Comparative genomics of plant growth promoting phosphobacteria isolated from acidic soils

Despite being one of the most abundant elements in soil, phosphorus (P) often becomes a limiting macronutrient for plants due to its low bioavailability, primarily locked away in insoluble organic and inorganic forms. Phosphate solubilizing and mineralizing bacteria, also called phosphobacteria, isolated from P-deficient soils have emerged as a promising biofertilizer alternative, capable of converting these recalcitrant P forms into plant-available phosphates. Three such phosphobacteria strains-Serratia sp. RJAL6, Klebsiella sp. RCJ4, and Enterobacter sp. 198-previously demonstrated their particular strength as plant growth promoters for wheat, ryegrass, or avocado under abiotic stresses and P deficiency. Comparative genomic analysis of their draft genomes revealed several genes encoding key functionalities, including alkaline phosphatases, isonitrile secondary metabolites, enterobactin biosynthesis and genes associated to the production of indole-3-acetic acid (IAA) and gluconic acid. Moreover, overall genome relatedness indexes (OGRIs) revealed substantial divergence between Serratia sp. RJAL6 and its closest phylogenetic neighbours, Serratia nematodiphila and Serratia bockelmanii. This compelling evidence suggests that RJAL6 merits classification as a novel species. This in silico genomic analysis provides vital insights into the plant growth-promoting capabilities and provenance of these promising PSRB strains. Notably, it paves the way for further characterization and potential application of the newly identified Serratia species as a powerful bioinoculant in future agricultural settings.

Proteomic response to phosphorus deficiency and aluminum stress of three aluminum-tolerant phosphobacteria isolated from acidic soils

Aluminum (Al)-tolerant phosphobacteria enhance plant growth in acidic soils by improving Al complexing and phosphorus (P) availability. However, the impact of Al stress and P deficiency on bacterial biochemistry and physiology remains unclear. We investigated the single and mutual effects of Al stress (10 mM) and P deficiency (0.05 mM) on the proteome of three aluminum-tolerant phosphobacteria: Enterobacter sp. 198, Enterobacter sp. RJAL6, and Klebsiella sp. RCJ4. Cultivated under varying conditions, P deficiency upregulated P metabolism proteins while Al exposure downregulated iron-sulfur and heme-containing proteins and upregulated iron acquisition proteins. This demonstrated that Al influence on iron homeostasis and bacterial central metabolism. This study offers crucial insights into bacterial behavior in acidic soils, benefiting the development of bioinoculants for crops facing Al toxicity and P deficiency. This investigation marks the first proteomic study on the interaction between high Al and P deficiency in acid soils-adapted bacteria.

A Comparative Study of the Synthesis and Characterization of Biogenic Selenium Nanoparticles by Two Contrasting Endophytic Selenobacteria

The present study examined the biosynthesis and characterization of selenium nanoparticles (SeNPs) using two contrasting endophytic selenobacteria, one Gram-positive (Bacillus sp. E5 identified as Bacillus paranthracis) and one Gram-negative (Enterobacter sp. EC5.2 identified as Enterobacter ludwigi), for further use as biofortifying agents and/or for other biotechnological purposes. We demonstrated that, upon regulating culture conditions and selenite exposure time, both strains were suitable "cell factories" for producing SeNPs (B-SeNPs from B. paranthracis and E-SeNPs from E. ludwigii) with different properties. Briefly, dynamic light scattering (DLS), transmission electron microscopy (TEM), and atomic force microscopy (AFM) studies revealed that intracellular E-SeNPs (56.23 ± 4.85 nm) were smaller in diameter than B-SeNPs (83.44 ± 2.90 nm) and that both formulations were located in the surrounding medium or bound to the cell wall. AFM images indicated the absence of relevant variations in bacterial volume and shape and revealed the existence of layers of peptidoglycan surrounding the bacterial cell wall under the conditions of biosynthesis, particularly in the case of B. paranthracis. Raman spectroscopy, Fourier transform infrared spectroscopy (FTIR), energy-dispersive X-ray (EDS), X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS) showed that SeNPs were surrounded by the proteins, lipids, and polysaccharides of bacterial cells and that the numbers of the functional groups present in B-SeNPs were higher than in E-SeNPs. Thus, considering that these findings support the suitability of these two endophytic stains as potential biocatalysts to produce high-quality Se-based nanoparticles, our future efforts must be focused on the evaluation of their bioactivity, as well as on the determination of how the different features of each SeNP modulate their biological action and their stability.

Melanin Induction Restores the Pathogenicity of Gaeumannomyces graminis var. tritici in Wheat Plants

One of the most challenging aspects of long-term research based on microorganisms is the maintenance of isolates under ex situ conditions, particularly the conservation of phytopathological characteristics. Our research group has worked for more than 10 years with Gaumannomyces graminis var. tritici (Ggt), the main biotic factor affecting wheat. In this sense we preserved the microorganisms in oil overlaid. However, several strains preserved for a long time lost their pathogenicity. These strains show white and non-infective mycelia. In this sense, we hypothesized that this is attributable to low melanin content. Melanin is a natural pigment mainly involved in UV protection, desiccation, salinity, oxidation, and fungal pathogenicity. Therefore, understanding the melanin role on Ggt pathogenicity is fundamental to developing melanin activation strategies under laboratory studies. In this study, we induce melanin activation by UV-A light chamber, 320 to 400 nm (T1) and temperature changes of 30 °C, 15 °C, and 20 °C (T2). Fungal pathogenicity was evaluated by determination of blackening roots and Ggt was quantified by real-time PCR in inoculated wheat plants. Results revealed that Ggt grown under UV-A (T1) conditions showed around 40% higher melanin level with a concomitant effect on root infection (98% of blackened roots) and 4-fold more Ggt genome copy number compared with the control (non-infective mycelia) being T1, a more inductor factor compared with T2. These findings would support the role of melanin in pathogenicity in darkly pigmented fungi such as Ggt and could serve as a basis for activating pathogenicity under laboratory conditions.

Protist–Lactic Acid Bacteria Co-Culture as a Strategy to Bioaccumulate Polyunsaturated Fatty Acids in the Protist Aurantiochytrium sp. T66

Thraustochytrids are aquatic unicellular protists organisms that represent an important reservoir of a wide range of bioactive compounds, such as essential polyunsaturated fatty acids (PUFAs) such as arachidonic acid (ARA), docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), which are involved in the regulation of the immune system. In this study, we explore the use of co-cultures of Aurantiochytrium sp. and bacteria as a biotechnological tool capable of stimulating PUFA bioaccumulation. In particular, the co-culture of lactic acid bacteria and the protist Aurantiochytrium sp. T66 induce PUFA bioaccumulation, and the lipid profile was evaluated in cultures at different inoculation times, with two different strains of lactic acid bacteria capable of producing the tryptophan dependent auxins, and one strain of Azospirillum sp., as a reference for auxin production. Our results showed that the Lentilactobacillus kefiri K6.10 strain inoculated at 72 h gives the best PUFA content (30.89 mg g−1 biomass) measured at 144 h of culture, three times higher than the control (8.87 mg g−1 biomass). Co-culture can lead to the generation of complex biomasses with higher added value for developing aquafeed supplements.

Engineering Multigenerational Host-Modulated Microbiota against Soilborne Pathogens in Response to Global Climate Change

Crop migration caused by climatic events has favored the emergence of new soilborne diseases, resulting in the colonization of new niches (emerging infectious diseases, EIDs). Soilborne pathogens are extremely persistent in the environment. This is in large part due to their ability to reside in the soil for a long time, even without a host plant, using survival several strategies. In this regard, disease-suppressive soils, characterized by a low disease incidence due to the presence of antagonist microorganisms, can be an excellent opportunity for the study mechanisms of soil-induced immunity, which can be applied in the development of a new generation of bioinoculants. Therefore, here we review the main effects of climate change on crops and pathogens, as well as the potential use of soil-suppressive microbiota as a natural source of biocontrol agents. Based on results of previous studies, we also propose a strategy for the optimization of microbiota assemblages, selected using a host-mediated approach. This process involves an increase in and prevalence of specific taxa during the transition from a conducive to a suppressive soil. This strategy could be used as a model to engineer microbiota assemblages for pathogen suppression, as well as for the reduction of abiotic stresses created due to global climate change.

Microbial Community Composition in Take-All Suppressive Soils

Gaeumannomyces graminis var. tritici (Ggt) is the main soilborne factor that affects wheat production around the world. Recently we reported the occurrence of six suppressive soils in monoculture areas from indigenous "Mapuche" communities, and evidenced that the suppression relied on the biotic component of those soils. Here, we compare the rhizosphere and endosphere microbial community structure (total bacteria, actinomycetes, total fungi, and ascomycetes) of wheat plants grown in suppressive and conducive soils. Our results suggested that Ggt suppression could be mediated mostly by bacterial endophytes, rather than rhizosphere microorganisms, since the community structure was similar in all suppressive soils as compared with conducive. Interestingly, we found that despite the lower incidence of take-all disease in suppressive soils, the Ggt concentration in roots was not significantly reduced in all suppressive soils compared to those growing in conducive soil. Therefore, the disease suppression is not always related to a reduction of the pathogen biomass. Furthermore, we isolated endophytic bacteria from wheat roots growing in suppressive soils. Among them we identified Serratia spp. and Enterobacter spp. able to inhibit Ggt growth in vitro. Since the disease, but not always pathogen amount, was reduced in the suppressive soils, we propose that take all disease suppressiveness is not only related to direct antagonism to the pathogen.

Effect of rhizobacterial consortia from undisturbed arid- and agro-ecosystems on wheat growth under different conditions

Plant growth-promoting rhizobacteria (PGPR) are studied as complements/alternatives to chemical fertilizers used in agriculture. However, poor information exists on the potential of PGPR from undisturbed ecosystems. Here, we have evaluated the plant growth-promoting (PGP) effect of rhizobacterial consortia from undisturbed Chilean arid ecosystems (Consortium C1) and agro-ecosystems (Consortium C2) on plant biomass production. The PGP effects of C1 and C2 were assayed in wheat seedlings (Triticum aestivum L.) grown in pots under growth chamber conditions and in pots placed in an open greenhouse under natural conditions, using two different Chilean Andisols (Piedras Negras and Freire series) kept either at 30 or 60% of their maximum water holding capacity (MWHC). PGP effects depended on the soil type, MWHC and the growth conditions tested. Although both consortia showed PGB effects in artificial soils relative to controls in growth chambers, only C1 provoked a PGP effect at 60% MWHC in phosphorus-poor soil of the 'Piedras Negras' series. At natural conditions, however, only C1 exhibited statistically significant PGP effects at 30% MWHC in 'Piedras Negras', yet and most importantly allowed to maintain similar plant biomass as at 60% MWHC. Our results support possible applications of rhizobacterial consortia from arid ecosystems to improve wheat growth in Chilean Andisols under water shortage conditions.

SIGNIFICANCE AND IMPACT OF THE STUDY

Wheat seedling inoculated with rhizobacterial consortia obtained from an undisturbed Chilean arid ecosystem showed improved growth in phosphorus-poor and partly dry soil. Arid ecosystems should be considered in further studies as an alternative source of microbial inoculants for agro-ecosystems subjected to stressful conditions by low nutrients and/or adverse climate events.