uncover the molecular mechanisms underlying its biofilm formation, root colonization, and plant growth-promoting traits. The SA190 genome consists of a single circular chromosome (5.07 Mb, 64

Desert ecosystems have limited resources and harsh climatic conditions and cannot support cropping in most farming models. Recently, microbial applications have emerged as promising strategies to enhance plant survival and adaptation in such extreme environments. However, the beneficial microbes and our understanding of their functional roles and adaptation mechanisms in desert ecosystems remain underexplored. This study reports the isolation and characterization of the Pseudomonas sp. R4-79 strain from the arid environment of Wadi Rum, Jordan, associated with the desert plant Ifloga spicata. The genome of Pseudomonas sp. R4-79, sequenced at 275 × PacBio coverage, consists of a 6.18 Mbp chromosome encoding 5,445 proteins, including gene clusters for siderophores, phenazines, hydrogen cyanide, and phytohormones, as well as secretion systems (T2SS, T4SS, T6SS, and TAT). Genomic and phenotypic analyses revealed that Pseudomonas sp. R4-79 belongs to the genus P. granadensis and exhibits plant growth-promoting attributes and substantial biocontrol potential. Pseudomonas sp. R4-79 effectively suppressed key phytopathogens, including the necrotrophic fungus Botrytis cinerea in vitro, as well as Pseudomonas syringae pv. tomato DC3000 and root-knot nematodes (Meloidogyne incognita) in vivo in Arabidopsis and tomato. This work suggests that P. granadensis R4-79 could represent an effective biocontrol agent to improve crop yield in sustainable agriculture.

Microbial communities associated with desert plants play a pivotal role in enhancing host survival under extreme environmental stressors, including drought, salinity, and nutrient limitation. The Darwin21 Endophytic Microbial Collection is one of the largest curated repositories of 2,500 cultivable endophytic bacteria isolated from 23 native desert plant species across Saudi Arabia, Jordan, and Pakistan. Representing a broad spectrum of arid microhabitats from inland deserts and mountain wadis to coastal mangroves and date palm oases, the collection supports integrative studies on microbial ecology and plant–microbe interactions in water-limited ecosystems. A central component of this initiative is the Darwin21 Genome Database, which currently hosts whole-genome sequences (WGS) of 534 endophytic bacterial isolates annotated with extensive ecological metadata, assembly statistics, functional traits, and host associations. The database interface provides tools for genome exploration, metadata filtering, and functional gene mining, enabling users to identify taxa and traits of agronomic interest, particularly for applications in sustainable agriculture and sustainable desert revegetation. By combining genomic, ecological, and functional data, the Darwin21 Genome Database serves as a foundational platform for the development of targeted microbial inoculants and fosters data-driven research into desert microbiomes and plant resilience mechanisms. Database URL ![Figure][1] ### Competing Interest Statement The authors have declared no competing interest. KAUST fund BAS/1/1062-01-01 [1]: pending:yes

Phenotypic switching in bacteria is a well-established evolutionary strategy that enhances fitness in response to changing environmental conditions. Here, we hypothesised that the observed phenotypic transition of the soil-dwelling Enterobacter sp. SA187-from yellow- to white-pigmented colonies upon plant root colonisation-reflects such an adaptive mechanism. This phenotypic switching is not host-specific but occurs consistently during the colonisation of various plant species. Through genome re-sequencing of switcher white colonies, we identified recurrent loss-of-function mutations in the rpoS gene compared to the yellow ancestral strain. Functional validation confirmed that mutations in rpoS are both necessary and sufficient to trigger the phenotypic switch, leading to widespread transcriptional changes affecting traits involved in plant colonisation, including motility, biofilm formation, metabolism, and growth rate. Metabolic profiling further revealed that the SA187 switcher variant exhibited enhanced fitness in conditions mimicking the acidic, sucrose-rich apoplastic environment of plant tissues, supporting the idea that this phenotypic switch represents a specific adaptation to the endophytic niche. Overall, our findings highlight the pivotal role of rpoS-mediated regulation in facilitating the transition of SA187 from a free-living to endophytic lifestyle and provide mechanistic insights into how bacterial symbionts dynamically adapt through phenotypic switching during host colonisation.

Plant-microbiome interactions are crucial in shaping plant growth, stress resilience, and disease resistance. Among these, the seed microbiome plays a pivotal role in early plant development and ecological adaptation. However, little is known about the factors that determine the abundance and functions of the seed microbiome, as well as the role of the host genome in shaping the microbial diversity across different ecotypes. In this study, we investigated the diversity of the Arabidopsis seed microbiomes that originate from multiple geographical locations. High-throughput sequencing identified key bacterial taxa that govern Arabidopsis seed microbiota diversity. Distinct compositions of bacterial taxa were identified in Arabidopsis accessions sharing geographical location and similar soil features. Genome-wide association studies (GWAS) revealed that both the abundance of key taxa and common functional traits are associated with specific host genetic loci such as the RNA-binding protein RPB47B, mutants of which showed altered physiological properties related to soil properties and microbial diversity. Overall, our study establishes that geographical, soil and genetic host factors shape the Arabidopsis seed microbiome.

Oxalotrophy refers to the ability of bacteria to utilize oxalate as a carbon and energy source. This is a critical process with significant implications for the global carbon cycle. Oxalate-degrading bacteria play a key role in carbon sequestration through the oxalate-carbonate pathway (OCP), contributing to stable inorganic carbon pools. In this study, we identified and cataloged 20 enzymes associated with various facets of oxalate metabolism to characterize the oxalotrophic potential of bacteria. Within this group, sets of enzymes were grouped into two functional categories in the context of carbon sequestration: a biomineralization toolkit for converting oxalate to inorganic carbon and an assimilation toolkit for incorporating oxalate into metabolic pathways such as amino acid biosynthesis and energy production. Using bioinformatic approaches, we analyzed a collection of 536 bacterial genomes from desert and dryland strains spanning 81 genera to identify oxalotrophs. To validate our findings, we tested several bacterial strains for growth on media supplemented with exogenous oxalate. Notably, while multiple bacterial strains grew on oxalate media, two Pseudomonas species, namely JZ043 and JZ097, failed to grow despite genomic predictions suggesting otherwise. Further investigation of these strains revealed several non-conservative amino acid substitutions in the glyoxylate carboligase enzyme (EC 4.1.1.47), a key player in oxalate metabolism, suggesting a potential link between these mutations and their inability to metabolize oxalate. Our findings highlight the significance of our approach for identifying oxalotrophic bacteria (OxB) and offer valuable insights into the molecular basis of oxalate metabolism. ### Competing Interest Statement The authors have declared no competing interest.

Fonio (Digitaria exilis), an orphan millet crop, is the oldest indigenous crop in West Africa. Although the yield is low due to pre-domestication characteristics, the quick maturation time, drought tolerance, and the ability to thrive on poor soils make fonio a climate-smart crop. Being holobionts, plants evolve in close interaction with microbial partners, which is crucial for plant phenology and fitness. As seeds are the bottleneck of vertically transmitting plant microbiota, we proposed to unravel the seed microbiome of the under-domesticated and resilient crop fonio. Our study investigated the bacterial seed endophyte diversity across 126 sequenced fonio accessions from distinct locations in West Africa. We conducted a correlation study of the structures and functions of the seed-associated microbiomes with the native geo-climate and soil structure data. We also performed Genome-wide association studies (GWAS) to identify genetic loci associated with seed endophyte diversity. We report that fonio millet has diverse heritable seed endophytic taxa. We analyzed the seed microbiomes of 126 fonio accessions and showed that despite the diversity of microbiomes from distinct geographical locations, all fonio genetic groups share a core microbiome. In addition, we observed that native soil composition, geo-climatic factors, and host genotype correlate with the seed microbiomes. GWAS analysis of genetic loci associated with endophyte seed bacterial diversity identified fonio SNPs associated with genes functioning in embryo development and stress/defense response. Analysis of the seed endophyte of the climate-smart crop fonio indicated that despite possessing a heritable core microbiome, native conditions may shape the overall fonio seed microbiomes in different populations. These distinct microbiomes could play important roles in the adaptation of fonio to different environmental conditions. Our study identified the seed microbiome as a potential target for enhancing crop resilience to climate stress in a sustainable way.

The scarcity of freshwater resources resulting in a significant yield loss presents a pressing challenge in agriculture. To address this issue, utilizing abundantly available saline water could offer a smart solution. In this study, we demonstrate that the genome sequence rhizosphere bacterium Tritonibacter mobilis AK171, a halophilic marine bacterium recognized for its ability to thrive in saline and waterlogged environments, isolated from mangroves, has the remarkable ability to enable plant growth using saline irrigation. AK171 is characterized as rod-shaped cells, displays agile movement in free-living conditions, and adopts a rosette arrangement in static media. Moreover, The qualitative evaluation of PGP traits showed that AK171 could produce siderophores and IAA but could not solubilize phosphate nor produce hydrolytic enzymes it exhibits a remarkable tolerance to high temperatures and salinity. In this study, we conducted a comprehensive genome sequence analysis of T. mobilis AK171 to unravel the genetic mechanisms underlying its plant growth-promoting abilities in such challenging conditions. Our analysis revealed diverse genes and pathways involved in the bacterium’s adaptation to salinity and waterlogging stress. Notably, T. mobilis AK171 exhibited a high level of tolerance to salinity and waterlogging through the activation of stress-responsive genes and the production of specific enzymes and metabolites. Additionally, we identified genes associated with biofilm formation, indicating its potential role in establishing symbiotic relationships with host plants. Furthermore, our analysis unveiled the presence of genes responsible for synthesizing antimicrobial compounds, including tropodithietic acid (TDA), which can effectively control phytopathogens. This genomic insight into T. mobilis AK171 provides valuable information for understanding the molecular basis of plant-microbial interactions in saline and waterlogged environments. It offers potential applications for sustainable agriculture in challenging conditions.

Global climate change increasingly challenges agriculture with flooding and salinity. Among strategies to enhance crop resilience to these stresses, we tested several endophytic bacterial strains from mangroves, which are permanently exposed to flooding and high salinity. We show several strains that can enhance flooding and salinity tolerance in Arabidopsis and rice plants. Two strains and their combination massively enhanced the growth and yield of Oryza sativa cv. Nipponbare under both soil and hydroponic growth conditions with and without salt treatment. The bacteria-induced transcriptome changes in O. sativa roots related to ABA-signaling with lignin and suberin deposition in root tissues explain the altered responses of colonized rice plants to hypoxic and saline stress conditions. While enhancing yield and grain quality, bacterially colonized rice plants also show much earlier flowering, thereby massively shortening the life cycle of rice plants and opening the possibility for an additional harvest per year. These results show that microbes can be a powerful tool for enhancing the yield and resilience of rice to hypoxic and saline stress conditions. ### Competing Interest Statement The authors have declared no competing interest.

High-light stress strongly limits agricultural production in subtropical and tropical regions owing to photooxidative damage, decreased growth, and decreased yield. Here, we investigated whether beneficial microbes can protect plants under high-light stress. We found that Enterobacter sp. SA187 (SA187) supports the growth of Arabidopsis thaliana under high-light stress by reducing the accumulation of reactive oxygen species and maintaining photosynthesis. Under high-light stress, SA187 triggers dynamic changes in the expression of Arabidopsis genes related to fortified iron metabolism and redox regulation, thereby enhancing the antioxidative glutathione/glutaredoxin redox system of the plant. Genetic analysis showed that the enhancement of iron and sulfur metabolism by SA187 is coordinated by ethylene signaling. In summary, beneficial microbes could be an effective and inexpensive means of enhancing high-light-stress tolerance in plants.

BackgroundAvicennia marina ecosystems are critical for coastal protection, water quality enhancement, and biodiversity support. These unique ecosystems thrive in extreme saline conditions and host a diverse microbiome that significantly contributes to plant resilience and growth. Global food security is increasingly threatened by crop yield losses due to abiotic stresses, including saline soils. Traditional plant breeding for salt tolerance is both costly and time-consuming. This study explores the potential of bacteria from A. marina to enhance plant growth under saline conditions, emphasizing their ecological significance.ResultsWe analyzed the microbiome of A. marina from the Red Sea coast using high-throughput Illumina sequencing and culture-dependent methods across various compartments (bulk soil, rhizosphere, rhizoplane, roots, and leaves). Our findings revealed distinct compartment-specific microbial communities, with Proteobacteria being the dominant phylum. Functional predictions indicated diverse microbial roles in metal uptake and plant growth promotion (PGP). Remarkably, our culture-dependent methods allowed us to recover 56% of the bacterial diversity present in the microbiome, resulting in the isolation and characterization of 256 bacterial strains. These isolates were screened for PGP traits, including salt and heat tolerance, siderophore production, and pectinase activity. Out of the 77 bacterial isolates tested, 11 demonstrated a significant ability to enhance Arabidopsis growth under salt stress.ConclusionsOur study highlights the ecological significance of mangrove microbiomes and the potential of culture collections in offering innovative solutions for ecological restoration and crop production in saline conditions. The unique collection of mangrove bacteria, particularly from the rhizosphere and endophytes, showcases significant PGP traits and stress tolerance capabilities. These findings emphasize the importance of functional traits, such as salt tolerance, in the recruitment of endophytic bacteria by plants over taxonomic affiliation. The identified bacterial strains hold potential not only for developing biofertilizers to improve crop productivity but also for ecological restoration projects aimed at rehabilitating saline-degraded lands, thereby contributing to overall ecosystem health and sustainability.

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.

Rice is one of the most essential crops since it meets the calorific needs of 3 billion people around the world. Rice seed development initiates upon fertilization, leading to the establishment of two distinct filial tissues, the endosperm and embryo, which accumulate distinct seed storage products, such as starch, storage proteins, and lipids. A range of systems biology tools deployed in dissecting the spatiotemporal dynamics of transcriptome data, methylation, and small RNA based regulation operative during seed development, influencing the accumulation of storage products was reviewed. Studies of other model systems are also considered due to the limited information on the rice transcriptome. This review highlights key genes identified through a holistic view of systems biology targeted to modify biochemical composition and influence rice grain quality and nutritional value with the target of improving rice as a functional food.