Isolation and Identification of Bacteria from Three Geothermal Sites of the Atacama Desert and Their Plant-Beneficial Characteristics

The Region of Arica and Parinacota (Atacama Desert) offers several unexplored remote sites with unique characteristics that would allow for the formulation of new bioproducts for agriculture. Among them, Jurasi Hot Springs, Polloquere Hot Springs, and Amuyo Lagoons represent a group of open pools fed by thermal water springing from the mountains. Their microbiomes remain unspecified, providing a unique opportunity to characterize the endemic community of these sites and develop new bioproducts for sustainable agriculture. Bacteria were isolated from the sediments of these geothermal sites and characterized by sequencing the 16S rRNA gene, microbiological characterization, and agricultural functional characterization. A total of 57 bacteria were isolated from three geothermal sites north of the Atacama Desert. The sequence analysis showed that the isolates belong to several bacterial genera, including Pantoea, Bacillus, and Pseudomonas, among others. The functional characterization revealed the presence of PGP traits, hydrolytic enzymes, and biocontrol activity against phytopathogenic fungi. These bacteria possess the potential to develop new biobased products for agriculture in arid conditions.

Rhizosphere microbiomes of resurrection plants Ramonda serbica and R. nathaliae: comparative analysis and search for bacteria mitigating drought stress in wheat (Triticum aestivum L.)

Rhizosphere microbial communities play an important role in maintaining the health and productivity of the plant host. The rhizobacteria Pseudomonas putida P2 of Ramonda serbica and Bacillus cereus P5 of R. nathaliae were selected for treatment of the Belija wheat cultivar because of their plant growth-promoting (PGP) properties. Compared to the non-treated drought-stressed plants, the plants treated with rhizobacteria showed increased activity of the two major antioxidant enzymes, superoxide dismutase, and ascorbate peroxidase. Plants treated with the B. cereus P5 strain exhibited higher proline content under drought stress, suggesting that proline accumulation depends on the relative water content (RWC) status of the plants studied. Inoculation of wheat seeds with the P. putida P2 strain improved water status by increasing RWC and alleviating oxidative stress by reducing H2O2 and malondialdehyde concentrations in plants exposed to severe drought, possibly also helping plants to overcome drought through its 1-aminocyclopropane-1-carboxylic acid deaminase activity. Analysis of data from Next Generation sequencing (NGS) revealed that the dominant bacterial taxa in the rhizosphere of resurrection plants R. serbica and R. nathaliae were extremophilic, thermotolerant, Vicinamibacter silvestris, Chthoniobacter flavus, and Gaiella occulta. From the fungi detected Penicillium was the most abundant in both samples, while Fusarium and Mucor were present only in the rhizosphere of R. serbica and the entomopathogenic fungi Metarhizium, and Tolypocladiumu only in the rhizosphere of R. nathaliae. The fungal communities varied among plants, suggesting a stronger environmental influence than plant species. Our study demonstrates the importance of in vivo experiments to confirm the properties of PGP bacteria and indicates that the rhizosphere of resurrection plants is a valuable source of unique microorganisms that can be used to improve the drought stress tolerance of crops.

Bacterial Community with Plant Growth-Promoting Potential Associated to Pioneer Plants from an Active Mexican Volcanic Complex

Microorganisms in extreme volcanic environments play an important role in the development of plants on newly exposed substrates. In this work, we studied the structure and diversity of a bacterial community associated to Andropogon glomeratus and Cheilanthes aemula at El Chichón volcano. The genetic diversity of the strains was revealed by genomic fingerprints and by 16S rDNA gene sequencing. Furthermore, a metagenomic analysis of the rhizosphere samples was carried out for pioneer plants growing inside and outside the volcano. Multifunctional biochemical tests and plant inoculation assays were evaluated to determine their potential as plant growth-promoting bacteria (PGPB). Through metagenomic analysis, a total of 33 bacterial phyla were identified from A. glomeratus and C. aemula rhizosphere samples collected inside the volcano, and outside the volcano 23 bacterial phyla were identified. For both rhizosphere samples, proteobacteria was the most abundant phylum. With a cultivable approach, 174 bacterial strains were isolated from the rhizosphere and tissue of plants growing outside the volcanic complex. Isolates were classified within the genera Acinetobacter, Arthrobacter, Bacillus, Burkholderia, Cupriavidus, Enterobacter, Klebsiella, Lysinibacillus, Pantoea, Pseudomonas, Serratia, Stenotrophomonas and Pandoraea. The evaluated strains were able to produce indole compounds, solubilize phosphate, synthesize siderophores, showed ACC deaminase and nitrogenase activity, and they had a positive effect on the growth and development of Capsicum chinense. The wide diversity of bacteria associated to pioneer plants at El Chichón volcano with PGPB qualities represent an alternative for the recovery of eroded environments, and they can be used efficiently as biofertilizers for agricultural crops growing under adverse conditions.

Salt-tolerant bacteria enhance the growth of mung bean (Vigna radiata L.) and uptake of nutrients, and mobilize sodium ions under salt stress condition

Salinity is one of the significant abiotic stresses that exert harmful effects on plant growth and crop production. It has been reported that the harmfulness of salinity can be mitigated by the use of salt-tolerant plant growth-promoting (PGP) bacteria. In this study, four bacteria were selected from a total of 30 cultures, based on salt-tolerant and PGP properties. The isolates were found to produce indole acetic acid (8.49-19.42 μg/ml), siderophore (36.04-61.77%), and solubilize potassium and inorganic phosphate. Identification based on 16S rRNA gene sequencing revealed that the isolates belonged to Cronobacter (two isolates) and Enterobacter (two isolates). Inoculation of PGP bacteria under 2 and 10% salinity stress showed enhanced plant growth parameters in Vigna radiata compared to both salinity and non-salinity control plants. The rate of germination (113.32-206.64%), root length (128.79-525.31%), shoot length (34.09-50.32%), fresh weight, and dry weight were 3-fold higher in bacteria-treated seeds than control plants. The estimation of chlorophyll (1-5-fold), carotenoids (1-4-fold), and proline content (3.65-14.45%) was also higher compared to control plants. Further, the bacterized seeds showed enhanced nitrogen and phosphorous uptake and mobilized sodium ions from roots to leaves. Overall the strains SS4 and SS5 performed well in both 2 and 10% salt-amended soils. These strains could be formulated as a bioinoculant to mitigate the salinity stress in salinized soils.

Compost-derived indole-3-acetic-acid-producing bacteria and their effects on enhancing the secondary fermentation of a swine manure-corn stalk composting

Composting, as an effectively bio-oxidative process, has been widely used for converting organic waste to organic fertilizer. However, the low fertilizer efficiency of composting product limited its application in agriculture. To improve the growth-promoting effect of composting product, the present study investigated the bioaugmentation strategy of inoculating indole-3-acetic-acid (IAA)-producing bacteria. Firstly, two IAA-producing bacteria (Bacillus safensis 33C and Rhodococcus rhodochrous YZ) were isolated from composting products with high IAA yields of 39.18 and 16.32 μg mL^-1, respectively. Secondly, the microbial inoculants were prepared with 33C, YZ and a previously isolated IAA-producing strain Corynebacterium stationis 29B. To increase the accumulation of microbial secondary metabolites, microbial inoculants were amended at the secondary fermentation stage of composting. Physicochemical characterization showed that the maturity of composting product was significantly promoted by inoculating microbial inoculants prepared with 33C and 29B (single and combined inoculants). Finally, bioaugmentation with 33C and 29B increased the IAA contents of composting products by 2.9-5.2 times, which benefited the germination and early vegetative growth of plants. In summary, inoculating proper IAA-producing bacteria during secondary fermentation of composting could improve the quality of composting product and expand its application.

Taxonomy and systematics of plant probiotic bacteria in the genomic era

Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics.

Characterization of culturable bacteria isolated from hot springs for plant growth promoting traits and effect on tomato (Lycopersicon esculentum) seedling

To elucidate the functional diversity of hot spring bacteria, 123 bacteria were isolated and screened for evaluating their multifunctional plant growth promoting (PGP) properties. The antagonistic activity against different phytopathogens showed the presence of a high amount of biocontrol bacteria in the hot springs. During screening for PGP properties, 61.0% isolates showed production of indole acetic acid and 23.6% showed inorganic phosphate solubilization qualitatively. For production of extracellular enzymes, it was found that 61.0% isolates produced lipase, 56.9% produced protease, and 43.9% produced cellulase. In extreme properties, half of the isolates showed tolerance to 5% NaCl (w/v) and 48.8% isolates survived heat shock at 70°C. The identification of 12 multipotential bacteria based on 16S rRNA gene sequencing revealed that the bacteria belonged to Aneurinibacillus aneurinilyticus and Bacillus spp. Bacterization of tomato seeds showed that the hot spring bacteria promoted shoot height, fresh shoot weight, root length, and fresh root weight of tomato seedlings, with values ranging from 3.12% to 74.37%, 33.33% to 350.0%, 16.06% to 130.41%, and 36.36% to 318.18%, respectively, over the control. This research shows that multifunctional bacteria could be isolated from the hot springs. The outcome of this research may have a potential effect on crop production methodologies used in saline and arid environments.

Characterisation of Pseudomonas spp. and Ochrobactrum sp. isolated from volcanic soil

Soil bacteria may have properties of plant growth promotion but not be sufficiently beneficial for plants under stress conditions. This challenge has led researchers to extend their searches into extreme environments for potential soil bacteria with multiple plant beneficial traits as well as abiotic stress tolerance abilities. In the current study, an attempt was made to evaluate soil bacteria from an extreme environment, volcano soils, based on plant growth promoting and abiotic stress mitigating characteristics. The screening led to the isolation of eight (NBRISH4, NBRISH6, NBRISH10, NBRISH11, NBRISH13, NBRISH14, NBRISH16 and NBRISH26) bacterial isolates capable of withstanding stresses, namely temperature (up to 45 °C), salt (up to 2 M NaCl) and drought (up to 60% Poly Ethylene Glycol 6000) in vitro. Further, the selected isolates were notable for their in vitro temporal performance with regards to survival (in terms of colony count), phosphate solubilisation, biofilm formation, auxin, alginate and exo-polysaccharide production abilities under abiotic stresses i.e. 40 °C temperature; 500 mM NaCl salt and drought (PEG) conditions. In vivo seed treatments of individual selected bacteria to maize plants resulted into significant enhancement in root and shoot length, root and shoot fresh and dry weight and number of leaves per plant. Overall, the plant growth promoting and abiotic stress tolerance ability was most evident for bacterial isolate NBRISH6 which was identified as an Ochrobactrum sp. using 16S rRNA based phylogenetic analysis.

An overview of siderophores for iron acquisition in microorganisms living in the extreme

Siderophores are iron-chelating molecules produced by microbes when intracellular iron concentrations are low. Low iron triggers a cascade of gene activation, allowing the cell to survive due to the synthesis of important proteins involved in siderophore synthesis and transport. Generally, siderophores are classified by their functional groups as catecholates, hydroxamates and hydroxycarboxylates. Although other chemical structural modifications and functional groups can be found. The functional groups participate in the iron-chelating process when the ferri-siderophore complex is formed. Classified as acidophiles, alkaliphiles, halophiles, thermophiles, psychrophiles, piezophiles, extremophiles have particular iron requirements depending on the environmental conditions in where they grow. Most of the work done in siderophore production by extremophiles is based in siderophore concentration and/or genomic studies determining the presence of siderophore synthesis and transport genes. Siderophores produced by extremophiles are not well known and more work needs to be done to elucidate chemical structures and their role in microorganism survival and metal cycling in extreme environments.