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Have we entered a 'post-model' era in plant biology?

Models such as arabidopsis (Arabidopsis thaliana) have underpinned genomic and physiological research in plant science. Advances in genome sequencing, pangenomics, and genome editing have prompted claims of a 'post-model' era, with model-crops and crops such as rice and bread wheat combining agricultural relevance with experimental tractability. We argue that the 'simplicity-to-complexity' approach remains valid, although model systems have evolved. Arabidopsis remains indispensable for interpreting multi-omics data, testing developmental hypotheses, and generating mechanistic insights difficult to obtain in crops. Linking these strengths to model-crops adds translational value by bridging discovery and breeding, while niche models such as Brachypodium distachyon and legumes address grass cell wall biology and nitrogen fixation. Future progress depends on diverse species with complementary strengths across fundamental and applied plant biology.

arabidopsis

Short-term virus-host interactions and functional dynamics in recently deglaciated Antarctic tundra soils.

Long-term chronosequence studies have shown that, as glaciers retreat, newly exposed soils become colonized through primary succession. To determine the key drivers of this process and their vulnerability to climate change, the short-term responses of these pioneering microbial communities also need to be elucidated. Here, we investigated how the taxonomic and functional structure of microbial communities, including viruses, changed over a 7-year period in an Antarctic glacier forefield. Using metagenomics and metatranscriptomics we assessed the influence of both abiotic and biotic factors on these communities. Our results revealed a highly heterogeneous bacteria-dominated microbial community, with Pseudomonas as the most abundant genus, followed by Lysobacter, Devosia, Cellulomonas, and Brevundimonas. This community exhibited the capacity for aerobic anoxygenic phototrophy, carbon and nitrogen fixation, and sulfur cycling, processes vital for survival in nutrient-poor environments. 52 high-quality metagenome-assembled genomes (MAGs) were recovered, representing both transient and cosmopolitan taxa, some of which were able to rapidly respond to environmental changes. A diverse and highly dynamic collection of lytic and temperate viruses was identified across all samples, with high clonal viral genomes typically detected in only one of the eight samples analyzed. Metatranscriptomic analyses confirmed the activity of lytic viruses, while prophage genomes featured much lower expression levels. Prophages appeared to influence host fitness through the expression of genes encoding membrane transporters. Additionally, the abundance of genes linked to antimicrobial compound synthesis and resistance, along with antiphage defense systems, highlights the importance of biotic interactions in driving microbial community succession and shaping short-term responses to environmental fluctuations.

Antarctica

Rhizobium zaerense sp. nov., a novel member of the Rhizobium leguminosarum species complex with a broad geographic distribution and multiple legume hosts.

A novel nitrogen-fixing rhizobial strain, designated Z1P35ᵀ, was isolated from root nodules of Pisum sativum grown in the Zaër region of Morocco. Phylogenetic analysis of the 16S rRNA gene placed strain Z1P35ᵀ within the genus Rhizobium, showing 100% sequence identity with several undescribed genospecies of the Rhizobium leguminosarum species complex (Rlc). Strain Z1P35ᵀ exhibited low average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values with all described Rhizobium species, but high ANI and dDDH values (97.62 and 78.8%, respectively) with Rhizobium sp. SRDI565, representing genospecies M (GsM) of the Rlc, suggesting that Z1P35ᵀ represents a novel species corresponding to GsM within this complex. FastANI screening against all Rhizobium genomes available in GenBank revealed that Z1P35ᵀ shares ANI values above the bacterial species delimitation threshold with 17 unclassified strains, which, together with Z1P35ᵀ and Rhizobium sp. SRDI565 (GsM), form a distinct lineage within the Rlc. These 17 strains originate from root nodules of diverse legume hosts and are distributed across the Mediterranean region and Australia, including representatives of the symbiovars viciae and trifolii. Phylogenomic analysis further confirms the clustering of Z1P35ᵀ with Rhizobium sp. SRDI565 (GsM) and several undescribed Rhizobium strains, forming a unique taxonomic unit clearly distinct from other members of the Rlc. Strain Z1P35ᵀ has a genome of 7.6 Mb with a G+C content of 61 mol% and carries numerous genes associated with chemotaxis, nodulation, nitrogen fixation, phosphate solubilization, iron acquisition and abiotic stress tolerance. Differentiation of Z1P35ᵀ from described Rhizobium species was further supported by phenotypic and chemotaxonomic analyses. Based on these results, we conclude that Z1P35T belongs to a novel species, corresponding to genospecies M within the Rlc, for which we propose the name Rhizobium zaerense sp. nov. The type strain is Z1P35ᵀ (DSM 120601ᵀ=CCMM B1365ᵀ).

Phylogeny

Metagenome-based diversity and functional analysis of culturable microbes in sugarcane.

UNLABELLED: Sugarcane is a key crop for sugar and energy production, and understanding the diversity of its associated microbes is crucial for optimizing its growth and health. However, there is a lack of thorough investigation and use of microbial resources in sugarcane. This study conducted a comprehensive analysis of culturable microbes and their functional features in different tissues and rhizosphere soil of four diverse sugarcane species using metagenomics techniques. The results revealed significant microbial diversity in sugarcane's tissues and rhizosphere soil, including several important biomarker bacterial taxa identified, which are reported to engage in several processes that support plant growth, such as nitrogen fixation, phosphate solubilization, and the production of plant hormones. The Linear discriminant analysis Effect Size (LEfSe) studies identified unique microbial communities in different parts of the same sugarcane species, particularly Burkholderia, which exhibited significant variations across the sugarcane species. Microbial analysis of carbohydrate-active enzymes (CAZymes) indicated that genes related to sucrose metabolism were mostly present in specific bacterial taxa, including Burkholderia, Pseudomonas, Paraburkholderia, and Chryseobacterium. This study improves understanding of the diversities and functions of endophytes and rhizosphere soil microbes in sugarcane. Moreover, the approaches and findings of this study provide valuable insights for microbiome research and the use of comparable technologies in other agricultural fields. IMPORTANCE: This work utilized metagenomics techniques for conducting a comprehensive examination of culturable microbes and their functional characteristics in various tissues and rhizosphere soil of four distinct sugarcane species. This study enhances comprehension of the diversity and functions of endophytes and rhizosphere soil microbes in sugarcane. Furthermore, the methodologies and discoveries of this work offer new perspectives for microbiome investigation and the use of similar technologies in other agricultural fields.

Saccharum

Comparative genomic analysis of a novel heat-tolerant and euryhaline strain of unicellular marine cyanobacterium Cyanobacterium sp. DS4 from a high-temperature lagoon.

BACKGROUND: Cyanobacteria have diversified through their long evolutionary history and occupy a wide range of environments on Earth. To advance our understanding of their adaptation mechanisms in extreme environments, we performed stress tolerance characterizations, whole genome sequencing, and comparative genomic analyses of a novel heat-tolerant and euryhaline strain of the unicellular cyanobacterium Cyanobacterium sp. Dongsha4 (DS4). This strain was isolated from a lagoon on Dongsha Island in the South China Sea, a habitat with fluctuations in temperature, salinity, light intensity, and nutrient supply. RESULTS: DS4 cells can tolerate long-term high-temperature up to 50 ℃ and salinity from 0 to 6.6%, which is similar to the results previously obtained for Cyanobacterium aponinum. In contrast, most mesophilic cyanobacteria cannot survive under these extreme conditions. Based on the 16S rRNA gene phylogeny, DS4 is most closely related to Cyanobacterium sp. NBRC102756 isolated from Iwojima Island, Japan, and Cyanobacterium sp. MCCB114 isolated from Vypeen Island, India. For comparison with strains that have genomic information available, DS4 is most similar to Cyanobacterium aponinum strain PCC10605 (PCC10605), sharing 81.7% of the genomic segments and 92.9% average nucleotide identity (ANI). Gene content comparisons identified multiple distinct features of DS4. Unlike related strains, DS4 possesses the genes necessary for nitrogen fixation. Other notable genes include those involved in photosynthesis, central metabolisms, cyanobacterial starch metabolisms, stress tolerances, and biosynthesis of novel secondary metabolites. CONCLUSIONS: These findings promote our understanding of the physiology, ecology, evolution, and stress tolerance mechanisms of cyanobacteria. The information is valuable for future functional studies and biotechnology applications of heat-tolerant and euryhaline marine cyanobacteria.

Cyanobacteria

Soybean α-Amylase Gene Family: Structure and Expression in Response to Abiotic Stresses.

α-Amylases are involved in starch breakdown, thereby influencing plant development. Information on the α-amylase genes in soybean is limited. Here, we identified five soybean α-amylase genes from subfamilies AtAMY1 (GmaAMY5), AtAMY2 (GmaAMY4), AtAMY3 (GmaAMY1, GmaAMY3), and AMY6 (GmaAMY2). In silico analysis indicated that all five genes were actively expressed in leaves, flowers, and pods but weakly in roots. GmaAMY1-GmaAMY5 mRNAs were predicted to be targets of miRNAs associated with stress response, organ development, and nitrogen fixation. Putative GmaAMY1-GmaAMY5 proteins contained α-amylase-specific catalytic domain, signatures, and active sites. Short-term abiotic stresses (100 mM NaCl, 2.5-20% PEG, and 4 °C cold) applied to the cv. Doka affected both GmaAMY1-GmaAMY5 expression and the content of starch and soluble sugars in leaves. GmaAMY1 gene expression increased in response to NaCl and PEG, GmaAMY2 in response to PEG, and GmaAMY5 in response to NaCl. Salt stress suppressed the expression of the GmaAMY2-GmaAMY4 genes. The mRNA levels of all five genes increased after 2 h of cold exposure. Under salinity stress, there was inverse correlation of starch content with GmaAMY4 expression (r = -0.5135, p = 0.0293) and overall GmaAMY1-GmaAMY5 expression (r = -0.6318, p = 0.0049), suggesting a possible role of GmaAMY genes in protecting soybean from salinity by maintaining the starch/soluble sugars balance. Our results may aid in the breeding of stress-tolerant soybean varieties.

Glycine max

Whole-Genome Analysis and Growth-Promoting Mechanism of Klebsiella pneumoniae YMK25 from Maize Rhizobacteria.

Plant growth-promoting rhizobacteria (PGPR) are microorganisms that enhance plant growth through various mechanisms. In the context of global agriculture, which faces fertilizer dependency and environmental pollution, developing eco-friendly microbial fertilizers has become crucial for enhancing agricultural sustainability. To identify highly effective PGPR, we isolated 102 bacterial strains from maize rhizosphere soil using the dilution plating method. The strains were screened for growth-promoting abilities using functional media, resulting in the selection of strain YMK25 for its exceptional capabilities in nitrogen fixation, solubilization of inorganic and organic phosphorus, indole-3-acetic acid (IAA) production, and siderophore production. Strain YMK25 produced IAA at a concentration of 80.49 ± 0.68 μg/mL and exhibited a relative siderophore expression level of 43.68%. Morphological analysis, 16S rDNA gene sequence analysis, and whole-genome sequencing confirmed that strain YMK25 is Klebsiella pneumoniae. Whole-genome analysis revealed a total genome length of 5,115,280 bp, a GC content of 57.61%, and it contained 4746 coding genes. Gene annotation results indicated genes involved in siderophore synthesis, phosphatase activity, and other plant growth-promoting functions, which align with the verified characteristics of strain YMK25. Furthermore, this strain exhibited significant metabolic capabilities. The pot experiment demonstrated that strain YMK25 promotes maize plant growth and assists in nutrient fixation in these plants. In conclusion, strain YMK25 is a high-quality PGPR with substantial potential for application in agricultural production, presenting promise for widespread use in sustainable agriculture.

Klebsiella pneumoniae

Genes associated with translation and oxidative phosphorylation as components of the translational response in nodulated and water-restricted soybean.

BACKGROUND: Soybean primarily acquires nitrogen through symbiosis with nitrogen-fixing bacteria. Water deficit (WD) is a major stress limiting crop yield. Nodulation may enhance drought tolerance in legumes by modulating nitrogen and hormone metabolism, osmotic adjustment, and antioxidant defenses; however, the molecular basis underlying the differential WD responses between N-fix and N-fed plants remain unclear. Translational control of gene expression is a key regulatory mechanism during stress. RESULTS: We compared the transcriptome and translatome of soybean roots from N-fix and N-fed plants exposed to WD across four combined treatments. N-fix plants under WD exhibited more complex responses in terms of total differentially expressed genes (DEGs) compared to N-fed plants. This increased complexity was also evident among translationally regulated DEGs and differentially expressed transcription factors, whose involvement in WD responses of N-fix plants is novel. Co-expression network analysis identified modules associated with core biological processes encompassing nodulation, WD, and notably, their interplay was particularly prominent in Module 1, which was enriched in genes related to ribosomal protein synthesis and oxidative phosphorylation (OXPHOS). Guilt-by-Association analysis enabled the prediction of novel functions for differentially expressed, uncharacterized hub genes related to stress and/or nodulation responses. CONCLUSIONS: Translational regulation of genes involved in OXPHOS and translation initiation emerged as a central response in N-fix plants under WD. These findings reveal distinct molecular adaptations in N-fix soybean roots facing WD and highlight translational control as a key regulatory layer. We also identified promising candidate genes-including transcription factors and uncharacterized hub genes under translational regulation-that represent potential targets for improving drought tolerance in legumes once validated functionally.

Glycine max

Description of two nitrogen-fixing bacteria, Azospirillum mesophilum sp. nov. and Azospirillum terrae sp. nov., isolated from paddy soils.

Two novel aerobic, rod-shaped, motile bacterial strains, designated as sgz302134T and sgz301742T, were isolated from paddy soil in Fujian Province. Strains sgz302134T and sgz301742T shared the highest 16S rRNA gene sequence similarities with the type strains Azospirillum isscasi C340-1T (98.2%) and Azospirillum thiophilum DSM 21654T (97.4%), respectively. The phylogenetic tree based on 16S rRNA gene sequences showed that two strains clustered with members of the genus Azospirillum. Growth of strains sgz302134T and sgz301742T was observed at 10-45 °C, pH 5.0-9.5 and 0-0.5% (w/v) NaCl and 15-37 °C, pH 6.0-9.0 and 0-1.0% (w/v) NaCl, respectively. Strains sgz302134T and sgz301742T contained Q-10 as the main quinone. The main fatty acids (>10%) of both strains were summed feature 2 (C12 : 0 aldehyde), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The genomic DNA G+C content of strains sgz302134T and sgz301742T was 68.4 and 68.3%, respectively. The digital DNA-DNA hybridization and average nucleotide identity values between the two strains and their related reference strains were 27.8 and 87.4% and 22.0 and 84.3%, respectively. Both strains possessed nif genes nifBDEHKN. Based on the above results, these two strains represent two novel species of the genus Azospirillum, for which the names Azospirillum mesophilum sp. nov. and Azospirillum terrae sp. nov. are proposed. The type strains are sgz302134T (=MCCC 1K09520T=KCTC 8840T) and sgz301742T (=MCCC 1K09804T=KCTC 18149T), respectively.

Soil Microbiology

Gluconacetobacter diazotrophicus as a plant growth-promoting endophyte: mechanistic insights and translational prospects for sustainable agriculture.

With the growing interest in sustainable agriculture, there has been a surge in exploration of multitrophic interactions between plants and microbes that can help plants adapt to changing environments and enhance their resilience to climate changes. One such beneficial microbe is Gluconacetobacter diazotrophicus, an aerobic, nitrogen-fixing endophyte currently being studied because of its ability to fix atmospheric nitrogen within plant tissues under aerobic conditions. This endophyte also promotes plant growth through processes like phytohormone production, nutrient solubilization, and improved stress tolerance of the plant. Recent advances in genomics and systems biology have provided valuable insights into the metabolism, interactions, and functions of this microorganism inside the host plants and its contribution to rhizosphere and endosphere dynamics. Despite considerable advances in understanding this organism, there are still limitations to its application due to its poor field performance, environmental variations, and difficulties in formulation production. This review consolidates the current knowledge on the ecology, physiology, and molecular mechanisms of Gluconacetobacter diazotrophicus, critically assesses its limitations, and identifies future research priorities to enhance its translational potential.

Gluconacetobacter

Mesorhizobium bavaricum sp. nov. and Mesorhizobium monacense sp. nov., two novel Lotus-associated species harbouring symbiotic plasmids.

Legumes establish a mutualistic interaction with nitrogen-fixing rhizobia. Lotus japonicus is a model for studying this symbiosis; however, only a limited number of rhizobial species nodulating this host have been taxonomically described. Here, we characterise four Mesorhizobium strains (DC-1.1T, Qj1B1, DC-1.5T, and Qj2B2) isolated from root nodules of Lotus japonicus and Lotus burttii. Multi-locus phylogeny and phylogenomic analyses resolved these isolates into two well-supported monophyletic clades. Genome-based comparisons supported their classification as distinct taxa, with strains DC-1.1T and Qj1B1 showing 95.2% average nucleotide identity (ANI) and 62.9-63.5% digital DNA-DNA hybridisation (dDDH) values relative to Mesorhizobium newzealandense ICMP 19545T, whereas DC-1.5T and Qj2B2 exhibited 92.5-92.8% ANI and 49.9-50.5% dDDH compared with Mesorhizobium waimense ICMP 19557T. Together with chemotaxonomic and physiological traits, these data support the proposal of two novel species, Mesorhizobium bavaricum sp. nov. (DC-1.1T and Qj1B1) and Mesorhizobium monacense sp. nov. (DC-1.5T and Qj2B2). Metagenomic analyses predicted high environmental prevalence for these novel taxa, particularly within soil habitats. Isolates DC-1.1T, Qj1B1, and DC-1.5T effectively nodulated Lotus burttii and significantly promoted plant growth, whereas Qj2B2 neither nodulated nor enhanced growth. Comparative genomic analysis revealed that the nodulating isolates harbour symbiotic genes (nod, fix, and nif) on symbiotic plasmids, a rare feature in Mesorhizobium strains, whereas Qj2B2 lacks essential nod and nif genes. Consistent with these genomic features, symbiotaxonomic analysis assigned the nodulating isolates to symbiovar loti. These results highlight the potential of these isolates as models for comparative analyses of symbiotic plasmid evolution and horizontal gene transfer.

Mesorhizobium

CRISPR/Cas9-mediated knockout of PsLykX gene of pea (Pisum sativum L.) leads to loss of symbiotic nodules.

Pea (Pisum sativum L.) symbiosis with nodule bacteria supplying plants with additional nitrogen is a very specific plant-microbial interaction. Mutual recognition of the partners occurs through perception of bacterial signal molecules (Nod factors) by plant receptors, enabling bacterial entry via root hairs and formation of nitrogen-fixing nodules. The pea gene Sym2, described but not yet cloned, exists in different allelic forms defining the symbiotic specificity, and is therefore thought to encode a Nod factor receptor. The PsLykX gene is a strong candidate for the Sym2, since its alleles coincide with high or low symbiotic specificity; however, to date, no genetic evidence has been obtained for a role of PsLykX in symbiosis. Here, we knocked-out the PsLykX in European pea cultivar Caméor using Agrobacterium-mediated hairy root transformation and CRISPR-Cas9 editing. The roots with editing events confirmed by sequencing lost the ability to form nodules, providing direct functional evidence that PsLykX is essential, at least, for the symbiosis between pea cultivar Caméor and Rhizobium ruizarguesonis RCAM1026.

Pisum sativum

Long-term PFOA and cadmium Co-contamination alters soil carbon, nitrogen, and phosphorus cycling: Insights from metagenomics and metabolomics.

The co-existence of perfluorooctanoic acid (PFOA) and cadmium (Cd) in soil poses a combined threat to microbial communities. However, the ecological effects and underlying mechanisms of their long-term combined exposure remain poorly understood. This study conducted a 90-day soil microcosm experiment to systematically investigate the effects of individual and combined effects of PFOA and Cd on microbial communities. Our results demonstrated that combined pollution of PFOA and Cd significantly affected four soil enzyme activities associated with carbon, nitrogen, and phosphorus cycling. It also influenced microbial thermal activity with an IC50 of PFOA at 0.94 mg/kg. The toxic interaction between PFOA and Cd varied with both toxicity indicators and exposure time. At the community level, PFOA and Cd synergistically reduced bacterial diversity and richness, while exerting more complex interactive effects on fungal communities. Metagenomic analysis revealed that PFOA and Cd significantly affected carbon, nitrogen, and phosphorus cycling by inhibiting inorganic phosphorus solubilization genes (gcd, pqqC) and altering key genes in carbon fixation and nitrogen transformation. Metabolomic profiling further demonstrated that PFOA disrupted membrane lipid homeostasis and amino acid metabolism. Meanwhile, the co-existence of Cd exacerbated disturbances in sugar and carbon metabolism. Our findings provide genetic-level insights into microbial responses to long-term PFOA and Cd co-contamination. These results are essential for risk assessment at such co-contamination sites.

Cadmium

Concurrent ecological and evolutionary processes contribute to mutualism breakdown between legumes and rhizobia.

Though they jointly shape community responses to environmental perturbations, ecology and evolution are often examined separately, even in microorganisms where both occur over short timescales. Here we examine ecological and evolutionary responses to 33 years of nitrogen fertilization using the legume-rhizobium mutualism. Pairing a manipulative inoculation study with full-length 16S rRNA gene amplicon sequencing and structural equation modeling allows us to synthesize across biological scales: whole bacterial community, genus Rhizobium, Rhizobium ASVs, and symbiosis plasmids. Clover's preferred partner decreases in N-addition soils, limiting host growth, while a diverse and largely uncharacterized Rhizobium community increases. This ecological change is compounded by a concurrent evolutionary degradation of symbiont partner quality via changing frequencies of symbiotic plasmids. Ecological (rarer symbionts) and evolutionary (inferior symbionts) processes each accounted for roughly half of this loss of host benefit, revealing that ecology and evolution jointly shape mutualism breakdown over the short timescales typical of microbial systems.

ecology

Nissolia brasiliensis as a nonnodulating model legume.

The nitrogen-fixing root nodule symbiosis is specifically formed by 4 orders of angiosperms. The largest of these 4 orders includes the legume family, the Fabaceae. Among legumes, historical model species have emerged, such as the root nodule symbiosis-forming Medicago truncatula and Lotus japonicus or, more recently, Aeschynomene evenia. By contrast, legume species that have lost root nodule symbiosis have been largely ignored. Here, we describe the first near chromosome-level assembly for a non-root nodule symbiosis-forming legume, the tropical Papilionoideae Nissolia brasiliensis. We compared its genome to closely related legumes and identified genes associated with root nodule symbiosis. Finally, we developed a stable transformation protocol that can be deployed in the future to reevolve root nodule symbiosis in legumes, a first step toward the goal of engineering root nodule symbiosis in nonlegume crops.

Fabaceae

Metagenome-assembled genomes for N2-fixing cyanobacterium Nostoc sp. TISTR 8405 and co-occurring microorganisms from a long-term laboratory culture.

We report here metagenome-assembled genomes from a long-term laboratory culture of the nitrogen-fixing cyanobacterium Nostoc sp. TISTR 8405, originally sourced from a Thai freshwater lake. The community consists of two additional co-occurring microorganisms, Erythrobacter sp. THAI-01 and Allorhizobium sp. THAI-01, and contains putative plasmids associated with Nostoc and Allorhizobium, respectively.

co-culture