Esther Menéndez

A novel halophilic actinobacterium, designated H202 ^T , was isolated from a Saharan soil in the Ahbès region (Béni-Isguen, Ghardaïa province, South Algeria), and its taxonomic position was determined by a genome-based polyphasic approach. Phylogenetic analysis of the 16S rRNA gene sequence revealed that the strain H202 ^T belonged to the genus Actinopolyspora and showed the highest sequence similarity to Actinopolyspora mzabensis DSM 45460 ^T (99.46%). Comparative genomic analysis based on digital DNA–DNA hybridization (dDDH), average nucleotide identity (ANI) and average amino acid identity (AAI) showed values below the recommended species cut-off thresholds of 70% (dDDH) and 95–96% (ANI and AAI), suggesting that the strain H202 ^T represents a novel species. This strain exhibits the typical characteristics of the genus Actinopolyspora . The cell-wall hydrolysates contained meso -diaminopimelic acid, and the diagnostic whole-cell sugars were arabinose and galactose. Phosphatidylcholine was identified as the diagnostic phospholipid, and the predominant menaquinones were MK-9(H ₄ ) and MK-10(H ₄ ). The major fatty acids (≥10%) were anteiso -C _17:0 , iso -C _15:0 , iso -C _16:0 and anteiso -C _15:0 . The genome size of strain H202 ^T was estimated to be 5.2 Mbp, with a G+C content of 67.5%. Based on these findings, strain H202 ^T is proposed as a representative of a novel species within the genus Actinopolyspora , named Actinopolyspora sabaoui sp. nov. The type strain is H202 ^T (=DSM 46671 ^T =CECT 31287 ^T ).

The family Rhizobiaceae of the class Alphaproteobacteria is highly diverse and currently consists of at least 276 validly published or proposed species across 38 genera. Despite several recent studies proposing revisions to the family Rhizobiaceae , anomalies and inconsistencies in the taxonomy of this family remain. Here, we revisit the taxonomy of the family Rhizobiaceae with a focus on the genus Rhizobium . First, we generated whole-genome sequences for 12 Rhizobium type strains that previously lacked publicly available genome sequences. We then applied an established phylogenomic framework to reappraise the taxonomic classification of 242 Rhizobiaceae type strains. Our data suggest that Rhizobium aegyptiacum is a later heterotypic synonym of Rhizobium aethiopicum , and they contradict a recent suggestion that Rhizobium azibense and Rhizobium gallicum are synonymous. In addition, we propose the formation of 8 new genera ( Allohoeflea gen. nov., Arminella gen. nov., Gillisella gen. nov., Limnomicrobium gen. nov., Martinezella gen. nov., Neohoeflea gen. nov., Parahoeflea gen. nov. and Velazquezella gen. nov.) and 32 novel combinations to fix paraphyletic genera or account for monophyletic type strains that are clearly distinguishable based on core-proteome average amino acid identity comparisons. Lastly, our data suggest that the type strain of Rhizobium arsenicireducens may have been lost and that a neotype should be designated.

The family Rhizobiaceae of the class Alphaproteobacteria is highly diverse and currently consists of at least 276 validly published or proposed species across 38 genera. Despite several recent studies proposing revisions to the family Rhizobiaceae, anomalies and inconsistencies in the taxonomy of this family remain. Here, we revisit the taxonomy of the family Rhizobiaceae with a focus on the genus Rhizobium. First, we generated whole genome sequences for 12 Rhizobium type strains that previously lacked publicly available genome sequences. We then applied an established phylogenomic framework to reappraise the taxonomic classification of 242 Rhizobiaceae type strains. Our data suggest that Rhizobium aegyptiacum is a later heterotypic synonym of Rhizobium aethiopicum, and they contradict a recent suggestion that Rhizobium azibense and Rhizobium gallicum are synonymous. In addition, we propose the formation of ten new genera (Allohoeflea gen. nov., Arminia gen. nov., Fluviimicrobium gen. nov., Gillisella gen. nov., Limnomicrobium gen. nov., Martinezia gen. nov., Neohoeflea gen. nov., Parahoeflea gen. nov., Velazquezia gen. nov., and Yannia gen. nov.) and 35 novel combinations to fix paraphyletic genera or account for monophyletic type strains that are clearly distinguishable based on core-proteome average amino acid identity (cpAAI) comparisons. Lastly, our data suggest that the type strain of Rhizobium arsenicireducens may have been lost, and that either a neotype should be designated or the taxonomic status of this species should be revised.

Rhizobia, Endophytes, Microbiome, Legumes, Plant Growth Promotion, Symbiosis, Plant Protection, Biological Nitrogen FixationDeciphering the Root Nodule Microbiome: Implications for Legume Fitness and Stress ResilienceThe legume-rhizobia symbiosis is a key plant-microbe interaction crucial for biological nitrogen fixation. Historically, it was believed that only nitrogen-fixing rhizobia colonized legume root nodules, influencing decades of research. This mutual relationship, in which rhizobia provide usable nitrogen to plants in exchange for carbon, plays a vital role in soil fertility and sustainable agriculture (Goyal et al., 2021). However, recent advances in molecular microbiology and the application of high-throughput omics technologies have challenged this classical view. Studies employing next-generation sequencing and metagenomic approaches have revealed that legume root nodules are more than just rhizobia habitats (Hakim et al., 2020, Liu et al., 2022, Zhang et al., 2018). Instead, they are complex microecosystems inhabited by diverse microbial consortia (Martínez-Hidalgo and Hirsch, 2017). In addition to rhizobia, these nodules also contain non-rhizobial bacteria, which were once dismissed as contaminants but are now recognized as consistent and potentially functional members of the nodule microbiome. These non-rhizobia include a wide range of bacterial taxa, some of which possess plant growth-promoting traits such as phosphate solubilization, phytohormone production, or pathogen suppression (Hassen et al., 2025).Their presence suggests that they may play synergistic or complementary roles in enhancing nodule function, influencing nutrient exchange, and contributing to plant resilience under stress (Etesami, 2022). Yet, despite these discoveries, the ecological roles, mechanisms of colonization, and interactions between these non-rhizobial microbes with rhizobia and host Alnus species with different chromosome ploidies. Using high-throughput sequencing of the 16S rRNA and nifH genes, the authors compared the microbial communities in A. glutinosa, A. formosana, and A. cremastogyne. In parallel, nitrogen levels in the nodules and the rhizosphere of these plants were also measured. They found that root nodules contained higher total and nitrate nitrogen, but lower ammonium nitrogen compared to rhizosphere soils. A. glutinosa exhibited the highest microbial diversity and nitrogen-fixing potential, with significantly greater abundance of Frankia and associated nitrogen cycle functions than the other two species. The study concludes that nitrogen content, particularly total nitrogen, strongly influences the abundance and diversity of nitrogen-fixing microbes like Frankia, highlighting A. glutinosa as a promising species for enhancing soil fertility through biological nitrogen fixation.Paenibacillus species, particularly those within the Paenibacillus polymyxa complex, as biocontrol agents and plant growth promoters. The authors screened strains isolated from legume root nodules for their ability to inhibit five major phytopathogenic fungi and evaluated their production of antifungal compounds like fusaricidins. Additionally, plant growth-promoting traits traits such as indole acetic acid production, phosphate solubilization, nitrogen fixation, and plant colonization were examined. It was found that several of these strains possess broad-spectrum antifungal activity, can effectively colonize wheat plants, promote plant growth, and control fungal diseases in planta, making them promising candidates for sustainable agriculture as biocontrol agents and biofertilizers.The systematic review by Hnini & Aurag consolidates findings on the prevalence and functionality of non-rhizobia, emphasizing their role in enhancing plant performance when co-inoculated with rhizobia. While traditionally thought to be solely inhabited by rhizobia, legume nodules also host a consistent and beneficial community of other bacteria, such as Bacillus, Pseudomonas and Paenibacillus. Although non-rhizobial endophytes (NREs) do not induce nodule formation, they enhance plant growth and resilience through mechanisms like nitrogen fixation, phosphate solubilization, siderophore production, and stress tolerance.The review also underscores that co-inoculation of legumes with both rhizobia and NREs generally leads to improved plant growth and yield compared to inoculation with rhizobia alone. It emphasized the specificity of plant-NRE associations, particularly in Phaseolus, and notes the consistent predominance of Bacillus and Pseudomonas across diverse legume species. The findings have important implications for sustainable agriculture, pointing out that targeted microbial inoculation strategies can enhance nutrient uptake, tolerance to different stresses, and overall crop performance and productivity under diverse environmental conditions.In conclusion, these studies collectively demonstrate that the root nodule environment harbors a high complexity of functionally active microbial communities with great potential for achieving advances towards sustainable agriculture. However, a critical knowledge gap remains in understanding the specific roles and interactions of non-rhizobial microbes. Future research should prioritize functional analyses to uncover how these microbial communities influence legume-rhizobia symbiosis, plant health, and agrosystems productivity.EM: Writing -review & editing, Writing -original draft. CB: Writing -review & editing, Writing -original draft.

The two-component signal transduction system EnvZ/OmpR is described to mediate response to osmotic stress, although it regulates genes involved in other processes such as virulence, fatty acid uptake, exopolysaccharide production, peptide transportation, and flagella production. Considering that some of these processes are known to be important for a successful symbiosis, the present study addresses the effects of extra envZ-like gene copies in the Mesorhizobium–chickpea symbiosis. Five Mesorhizobium-transformed strains, expressing the envZ-like gene from M. mediterraneum UPM-Ca36T, were evaluated in terms of symbiotic performance. Chickpea plants inoculated with envZ-transformed strains (PMI6envZ⁺ and EE7envZ⁺) showed a significantly higher symbiotic effectiveness as compared to the corresponding control. In plants inoculated with PMI6envZ+, a higher number of infection threads was observed, and nodules were visible 4 days earlier. Overall, our results showed that the overexpression of Env-like protein may influence the symbiotic process at different stages, leading to strain-dependent effects. This study contributes to elucidating the role of an EnvZ-like protein in the rhizobia–legume symbioses.

Bacteria can sense changes in the environment and adapt to survive under different conditions. The two-component signal transduction system EnvZ/OmpR is described to mediate response to osmotic stress. This system also regulates genes involved in other processes such as virulence, fatty acid uptake, exopolysaccharide production, peptide transportation and flagella production. Considering that some of these processes are known to be important for a successful symbiosis, the present study addresses the role of EnvZ in rhizobia-legume interaction, evaluating the effects of extra envZ-like gene copies in the Mesorhizobium-chickpea symbiosis. Five Mesorhizobium-transformed strains, expressing the envZ-like gene from M. mediterraneum UPM-Ca36T, were evaluated in terms of symbiotic performance. Chickpea plants inoculated with envZ-transformed strains (PMI6envZ+ and EE7envZ+) showed significant higher symbiotic effectiveness as compared to the corresponding empty-vector strains. In plants inoculated with PMI6envZ+, a higher number of infection threads was observed, and nodules were visible 4 days earlier. Overall, our results showed that the expression of extra-copies of the envZ-like gene influenced the symbiotic process at different stages, leading to strain-dependent effects. This study represents the first report on the involvement of an EnvZ-like protein in the rhizobia-legume symbiosis and contributes to elucidate the role of these systems in bacteria-host interaction.

Frontiers has taken a commendable initiative to celebrate International Women's Day by launching a series of research topics designed to highlight and empower women researchers. The topic "Women in Microbe and Virus Interactions with Plants: 2022/2023" celebrates the women's achievements in this field, providing a platform to showcase and advance their research.The UNESCO has emphasized the need for gender equality in science as essential for sustainable worldwide development (UNESCO Call to Action, 2024). Gender equality has been discussed for decades, achieving it remains challenging, particularly in STEM (Science, Technology, Engineering, and Mathematics) fields, where women comprise only 30% of the researchers worldwide (UNESCO Institute for Statistics, 2019). Women scientists frequently face obstacles in obtaining authorships, and their contributions are often underevaluated in scientific papers (Broderick and Casadevall, 2019). This perpetuates a cycle of reduced impact and limited opportunities for women scientists (Sarabi and Smith, 2023). Adressing these challenges is imperative to improve the well-being, productivity, and equity of female scientists in STEM (Van den Besselaar and Sandström, 2017). This research topic highlights the impactful contributions of women in the field of plant interactions with microbes and viruses. The collection includes five high-quality research papers that explore the complexities of plant-microbe interactions, including colonization, detection, and disease control, providing critical insights for sustainable agriculture. Crop production is significantly affected by various pathogens and pests. Addressing these challenges requires a comprehensive understanding of plant-microbe interactions, which encompass competition, commensalism, mutualism, and parasitism. Women scientists have played a pivotal role in advancing our understanding of these processes. The groundbreaking work of Lynn Margulis (Margulis, 1967) on symbiosis exemplifies this contribution. Margulis highlighted that cooperation is as important as competition in evolution, an idea that has profoundly influenced our understanding of plant-microbe interactions and has shaped critical areas of plant health and crop productivity. In summary, this research topic offers fresh insights, recent advancements, and future perspectives in the complex relationships between plants with microbes and viruses, while also addressing current challenges in agriculture and food security. Additionally, by showcasing the latest scientific advances made by women researchers, this topic promotes gender equality and encourages more women to pursue careers in STEM fields.SC: Writing -original draft; SC, NM and EM: Writing -review & editing.

The challenges posed to modern agriculture such as climate change, depleting groundwater resources, and increased global population (Ivanovish et al 2023; Khatri et al 2024), underscore the urgent need for innovative and sustainable strategies to mitigate plant stress. Plants face a multitude of biotic and abiotic stressors, which can severely affect their growth, development, and productivity. Despite these challenges, plants have evolved complex defense mechanisms that are tightly regulated at various molecular levels (Zandalinas et al., 2021;Zandalinas & Mittler, 2022). However, the ways in which biotic and abiotic stresses together influence plant responses at molecular level remain poorly understood. This Research Topic includes comprehensive studies exploring the interplay between biotic and abiotic stresses, with a particular focus on how abiotic stress can either enhance or reduce plant susceptibility to pathogens and pests. The collection includes a balanced mix of original research and review articles, with an emphasis on molecular and multi-omic approaches. Some studies underscore the critical role of transcription factors and kinases in regulating integrative plant responses, utilizing a variety of omics and molecular studies a more 35 applied emphasizing the importance of in situ measurements for practical 36

This study aims to evaluate the in silico genomic characteristics of five species of the genus Planotetraspora: P. kaengkrachanensis, P. mira, P. phitsanulokensis, P. silvatica, and P. thailandica, with a view to their application in therapeutic research. The 16S rRNA comparison indicated that these species were phylogenetically distinct. Pairwise comparisons of digital DNA-DNA hybridization (dDDH) and OrthoANI values between these studied type strains indicated that dDDH values were below 62.5%, while OrthoANI values were lower than 95.3%, suggesting that the five species represent distinct genomospecies. These results were consistent with the phylogenomic study based on core genes and the pangenome analysis of these five species within the genus Planotetraspora. However, the genome annotation showed some differences between these species, such as variations in the number of subsystem category distributions across whole genomes (ranging between 1979 and 2024). Additionally, the number of CAZYme (Carbohydrate-Active enZYme) genes ranged between 298 and 325, highlighting the potential of these bacteria for therapeutic research applications. The in silico physico-chemical characteristics of cellulases from Planotetraspora species were analyzed. Their 3D structure was modeled, refined, and validated. A molecular docking analysis of this cellulase protein structural model was conducted with cellobiose, cellotetraose, laminaribiose, carboxymethyl cellulose, glucose, and xylose ligand. Our study revealed significant interaction between the Planotetraspora cellulase and cellotetraose substrate, evidenced by stable binding energies. This suggests that this bacterial enzyme holds great potential for utilizing cellotetraose as a substrate in various applications. This study enriches our understanding of the potential applications of Planotetraspora species in therapeutic research.