Microorganisms

BackgroundMicrobial communities in the rhizosphere are key drivers of plant immunity, mediating plant responses to stress. Under specific stresses plants are capable of recruiting beneficial microorganisms into their rhizosphere with the potential to alleviate these stresses. Among these stresses, herbivorous pests remain a major agricultural challenge. Despite this, the impact of leaf herbivory on root-associated microbiomes, and how this impact can shape plant defense phenotypes are still understudied. In this study, our main objective was to determine the extent to which leaf herbivory affects the rhizosphere microbiome, and whether and how these herbivory-induced changes modulate plant defense phenotypes through plant-soil feedback. To that end, we designed a two-phase assay in which we challenged sunflower (Helianthus annuus L.) with Spodoptera exigua and later tested the effect of the microbial legacy after infestation on sunflower defense phenotype, considering resistance and tolerance as major drivers. ResultsWe found that herbivory triggered significant changes in the bacteriome structure and dynamics, and microbiome functional profile, while effects on mycobiome were comparatively less pronounced. Under herbivory, several bacterial taxa and functional groups were enriched, the bacterial co-occurrence network was more complex and assembly processes were slightly more stochastic. Furthermore, after evaluating the plant-soil feedbacks of herbivory-induced microbiomes we observed no effect on plant resistance proxies such as herbivore growth and survival, and leaf phenolic and flavonoid content. We did observe differences on tolerance proxies, while plants grown on herbivore-challenged microbiome were overall smaller, the biomass loss to herbivory was significantly lower while the elemental nutrient content and photosynthetic pigments content was enhanced. ConclusionsOur study demonstrates that insect herbivory by S.exigua reshapes sunflower rhizosphere microbiome and generates a soil legacy that promotes herbivory tolerance on subsequent plant generations. This highlights the broader potential of microbiome-mediated plant-soil feedbacks in shaping plant adaptation to herbivory.

Marine non-cyanobacterial diazotrophs (NCDs) are recognized as globally distributed, however, few representatives have been isolated in pure cultures. As a result, understanding the physiology, growth rate, substrate preference and dinitrogen (N2) fixation capabilities proves difficult. Thalassolituus haligoni. sp. nov., BB40 was isolated from a fjord-like inlet within Kjipuktuk (Halifax), Nova Scotia. The fully sequenced genome displayed all necessary genes required for N2 fixation, and various carbon uptake pathways. The gram-negative flagellated rod shape bacterium displayed significantly higher growth rates in medium amended with nitrate (NO3-) or ammonia (NH3), compared to dissolved N2, as the sole nitrogen source. Biological N2 fixation rates were detectable across all conditions, measuring a range from 9.34 x 10-6 to 1.4 x 10-1 fmol N cell-1 day-1. Growth of the isolate was successful between 4 {degrees}C up to 35 {degrees}C, with a Topt of 20 {degrees}C for N2, and between 27 - 30 {degrees}C for fixed nitrogen (NO3- and NH3). The closest relatives to T. haligoni, were found to be the uncultured Arc-gamma-03 (99% average nucleotide identity (ANI)) and Oceanobacter antarcticus (81% ANI). T. haligoni also displays versatile capabilities for growth on various carbon, and nitrogen sources, and antibiotics. Collectively this study provides an in-depth physiological assessment of an Oceanospirillales diazotrophic species which we presently have limited knowledge of.

BackgroundThe composition and function of the gut microbiome have been shown to contribute to both health and disease. One of the most powerful modulators of microbial composition and function is diet. Materials & MethodsUsing the E{micro}-TCL1 murine model of B-cell chronic lymphocytic leukemia (CLL), we assigned male and female mice to a high-fat, high-carbohydrate Western diet (HF) or standard chow (CH) diet. ResultsMice consuming a HF diet had significantly shorter survival than those consuming a CH diet, irrespective of sex, with female mice exhibiting particularly poor outcomes. We also observed a significant increase in splenic involvement by CLL in the HF diet-fed mice at time of sacrifice. Mice receiving the HF diet demonstrated immediate and profound effects on the gut microbiome, marked by reduced alpha diversity and significantly different community composition as measured by beta diversity. Notably, there was a sustained increase in Akkermansia muciniphila and Bacteroidetes thetaiotaomicron in HF diet-fed mice, coupled with a corresponding increase in microbiome functional pathways related to arginine and histidine biosynthesis, chitin degradation, and nucleotide biosynthesis. DiscussionCollectively our data provides evidence of the profound and sustained impact of a high-fat Western diet upon the gut microbiome community and CLL pathogenesis in the E{micro}-TCL1 murine model of CLL.

The growth of cultures and formation of mucilage blooms in reaction to salt stress of cyanobacterial cultures are investigated with a focus on the influence of pH. In non-buffered medium, cultures show their pH increasing from 6.5 just after inoculation, up to 11 during the exponential phase. We record the time-evolution of concentration and pH, with different initial OD0. In a second set of experiments, we extract the doubling time of the unbuffered cultures in comparison with those inoculated in pH-buffered BG11 media at four different pH from 6.3 to 10.5 : in the most acid media, all cultures die or grow very slowly. At pH = 10.5, we obtain the fastest growth for all four strains, allowing to qualify these cyanobacteria as being alkaliphiles, though for all strains with comparable initial OD0, the doubling time is shorter for unbuffered cultures. Following a previous study [31]), we finally investigate the influence of pH on mucilage formation and biomass uplift induced by salt stress, involving EPS floculation by cations. Our results show that operating in buffered media significantly influences the mucilage formation, though the observed regimes cannot be simply correlated to the pH value.

Currently, there are three recognized rhizobial genera belonging to the beta branch of the proteobacteria; Trinickia, Paraburkholderia, and Cupriavidus. These beta-rhizobia have been found associated with legume species mainly within the Mimosoideae and Papillonoideae. Most diversity, evolutionary, and functional studies have focused on Paraburkholderia, whereas few have addressed the diversity and evolution of symbiosis in the Cupriavidus genus. The present work aimed to provide an actual view of the symbiotic Cupriavidus diversity and to analyse the origin and evolution of their symbiotic genes. Using whole-genome information for phylogenetic reconstruction, we showed that the described symbiotic Cupriavidus strains belong to five distinct lineages, although they are intermixed with non-symbiotic species. The high synteny and sequence conservation of symbiotic genes suggest a common origin of acquisition for all rhizobial Cupriavidus described so far. However, we observed very low sequence conservation among (mega)plasmids carrying the symbiotic island, excluding the existence of a conserved symbiotic plasmid within beta-rhizobia. We can conclude that up to now there are five rhizobial species within the Cupriavidus genus, and we predict the description of new symbiotic species in the near future.

Non-pathogenic Xanthomonas (NPX) from a diverse plant hosts are being reported on an increasing basis. There are also reports of multiple species forming communities on a single host plant, such as rice, and, given their role as core endophytes in protecting plants from pathogens, it is essential to isolate and characterization of more NPX species from diverse host plants. Using phylogenomic analysis of publicly available Xanthomonas genome sequences, we identified a novel clade comprising NPX strains from diverse hosts. One of the strains previously reported from our lab is from healthy rice seeds and was reported to be non-pathogenic, with bio-protection function against the bacterial leaf blight pathogen. Genomic investigation confirmed the lack of type III secretion system and its effectors, consistent with their non-pathogenic nature. These strains also harbour core and unique biosynthetic loci identified in other non-pathogenic Xanthomonas (NPX) strains. Further investigation using multiple genomic-based taxonomic indices indicates that these strains represent a potential new species. Hence, we propose Xanthomonas imtechensis sp. nov. as a new species of the genus Xanthomonas, with the type strain being PPL568 = MTCC 13186 = CFBP 9040 = ICMP 24395.

European ash dieback caused by the invasive ascomycete species Hymenoscyphus fraxineus poses the most prominent danger to common ash trees (Fraxinus excelsior) in Europe. The disease is widely distributed in Europe and currently no efficient management strategy is available. Host-induced gene silencing and exogenous dsRNA applications have shown great potential for controlling fungal diseases in crop plants. In this study, we reported in silico evidence for the presence of a functional RNA interference pathway in Hymenoscyphus fraxineus. Moreover, we showed that the transgenic expression of a double stranded RNA (dsRNA) leads to inhibition of translation of its target polyketide synthase-like gene, a fungal endogene. We explored whether the dsRNA could be introduced exogenously and demonstrated that H. fraxineus can take up externally applied dsRNA molecules. This study highlights the RNA interference mechanism in H. fraxineus and suggests exoRNA applications as a promising approach to control European ash dieback.

BackgroundRespiratory tract infections range from asymptomatic colonisation to an invasive disease. Recent studies suggest that nasopharyngeal microbiota may influence this variability. Emerging evidence points to Dolosigranulum pigrum, a nasopharyngeal commensal, as a potentially protective bacterium. This study aimed to identify variables associated with the presence of D. pigrum in the nasopharynx of children with varying respiratory health statuses. MethodsNasopharyngeal aspirates were collected from children <18 years who were asymptomatic (n=65), had banal viral infection (n=48), or Invasive Pneumococcal Disease (IPD) (n=27). The presence of D. pigrum was defined as >0.1% of total sequences obtained by 16S rRNA gene sequencing. Variables included sex, breastfeeding, delivery mode, S. pneumoniae carriage, respiratory viruses and clinical features. ResultsAmong 140 children (73 males, 67 females), D. pigrum was detected in 79 (56.4%): 44/65 in the healthy group; 26/48 of viral and 9/27 IPD cases. Multivariate analysis revealed significant associations with health status and sex. Healthy children were more likely to carry D. pigrum than IPD cases (44/79 vs. 26/79; p= 0.028). Males were more frequently D. pigrum carriers than females (48/79 vs. 31/79; p= 0.033). ConclusionD. Pigrum was associated with respiratory health, being more prevalent in healthy children, and showed potential sex-related differences.

Purine moieties are essential for many functions within the eukaryotic cell, including energy, signaling and nucleic acid synthesis. While purine starvation is known to induce stress resistance in eukaryotic model organism budding yeast Saccharomyces cerevisiae, it remains unclear whether the physiological response is related to disruption of synthesis pathway in particular position or it is uniform across all genetic deficiencies within the de novo adenine biosynthesis pathway. It is also not known how purine starved cells perceive purine shortage - weather they share the same signaling elements with nitrogen starvation or not. MethodsWe characterised physiology of strains with deletions in adenine biosynthesis pathway when cultivated in full or purine deficient and compared to cell physiological parameters when cultivated in nitrogen deficient media. We tested stress tolerance, carbon flux, cell cycle arrest and did transcription profiling (RNA-seq). ResultsOur findings demonstrate that purine starvation-induced stress resistance is significantly modulated by the specific step at which the pathway is interrupted. Transcriptional analysis revealed that purine starvation in many aspects phenocopies nitrogen starvation, particularly - in both starvations strong downregulation of ribosome related genes occurs. In the same time several metabolic features which differ from N- and ade- starvations: pentose phosphate pathway is specifically upregulated within ade4{Delta}-ade2{Delta} and downregulated in N-cells. Notably, the expression of stress-responsive genes such as HSP12, HSP26, and GRE1 varied between mutants, suggesting that the accumulation of pathway intermediates (e.g., AIR in ade2{Delta}) or the absence of downstream precursors (AICAR) alters the perception of starvation especially in the case of ade16{Delta}ade17{Delta} strain. ConclusionsMetabolic and stress-tolerance phenotypes of purine auxotrophs are not merely a result of purine depletion but seems that the response is signalled via the same pathways, like TOR1. The results suggest that strains having mutations within various positions of the purine pathway "perceive" purine limitation a bit differently - especially when we compare the end of the pathway with the other mutants. Different phenotypic outcomes of the occasional purine depletion might give preferences for organisms which have mutations in the beginning rather at the end of the pathway. Besides, our findings might have implications in the design of synthetic pathways and the use of auxotrophic markers in yeast research.

The emergence of vaccine covered serotypes causing invasive pneumococcal disease (IPD) is a serious concern worldwide. We investigated the unexpected rise of serotype 4 causing IPD primarily in non-vaccinated young adults after the COVID-19 pandemic that further spread to adults [&ge;] 65 years in recent years. For this purpose, we conducted a retrospective study of serotype 4 IPD cases (n=827) reported in Spain between 2009 and 2024. Whole-genome sequencing was performed to assess clonal lineages and phylogenetic relationships. Clinical and epidemiological data were compared between serotype 4 and all other serotypes causing IPD. Epidemiological and genomic analysis confirmed that the rise started as an abrupt cluster of IPD cases in Seville (Andalusia) in the year 2022 due to the ST15063 within GPSC12 lineage. This outbreak initially caused pneumonia episodes that required hospitalization in young individuals associated with high rates of tobacco smoking, alcohol, and inhaled drugs such as cannabis and cocaine, followed by a general distribution pattern throughout the country in the following years, affecting the elderly population. Experimental studies to evaluate potential underlying mechanisms confirmed that ST15063 serotype 4 strains displayed enhanced infection rates of human lung cells that significantly increased in the presence of cigarette smoke exposure and by influenza H3N2 virus coinfection, but not with H1N1. These findings highlight the need for targeted vaccination strategies not only against pneumococcus but also against respiratory viruses such as influenza, RSV and COVID-19 and demonstrate the importance of molecular surveillance to establish effective interventions in high-risk populations.

The transcription factor Pho4 is crucial for the response to phosphate starvation in many fungi, and it has been linked to tolerance to alkalinization of the medium and to pathogenicity. It is widely accepted that it is encoded by a single gene. However, the industrially relevant yeast Komagataella phaffii might contain two Pho4-encoding genes (PAS_chr1-1_0265 and PAS_chr2-1_0177, designated here PHO4(A) and PHO4(B), respectively), which have never been functionally characterized. The phenotypic analysis of single and double mutants suggests that Pho4(B) plays a major role in the adaptation to Pi scarcity. While single mutants exhibited limited and non-overlapping phenotypic defects, the pho4(A) pho4(B) strain was sensitive to multiple types of stress, including phosphate starvation and alkaline pH. Transcriptomic analysis confirms that Pho4(B) is crucial for the transcriptional response to phosphate starvation, including induction of typical gene markers (PHO5, PHO89, VTC1, etc.). However, by using a GFP reporter we found that PHO4(A) also participates in the induction of PHO89 under high pH stress. Expression of both PHO4(A) and PHO4(B) in S. cerevisiae complemented the pho4 mutation under phosphate limitation by restoring growth, expression of the Pho84 transporter and secreted phosphatase activity. These results indicate that both transcription factors display partially overlapping functions, responding differently to diverse stimuli, and that together they constitute a key component in the adaptation to a variety of stresses. Therefore, K. phaffii is an exceptional example among fungi that encodes two Pho4 functional transcription factors.

BackgroundPotato is an important crop worldwide, yet its production is severely threatened by Phytophthora infestans, the causal agent of late blight. Alternatives to the current control strategies are needed, as these rely heavily on environmentally harmful treatments. The recruitment of beneficial microbes by plants upon stress ("cry-for-help" mechanism) may represent an opportunity to find new biocontrol agents but this has not yet been reported for potato. The aim of this study was to analyse whether foliar late blight infection induces shifts in the phyllosphere, rhizosphere and soil bacterial communities associated with two potato cultivars of differing sensitivity to late blight. Moreover, we aimed at isolating members of the plant microbiota to test whether bacteria putatively recruited upon infection would be particularly active in protecting the plant against late blight. ResultsControlled foliar infection triggered substantial, cultivar-specific shifts in the rhizosphere communities across two successive generations. Despite the number of differentially abundant ASVs detected being ten times higher in the second generation than in the first one, the same taxonomic groups were concerned by the shifts: Burkholderiales, Flavobacteriales, and Bacillales. Furthermore, the communities linked to the susceptible cultivar consistently shifted more strongly than the communities linked to the resistant cultivar. The obtained ASV sequences were used to identify 163 corresponding isolates. The inhibition potential of these strains against P. infestans spores was assessed through biological assays, which revealed the biocontrol potential of strains otherwise not yet known to inhibit phytopathogenic organisms, such as Advenella, Nocardioides and Phyllobacterium strains. Although we found no correlation between the relative abundance shift of the ASVs upon infection and the activity of the corresponding strains, we observed that the overall activity of strains isolated from the resistant cultivar was higher than that of the strains isolated from the susceptible one. ConclusionTaken together, the higher activity of the strains isolated from the resistant cultivar, along with its comparatively modest microbiome shifts upon infection suggest that the investigated resistant cultivar might harbour specific microbiota enriched in strains with efficient protective abilities against their host plants pathogens, which possibly contribute to its higher resistance against P. infestans.

BackgroundTuberculosis (TB) is the second-leading cause of deaths from infectious agents and remains a global health threat. Ethionamide (ETH) is a prodrug used in regimens for multidrug-resistant TB, and, partly due to side effects that can lead to low treatment adhesion, resistance arises. Changes in EthA, the monooxygenase that activates ETH, are the main mechanism of resistance. Yet, of hundreds of EthA substitutions found in resistant isolates, only a handful have been annotated as resistance determinants. ResultsAn in silico analysis was carried out on a previously described panel of Mycobacterium tuberculosis clinical isolates for which genomes and ETH susceptibility testing results were available. EthA substitutions were mapped, revealing the existence of hotspots in its sequence. Visualization of the hotspots in the EthA structural model shows that they cluster in three regions, including ligand binding pockets. Models were built of twenty-three variants found in resistant isolates and changes in local configuration was mapped to identify investigate impact on ETH activation. Information from these models contributed to establishing five criteria for scoring whether substitutions are most likely to lead to resistance. Using these criteria, EthA D58G was selected and its expression is shown to increase growth in high ETH concentrations. ConclusionFunctionally relevant regions of EthA are revealed and point out priority substitutions for functional studies, enhancing identification and detection of substitutions not been previously associated with resistance.

Toxoplasma gondii is a globally prevalent zoonotic parasite with multiple life stages and transmission routes, including ingestion and transplacental transmission. It is a major cause of abortion in sheep, goats and pigs, among other production animals, worldwide. While Type II strains are common in livestock in North America and Europe, non-archetypal, non-clonal genotypes are highly prevalent in South America. This study aimed to determine the molecular epidemiology of T. gondii strains causing sheep abortion in Uruguay. Phylogenomic analyses confirmed significant divergence among typed strains and revealed similarities with genotypes previously detected in the human population. Two novel strains, were isolated and characterized, uncovering the connection between their genetic makeup and phenotypes. Differences in virulence could be correlated to differences in gene copy number of the pseudo kinase ROP5 - further highlighting this virulence factor as relevant in wild strains. Whole-genome sequencing further confirmed the divergence among Uruguayan isolates, uncovering at least three distinct evolutionary origins. Overall, our findings highlight the circulation of virulent non-clonal lineages with links to human infections and underscore the importance of furthering genomic surveillance in South America to better understand Toxoplasmas transmission dynamics, pathogenic potential, and zoonotic risk.

Glutathione has important roles in diverse infections, yet its involvement in the interaction between the deadly fungal pathogen Batrachochytrium dendrobatidis (Bd) and its amphibian hosts is still unclear. Using in vitro assays and a cell infection model, we examined how glutathione influences Bd virulence traits and cellular host disease resistance. For Bd, inhibition of glutathione reductase rapidly killed zoospores, indicating that glutathione is essential for this pathogen. In addition, exposure to exogenous glutathione promoted the potential for virulence through accelerated and increased zoospore release. In host amphibian cells, Bd infection decreased intracellular glutathione content and increased reactive oxygen species, suggesting that chytridiomycosis pathogenesis may involve oxidative stress. Depletion of host glutathione before exposure to Bd increased infection severity and Bd growth, whereas amphibian cells with slightly elevated glutathione levels were partially protected against Bd. However, manipulation of host glutathione levels after the establishment of Bd infection did not impact its intracellular growth, implying that the host glutathione-mediated resistance only occurs during the initial Bd invasion process. Importantly, this effect of glutathione on host resistance is not a general response to pathogens, as it was not observed in cells exposed to viral pathogen FV3. As glutathione increased both infectious zoospore production and host resistance to zoospore infection, our study suggests that this antioxidant may play an important role in the host/pathogen interaction during chytridiomycosis. Thus, environmental conditions and therapeutic approaches that affect glutathione systems in the host and/or pathogen have the potential to alter chytridiomycosis dynamics and should be further explored.

The strain LEGE 10371, isolated from the surface of a marine sponge at Praia da Memoria, Portugal, was characterized as a new Thalassoporum species (Pseudanabaenales) using a polyphasic approach that included 16S rRNA gene phylogenetic analysis (Maximum Likelihood and Bayesian Inference), 16S-23S ITS secondary structures, p-distance calculations, MALDI-TOF MS profiling, and morphological analysis by optical and scanning electron microscopy, as well as ecological and biochemical characterization. Phylogenetically, LEGE 10371 clustered within the Thalassoporum clade, however distant from the other existent species of the genus. The p-distance analysis revealed low sequence identity with other Thalassoporum species, with a maximum value of 97.2% to Th. komareki. The MALDI-TOF profile displayed high-intensity peaks at approximately 3,000, 4,000, 6,000 and 8,000 m/z, representing strong candidates for diagnostic markers of the new species. Morphologically, the new species differ from the other species of the genus by presenting trichomes with more than 10 cells and lack of aerotopes. Biocompatibility of the fractions was evaluated in HaCaT keratinocytes, showing no cytotoxic effects at most tested concentrations. PCR screening targeting mcyE, sxtG, anaC, and cyrA confirmed the absence of the genetic potential for the production of major cyanotoxins. Chemical characterization revealed a pigment-rich profile dominated by chlorophyll-a and carotenoids, including {beta}-carotene, zeaxanthin, lutein, and mixoxanthophyll. Bioactivity assays showed superoxide anion radical scavenging by the aqueous fraction (IC2 {approx} 0.042-0.045 mg mL-{superscript 1}), strong nitric oxide radical scavenging by the acetonic fraction (IC = 0.045 mg mL-{superscript 1}), and lipoxygenase inhibition ([~]41%, for a fraction concentration of 0.25 mg mL-), suggesting a potential contribution of these fractions to modulate inflammation-related pathways. Additionally to this results, the polyphasic analysis permitted to confirm previous data that Pseudanabaena and Limnothrix represent the same generic entity. Both genera clustered together, presented high 16S rRNA gene identity (up to 99.9%) and share the same morphological and ecological features. Consequently, we formally proposed the synonimization of Limnothrix into Pseudanabaena.

BackgroundPeriodontitis (Perio) is a progressive oral disease characterized by inflammation and degradation of the periodontal apparatus and is associated with local and systemic morbidity including loss of teeth, cardiovascular disease, and diabetes mellitus, among others. Perio is highly prevalent in domestic canines and exhibits certain parallels in pathogenesis and pathophysiology to Perio in humans, although standard treatments are less effective. In both species, a complex interplay between oral microbiota and host immune response is implicated in the etiology of Perio but is not fully understood. ResultsUsing shotgun metagenomics and RNA-seq on oral samples from companion dogs, we identify features of the oral microbiome and host transcriptional profile that are associated with Perio and its progression. We observe differences in microbiota composition between Perio and non-Perio animals that are largely consistent with what has been described in humans but also identify several species that are distinctly associated with canine Perio. We observe an abrupt shift in host gene expression related to immune response and tissue structure that is associated with disease severity, specifically the progression from mild periodontal disease (PD) to more severe Perio and the initiation of clinical attachment loss. The gingival plaque microbiota exhibits a parallel dynamic, with distinct compositional profiles in mild, moderate, and severe PD. We then examine several of the known mechanistic components of the keystone pathogen hypothesis of PD, identifying specific commonalities between canine and human pathologies, including the involvement of Porphyromonas species and related virulence factors. Additionally, we show infiltration of gingival tissue by Porphyromonas and Tannerella spp. via fluorescence microscopy. Finally, we assess correlations between host gene expression and microbial metabolic pathways which suggest additional potential virulence factors. ConclusionsThis work elucidates the metagenomic and transcriptomic signatures of Perio in companion dogs with the goals of informing veterinary medicine, evaluating the potential of canines as a model organism for the study of Perio, and clarifying the relationship between Perio development and progression, the oral microbiota, and the localized host response. Our findings provide insight into the etiopathogenesis of canine Perio and its relationship to human Perio and suggest novel targets of potential translational interest.

BackgroundGlobally, seagrass ecosystems are threatened by anthropogenic activities that are leading to increased levels of eutrophication, coastal pollution and thermal conditions. Consequently, there is a growing need to develop new approaches that work to mitigate these stressors and enhance restoration efforts in seagrass meadows. One promising strategy is to identify, isolate and characterize microbial consortia that are likely to support seagrass productivity. However, our current understanding of key microbial functions that support plant growth in marine systems is limited. Based on evidence from terrestrial plant-microbe systems, seagrass-associated bacteria are expected to provide the plant with nitrogen and phosphorus resources while detoxifying sulfur and producing phytohormones. Here, we sequenced 61 bacterial cultures isolated from the rhizosphere, rhizoplane, and endosphere of the seagrass, Zostera marina to identify a consortium of six putative plant growth promoting (PGP) candidates. ResultsOur cultivation approach using plant-based media allowed us to isolate 201 bacteria from Z. marina, which reflected 18% of the total microbial diversity of the starting inoculum. Genomic and phenotypic analyses of the 61-sequenced pure-cultures revealed that most of the sequenced taxa were able to mobilize nitrogen primarily through catabolic pathways, including denitrification (51%), dissimilatory nitrate reduction to ammonia (71%), and C-N bond cleavage (83%). Six of the isolates, which represent new lineages of Agarivorans, coded for the nitrogenase gene cassette. Additionally, 52% of the genomes had genes for sulfur and/or thiosulfate oxidation, 88.5% for phosphorus solubilization, and 60.5% for IAA production. Genomic analysis also revealed that some pathways, including denitrification and dissimilatory nitrite to ammonia DNRA, required cross-species cooperation as no one taxa contained all the genes needed to complete these metabolic pathways. Based on draft genome models and results from phenotypic assays, isolates Streptomyces sp. (Iso23 and Iso384), Mesobacillus sp (Iso127), Roseibuim sp. (Iso195), Peribacillus sp. (Iso49), and Agarivorans sp. (Iso311) represent a minimal microbial community that is likely to promote seagrass growth and enhance restoration efforts. ConclusionOur work provides a detailed genomic and phenotypic analysis of bacteria isolated from Z. marina and identifies a minimal microbial community with complementary PGP traits. Isolating, identifying and characterizing bacteria that promote seagrass growth is critical towards enhancing restoration efforts of seagrass meadows.

BackgroundThe global rise of antimicrobial resistance has intensified the search for new microbial metabolites from underexplored environments and taxonomic groups. Extreme and geographically isolated habitats, such as Antarctic terrestrial ecosystems, represent promising reservoirs of novel biosynthetic diversity, particularly among rare and difficult-to-cultivate actinomycetes, where chemical mediators are thought to play key roles in microbial persistence and interaction under resource-limited conditions. ResultsHere, we report the characterization of kineochelins, a previously undescribed group of siderophores produced by an Antarctic isolate, Actinokineospora sp. UV203 representing difficult to cultivate actinomycetes. Structural elucidation revealed a set of closely related congener molecules with a mixed-ligand architecture consistent with metal-chelating activity. Genome mining combined with transcriptomic analysis identified the involvement of a dedicated nonribosomal peptide synthetase-encoding biosynthetic gene cluster responsible for kineochelin production. Comparative genomic analyses showed that, although kineochelin biosynthetic genes share limited homology with those of known mixed-ligand siderophores, their biosynthetic pathways differ substantially in gene content and organization, indicating a distinct evolutionary lineage. Functional characterization of kineochelins demonstrated strong and selective iron chelation, with pronounced affinity for ferric and ferrous iron. Crude culture extracts inhibited the growth of bacterial strains isolated from the same Antarctic environment, suggesting that kineochelin-associated chemistry contributes to iron-mediated competitive interactions within native microbial communities. In addition, kineochelin-enriched fractions exhibited selective inhibitory activity against the opportunistic yeast pathogen Nakaseomyces glabratus and a clinical isolate of Saccharomyces cerevisiae associated with invasive infection. ConclusionsTogether, these findings expand the known chemical and biosynthetic diversity of the genus Actinokineospora and demonstrate that Antarctic rare actinomycetes are a valuable source of novel natural products with potential relevance for microbial ecology and biotechnology. The ecological activities of kineochelins highlight the role of iron acquisition in shaping microbial interactions in extreme environments and underscore the biotechnological potential of metabolites derived from underexplored polar microorganisms.

BACKGROUNDEndophytic fungi are naturally inhabiting plant organs without causing disease symptoms. They can also contribute to their hosts pest and disease resistance by displaying entomopathogenic and/or antifungal traits. In this study, we evaluated the ability of 11 strains of avocado fungal endophytes to antagonize three important avocado plant pathogens: Colletotrichum gloeosporioides, Fusarium solani, and Phytophthora cinnamomi, and two insect pests: Sitophilus zeamais and Xyleborus bispinatus. RESULTSThe results show that Trichoderma spp. strains were the most effective against the evaluated plant pathogens in terms of growth inhibition, in direct contact assays or through metabolite production. Other fungi, such as Purpureocillium sp. and Pochonia sp., only exhibited pathogen inhibition through diffusible metabolites but displayed strong insecticidal capacity against the evaluated pests, hence being identified as promising multi-target biocontrol agents in the integrative analysis. CONCLUSIONOur findings evidence the potential of avocado fungal endophytes and their metabolites as multi-target biocontrol agents of crop pests and pathogens.