Commonalities between the Atacama Desert and Antarctica rhizosphere microbial communities.

Plant-microbiota interactions have significant effects on plant growth, health, and productivity. Rhizosphere microorganisms are involved in processes that promote physiological responses to biotic and abiotic stresses in plants. In recent years, the interest in microorganisms to improve plant productivity has increased, mainly aiming to find promising strains to overcome the impact of climate change on crops. In this work, we hypothesize that given the desertic environment of the Antarctic and the Atacama Desert, different plant species inhabiting these areas might share microbial taxa with functions associated with desiccation and drought stress tolerance. Therefore, in this study, we described and compared the composition of the rhizobacterial community associated with Deschampsia antarctica (Da), Colobanthus quitensis (Cq) from Antarctic territories, and Croton chilensis (Cc), Eulychnia iquiquensis (Ei) and Nicotiana solanifolia (Ns) from coastal Atacama Desert environments by using 16S rRNA amplicon sequencing. In addition, we evaluated the putative functions of that rhizobacterial community that are likely involved in nutrient acquisition and stress tolerance of these plants. Even though each plant microbial rhizosphere presents a unique taxonomic pattern of 3,019 different sequences, the distribution at the genus level showed a core microbiome with a higher abundance of Haliangium, Bryobacter, Bacillus, MND1 from the Nitrosomonadaceae family, and unclassified taxa from Gemmatiamonadaceae and Chitinophagaceae families in the rhizosphere of all samples analyzed (781 unique sequences). In addition, species Gemmatirosa kalamazoonesis and Solibacter usitatus were shared by the core microbiome of both Antarctic and Desert plants. All the taxa mentioned above had been previously associated with beneficial effects in plants. Also, this microbial core composition converged with the functional prediction related to survival under harsh conditions, including chemoheterotrophy, ureolysis, phototrophy, nitrogen fixation, and chitinolysis. Therefore, this study provides relevant information for the exploration of rhizospheric microorganisms from plants in extreme conditions of the Atacama Desert and Antarctic as promising plant growth-promoting rhizobacteria.

Metagenomic and Functional Characterization of Two Chilean Kefir Beverages Reveals a Dairy Beverage Containing Active Enzymes, Short-Chain Fatty Acids, Microbial ß-Amyloids, and Bio-Film Inhibitors.

Kefir beverage is a probiotic food associated with health benefits, containing probiotic microorganisms and biomolecules produced during fermentation. The microbial composition of these beverages varies among countries, geographical regions, and the substrates, therefore, the characterization of kefir beverages is of great relevance in understanding their potential health-promoting and biotechnological applications. Therefore, this study presents the metagenomic and functional characterization of two Chilean kefir beverages, K02 and K03, through shotgun and amplicon-based metagenomic, microbiological, chemical, and biochemical studies. Results show that both beverages' microbiota were mainly formed by Bacteria (>98%), while Eukarya represented less than 2%. Regarding Bacteria, the most abundant genera were Acetobacter (93.43% in K02 and 80.99% in K03) and Lactobacillus (5.72% in K02 and 16.75% in K03), while Kazachstania was the most abundant genus from Eukarya (42.55% and 36.08% in K02 and K03). Metagenomic analyses revealed metabolic pathways for lactose and casein assimilation, biosynthesis of health-promoting biomolecules, and clusters for antibiotic resistance, quorum sensing communication, and biofilm formation. Enzymatic activities, microbial ß-amyloids, and short-chain fatty acids (acetic acid and propionic acid) were also detected in these beverages. Likewise, both kefir beverages inhibited biofilm formation of the opportunistic pathogen Pseudomonas aeruginosa.

Draft Genome Sequences of Lactobacillus plantarum Strain K03D08 and Acetobacter syzygii Strain K03D05, Isolated from a Kefir Beverage Collected in Chile.

Kefir is an ancestral food produced using microbial consortia whose composition varies depending on the geographical origin and the substrate used for fermentation. This dairy beverage is considered a probiotic food, and its consumption has been associated with several health benefits. This report describes the isolation of bacterial strains from Chilean kefir.

Acidiferrimicrobium australe gen. nov., sp. nov., an acidophilic and obligately heterotrophic, member of the Actinobacteria that catalyses dissimilatory oxido-reduction of iron isolated from metal-rich acidic water in Chile.

A novel acidophilic member of the phylum Actinobacteria was isolated from an acidic, metal-contaminated stream draining from an abandoned underground coal mine (Trongol mine), situated close to Curanilahue, Biobío Region, Chile. The isolate (USS-CCA1T) was demonstrated to be a heterotroph that catalysed under aerobic conditions the oxidation of ferrous iron and the reduction of ferric iron under anaerobic conditions, but not the oxidation of sulfur nor hydrogen. USS-CCA1T is a Gram-positive, motile, short rod-shaped, mesophilic bacterium with a temperature growth optimum at 30 °C (range 20-39 °C). It was categorized as an extreme acidophile growing between 1.7 and 4.5 and optimally at pH 3.0. The G+C content of the chromosomal DNA of the isolate was 74.1 mol%, which is highly related to Aciditerrimonas ferrireducens IC-180T , (the most closely related genus; 94.4 % 16S rRNA gene identity), and higher than other acidophilic actinobacteria. The isolate (USS-CCA1T) was shown to form a distinct 16S rRNA clade from characterized acidophilic actinobacteria, well separated from the genera Acidimicrobium, Ferrimicrobium, Ferrithrix, 'Acidithrix' and Aciditerrimonas. Genomic indexes (ANIb, DDH, AAI, POCP) derived from the USS-CCA1T draft genome sequence (deposited at DDBJ/ENA/GenBank under the accession WJHE00000000) support assignment of the isolate to a new species and a new genus within the Acidimicrobiaceae family. Isolate USS-CCA1T is the designated type strain of the novel species Acidiferrimicrobium australe (=DSM 106828T,=RGM 2506T).

16S rRNA Amplicon Sequencing of Seawater Microbiota from Quintero Bay, Chile, Affected by Oil Spills, Shows the Presence of an Oil-Degrading Marine Bacterial Guild Structured by the Bacterial Genera Alcanivorax, Cobetia, Halomonas, and Oleiphilus.

The Quintero Bay, located along the central coast of Chile, has suffered different oil spills during the past 5 years, impacting marine ecosystems. This report describes the microbial community structure of seawater samples obtained from the Quintero Bay through 16S rRNA amplicon sequencing.

A new functional biofilm biocatalyst for the simultaneous removal of dibenzothiophene and quinoline using Rhodococcus rhodochrous and curli amyloid overproducer mutants derived from Cobetia sp. strain MM1IDA2H-1.

Biocatalyst systems based on biofilms were developed to remove nitrogen and sulfur-containing heterocyclic hydrocarbons using Cobetia sp. strain MM1IDA2H-1 and Rhodococcus rhodochrous. The curli overproducers mutants CM1 and CM4 were derived from Cobetia sp. strain and used to build monostrain biofilms to remove quinoline; and together with R. rhodochrous to simultaneously remove quinoline and dibenzothiophene using mixed biofilms. The quinoline removal using biofilms were 96% and 97% using CM1 or CM4 curli overproducers respectively, whereas bacterial suspensions assays yielded 19% and 24% with the same strains. At the other hand, the simultaneous removal of quinoline and dibenzothiophene using mixed biofilms were respectively 50% and 58% using strains R. rhodochrous with CM1 and 75% and 50% using R. rhodochrous with CM4. Results show that biofilms were more efficient than bacterial suspension assays and that in mixed biofilms the shared surface area by two or more bacteria could affect the final yield.

Genome Sequence of Cobetia sp. Strain MM1IDA2H-1, a Hydrocarbon-Degrading and Biosurfactant-Producing Marine Bacterium.

Cobetia sp. strain MM1IDA2H-1 is a marine bacterium isolated from seawater samples that uses the heterocyclic aromatic hydrocarbon dibenzothiophene as the sole carbon source and produces a biosurfactant that inhibits bacterial quorum sensing. The Cobetia sp. MM1IDA2H-1 genome was sequenced, processed, assembled, and annotated for basic and applied studies.

Removal of sulfur-containing organic molecules adsorbed on inorganic supports by Rhodococcus Rhodochrous spp.

OBJECTIVE: To remove dibenzothiophene (DBT) and 4,6-dimethyl-dibenzothiophene (4,6-DMDBT) adsorbed on alumina, silica and sepiolite through biodesulfurization (BDS) using Rhodococcus Rhodochrous spp., that selectively reduce sulfur molecules without generating of gaseous pollutants. RESULTS: The adsorption of DBT and 4,6-DMDBT was affected by the properties of the supports, including particle size and the presence of surface acidic groups. The highest adsorption of both sulfur-containing organic molecules used particle sizes of 0.43-0.063 mm. The highest percentage removal was with sepiolite (80 % for DBT and 56 % for 4,6-DMDBT) and silica (71 % for DBT and 37 % for 4,6-DMDBT). This is attributed to the close interaction between these supports and the bacteria. CONCLUSIONS: Biodesulfurization is effective for removing the sulfur-containing organic molecules adsorbed on inorganic materials and avoids the generation of gaseous pollutants.

Biodesulfurization of gas oil using inorganic supports biomodified with metabolically active cells immobilized by adsorption.

The immobilization of Pseudomonas stutzeri using adsorption on different inorganic supports was studied in relation to the number of adsorbed cells, metabolic activity and biodesulfurization (BDS). The electrophoretic migration (EM) measurements and Tetrazolioum (TTC) method were used to evaluate adsorption and metabolic activity. Results indicate that maximal immobilization was obtained with an initial load of 14 x 10(8) cells mL(-1) for Al and Sep, whereas Ti requires 20 x 10(8) cells mL(-1). The highest interaction was observed in the P. stutzeri/Si and P. stutzeri/Sep biocatalysts. The IEP values and metabolic activities indicate that P. stutzeri change the surface of supports and maintains metabolic activity. A direct relation between BDS activity and the adsorption capacity of the bacterial cells was observed at the adsorption/desorption equilibrium level. The biomodification of inorganic supports by the adsorption process increases the bioavailability of sulphur substrates for bacterial cells, improving BDS activity.

Analysis of s-triazine-degrading microbial communities in soils using most-probable-number enumeration and tetrazolium-salt detection.

A simple and sensitive method for the detection and enumeration of microbial s-triazine-degrading microorganisms in soil was designed. The procedure is based on the ability of some microbes to use s-triazines, such as simazine, atrazine, and cyanuric acid, as sole nitrogen source. It employs the respiration indicator 2,3,5-triphenyl-2H-tetrazolium chloride (TTC) to detect metabolic activity and the most-probable-number (MPN) enumeration in microtiter plates. The method was used to identify simazine- and cyanuric acid-degrading activities in agricultural soils treated with the herbicide simazine. The MPN-TTC method showed that the number of simazine- and cyanuric acid-degrading microorganisms increased four weeks after the herbicide simazine had been applied.

Expression of the Pseudomonas putida OCT plasmid alkane degradation pathway is modulated by two different global control signals: evidence from continuous cultures.

Expression of the genes of the alkane degradation pathway encoded in the Pseudomonas putida OCT plasmid are subject to negative and dominant global control depending on the carbon source used and on the physiological status of the cell. We investigated the signals responsible for this control in chemostat cultures under conditions of nutrient or oxygen limitation. Our results show that this global control is not related to the growth rate and responds to two different signals. One signal is the concentration of the carbon source that generates the repressing effect (true catabolite repression control). The second signal is influenced by the level of expression of the cytochome o ubiquinol oxidase, which in turn depends on factors such as oxygen availability or the carbon source used. Since under carbon limitation conditions the first signal is relieved but the second signal is not, we propose that modulation mediated by the cytochrome o ubiquinol oxidase is not classical catabolite repression control but rather a more general physiological control mechanism. The two signals have an additive, but independent, effect, inhibiting induction of the alkane degradation pathway.

Inactivation of cytochrome o ubiquinol oxidase relieves catabolic repression of the Pseudomonas putida GPo1 alkane degradation pathway.

Expression of the alkane degradation pathway encoded by the OCT plasmid of Pseudomonas putida GPo1 is regulated by two control systems. One relies on the transcriptional regulator AlkS, which activates expression of the pathway in the presence of alkanes. The other, which is a dominant global regulation control, represses the expression of the pathway genes when a preferred carbon source is present in the growth medium in addition to alkanes. This catabolite repression control occurs through a poorly characterized mechanism that ultimately regulates transcription from the two AlkS-activated promoters of the pathway. To identify the factors involved, a screening method was developed to isolate mutants without this control. Several isolates were obtained, all of which contained mutations that mapped to genes encoding cytochrome o ubiquinol oxidase, the main terminal oxidase of the electron transport chain under highly aerobic conditions. Elimination of this terminal oxidase led to a decrease in the catabolic repression observed both in rich Luria-Bertani medium and in a defined medium containing lactate or succinate as the carbon source. This suggests that catabolic repression could monitor the physiological or metabolic status by using information from the electron transport chain or from the redox state of the cell. Since inactivation of the crc gene also reduces catabolic repression in rich medium (although not that observed in a defined medium), a strain was generated lacking both the Crc function and the cytochrome o terminal oxidase. The two mutations had an additive effect in relieving catabolic repression in rich medium. This suggests that crc and cyo belong to different regulation pathways, both contributing to catabolic repression.