Delftia sp. JD2 is a heavy metal-resistant bacterium that promotes alfalfa, soybean, and clover root development and early nodulation when co-inoculated with their corresponding rhizobial strains. It also increases the grain yield of soybean plants. This strain could be considered for biotechnological applications, which requires the study of its harmlessness or toxicity. Thus, we analyzed the genome of JD2 by searching for pathogenicity factors. We also examined the potential toxicity of JD2 in some animals such as earthworms, planktonic crustaceans, fishes, and mammalians using Eisenia foetida , Daphnia magna , Danio rerio (zebrafish), and Mus musculus (mouse) as model organisms, following standard toxicity protocols. We found that JD2 genome codes for antibacterial virulence factors, active efflux pumps, and a versatile type VI secretion system that could participate in virulence and also other processes such as mobility, biofilm formation, and root infection. We also found that JD2 could be considered a safe microbe, at least in the tested organisms and according to the analyzed parameters.

In Uruguayan soils, populations of native and naturalized rhizobia nodulate white clover. These populations include efficient rhizobia but also parasitic strains, which compete for nodule occupancy and hinder optimal nitrogen fixation by the grassland. Nodulation competitiveness assays using gusA-tagged strains proved a high nodule occupancy by the inoculant strain U204, but this was lower than the strains with intermediate efficiencies, U268 and U1116. Clover biomass production only decreased when the parasitic strain UP3 was in a 99:1 ratio with U204, but not when UP3 was at equal or lower numbers than U204. Based on phylogenetic analyses, strains with different efficiencies did not cluster together, and U1116 grouped with the parasitic strains. Our results suggest symbiotic gene transfer from an effective strain to U1116, thereby improving its symbiotic efficiency. Genome sequencing of U268 and U204 strains allowed us to assign them to species Rhizobium redzepovicii, the first report of this species nodulating clover, and Rhizobium leguminosarun, respectively. We also report the presence of hrrP- and sapA-like genes in the genomes of WSM597, U204, and U268 strains, which are related to symbiotic efficiency in rhizobia. Interestingly, we report here chromosomally located hrrP-like genes.

Herein we present the draft genome (7.32 Mb and 62% GC content) of melanin- and laccase-producing Sinorhizobium ( Ensifer ) meliloti strain CE52G isolated from alfalfa nodules. We analyzed the genome and, performed a few in-bench experiments to corroborate some information. We found the gene for the laccase, probably involved in the production of the pigment melanin. CE52G shows genes for: (i) Embden-Meyerhof (EMP) and Entner-Doudoroff (ED) pathways; (ii) dissimilation and assimilation of nitrate, assimilation to ammonia, and conversion of nitrous oxide to nitrogen; (iii) Nodulation Factor and Mo-nitrogenase synthesis; (iv) synthesis and degradation of polyhydroxybutyrate and glycogen; (v) succinoglycan (EPS I) and galactoglucan (EPS II); and (vi) acidic and oxidative stress endurance. This bacterium does not produce siderophores but has the genomic machinery for the acquisition of siderophores (produced by other organisms) and hemophores for the uptake of heme from the environment. Among others, we found genes for two-component systems involved in the uptake of dicarboxylic acids and, the response to acidic conditions. The general information is discussed in terms of their relevance during CE52G association with plants and environmental adaptation.

Resistance to antibiotics and heavy metals in Antarctic bacteria has been investigated due to anthropogenic impact on the continent. However, there is still much to learn about the genetic determinants of resistance in native bacteria. In this study, we investigated antibiotic, heavy metal, and metalloid resistance in Pseudomonas sp. AU10, isolated from King George Island (Antarctica), and analyzed its genome to look for all the associated genetic determinants (resistome). We found that AU10 displayed resistance to Cr(VI), Cu(II), Mn(II), Fe(II), and As(V), and produced an exopolysaccharide with high Cr(VI)-biosorption capacity. Additionaly, the strain showed resistance to aminopenicillins, cefotaxime, aztreonam, azithromycin, and intermediate resistance to chloramphenicol. Regarding the resistome, we did not find resistance genes in AU10's natural plasmid or in a prophage context. Only a copper resistance cluster indicated possible horizontal acquisition. The mechanisms of resistance found were mostly efflux systems, several sequestering proteins, and a few enzymes, such as an AmpC β-lactamase or a chromate reductase, which would account for the observed phenotypic profile. In contrast, the presence of a few gene clusters, including the terZABCDE operon for tellurite resistance, did not correlate with the expected phenotype. Despite the observed resistance to multiple antibiotics and heavy metals, the lack of resistance genes within evident mobile genetic elements is suggestive of the preserved nature of AU10's Antarctic habitat. As Pseudomonas species are good bioindicators of human impact in Antarctic environments, we consider that our results could help refine surveillance studies based on monitoring resistances and associated resistomes in these populations.

This review presents a summary of the work done in Uruguay on the diversity and agricultural use of rhizobia, a group of soil bacteria able to establish symbiotic associations almost exclusively with legumes and fix atmospheric nitrogen. Uruguay has a long tradition regarding the use of microbial inoculants for agriculture. It is worth mentioning that since 1960, Uruguay has formally regulated the use of microorganisms in agriculture, being considered one of the pioneer countries where state policies on microbial inoculants have been implemented. In general, the vast majority of the work carried out in Uruguay has focused on the selection and characterization of promising bacteria to be used as biofertilizers. Therefore, the most studied symbiotic associations were those established with legumes of agricultural interest for the country, such as alfalfa, clover, lotus and soybean. The studies carried out with autochthonous alpha- and beta- rhizobia associated with diverse legume species are also considered, taking into account their ecological importance and the interest in knowing and preserving native germplasm.

Delftia sp. strain JD2 is a soil bacterium that produces auxins and acts as a nodulation-assisting bacterium in legumes inoculated with rhizobia. The co-inoculation of soybean (Glycine max) seeds with Bradyrhizobium elkanii and JD2 enhances plant growth, nitrogen fixation, and grain yield. This work aimed to characterize bioactive compounds in soybean plants under different inoculation treatments. Metabolomic profiling by Ultra-High-Performance Liquid Chromatography coupled with High-Resolution Mass Spectrometry (UHPLC-HRMS) was carried out on freeze-dried rhizospheric exudates and root extracts from hydroponic or greenhouse plants experiments, respectively. The differential metabolomic profiling between treatments was analyzed by pair-wise comparisons. Statistical results showed that both root and rhizospheric samples clustered according to the inoculation treatment and the sampling time of plants. This classification derives from the different production of cinnamic acids, coumarins, benzoic acids, and flavonoids, among other discriminant compounds between treatments. We observed the over-production of nod genes inducers in roots from plants inoculated with JD2. In contrast, a reduction in the discriminant flavonoids occurred in co-inoculated plants. JD2 positively influences the production of auxins. These changes in the composition of flavonoids and auxins are likely to explain the differences observed in the growth and nodulation of co-inoculated plants. This study emphasizes some metabolic changes that positively affect the co-inoculation of soybean seeds with bradyrhizobia and JD2.

In this study, we report the draft genome sequence of Bradyrhizobium sp. strain Oc8, a rhizobium isolated from Crotalaria ochroleuca,efficient in C. ochroleuca, C. juncea, C. spectabilis, and Cajanus cajan. The whole genome of the strain Oc8 contains 46 scaffolds, 8,283,342 bp, and 63.27% of GC content. Bradyrhizobium sp. Oc8 is an effective nitrogen-fixing bacterium with potential use as an inoculant for legumes used as cover crops and green manures.

Cold-adapted (CA) microorganisms (= psychrophiles or psychrotolerants) are key players of many ecological interactions in natural ecosystems. Some of them can colonize the rhizosphere of plants and cause damage to their hosts; others, on the contrary, protect plants from their pathogens through direct and indirect mechanisms, thus promoting plant growth and development. These "protective" microbes are known as biocontrol agents (BCA). BCA either limit or inhibit the growth of plant pathogens, owing to the excretion of a panoply of secondary metabolites (including soluble and volatile antibiotics, siderophores, quorum sensing interfering agents). BCA can also control plant pathogens through indirect mechanisms, including competence for nutrients and space, or else by interfering with their chemical communication. That explains why some of these BCA have been included in the formulation of commercial biopesticides, which are environmentally friendly products containing live cells used to control plant diseases and pests. At present, the development of biopesticides from mesophilic microorganisms is an established technology. Unfortunately, these biopesticides are not active at low temperatures. On the other hand, the information concerning the potential use of CA-BCA for the same goal is at its infancy. Here, we review the current knowledge concerning the isolation, identification, and characterization of CA microbes which act as antagonists of plant pathogens, including the mechanisms they deploy to antagonize plant pathogens. We also illustrate their biotechnological potential to develop CA biopesticides and discuss their utility in the context of mountainous agriculture. KEY POINTS: • Many naturally occurring cold-active microbes antagonize plant pathogens. • The mechanisms of biocontrol exerted by these microbes are either direct or indirect. • Cold-active biocontrol agents can be used to develop biopesticides. • Cold-active biopesticides are crucial for sustainably intensifying agriculture in cold climates.

Flavonoids produced by roots are secondary metabolites involved in the induction of nod genes in rhizobial cells and nodule organogenesis. We describe the development and quality control of a new formulation for soybean (Glycine max (L.) Merr.) based on Bradyrhizobium elkanii cells grown in a culture medium containing isoflavones. As opposed to B. japonicum, the performance of B. elkanii pre-incubated with isoflavones is unknown. Its evaluation implied in vitro, greenhouse, and field research trials. Greenhouse and in vitro treatments comprised: seeds inoculated with a traditional inoculant based on B. elkanii; seeds inoculated with a new formulation based on isoflavones-cultivated B. elkanii cells, the exogenous application of isoflavones into the growth substrate, and the non-inoculated control. Field treatments included non-inoculated controls with and without N-fertilizer and seeds inoculation with the traditional or the new formulation. No changes in quality parameters (bacterial survival on both seeds and liquid formulation) were observed, as compared with the traditionally produced bradyrhizobial cells. Also, improved plant response (nodulation, plant growth, and seed yield) was observed when seeds were inoculated with the new formulation. The exogenous application of isoflavones directly into the substrate had deleterious effects on soybean growth and nodulation; however, the increased values of agronomical parameters in field conditions show that the addition of isoflavones during the industrial fermentation of B. elkanii is a better option over the common bradyrhizobial inoculant.

New educational resources are being implemented as an initiative to foster learning. In order to contribute to the toolkit of innovative educational resources, we developed a microbiology comic book. The aim of this comic is to provide educators with a fun, accessible, and rigorous way to generate awareness of the invisible world that surrounds us and that inhabits us. Bacteria have a reputation as harmful and disgusting entities. Mass media, with advertisements of disinfectants, soaps, and house cleaning products, are sending a distorted message about microbes. We must debunk these misconceptions and emphasize the importance of microorganisms, and particularly bacteria, in the environment and our lives. Education is the means to this end, and therefore this comic is intended to help educators teach microbiology in an attractive, accurate, and straightforward way. Here, we present this educational tool and give some tips on the different themes that can be addressed in the classroom using this resource.

For microbiologists, the importance of microorganisms in our daily lives and their impact on our well-being is evident. However, microbiology literacy in our society is far from being enough for individuals to make informed choices and to demand actions based on that information. The vaccine hesitation movement and the alarming increase in antimicrobial resistance due to overuse and misuse of antibiotics are just two examples of how much work is needed to make our society literate in topics related to microbiology. Considering the challenges of communicating a discipline surrounded by misconceptions, which studies the role of living organisms that cannot be seen in plain sight, we need to explore different strategies to effectively contribute to microbiology literacy in our society. Here, we will comment on the use of comics for such a task.

The family Comamonadaceae belongs to the Beta subdivision of the phylum Proteobacteria. Members of this family display differential biological properties, mainly related to physiological and/or ecological traits. There are a few studies (if any) about features related with the molecular evolution of this group. In this work we report the analysis of the codon usage patterns using the data obtained from completely and draft sequenced bacterial genomes that belong to this family. The effect of natural selection in translation acting at the levels of speed and accuracy are described and discussed in a phylogenetic framework. Preferred (optimal) codons were identified. We found that there is an important level of variation in the strength of selection among the analyzed microorganisms, which is probably associated with lineage-specific ecological and/or physiological trends. Although the codon usage bias in highly expressed genes is not conserved across the evolutionary time of the family, it is conserved among species within a genus, suggesting a major role of negative selection at this level.

Delftia sp. strain JD2 is a betaproteobacterium characterized as a plant growth-promoting bacterium with a 'helper' function, enhancing the performance of rhizobial inoculant strains during the coinoculation of alfalfa and clover. In this work we analyzed i) the effect of the coinoculation with Bradyrhizobium elkanii and Delftia sp. strain JD2 strains on the performance of soybean plants and ii) the production of a few secondary plant metabolites that would explain the positive effect of coinoculation on the growth and development of soybean plants. The results showed a beneficial effect of coinoculation on soybean growth, nodulation rate, and pulse yield, with the concomitant benefit for the agricultural economy. In addition, based on a metabolomics approach, we demonstrated that a different pattern of plant metabolites is being produced at different stages of plant growth. The new information suggests that the coinoculation of soybean changes the primary and secondary metabolism of the plant, including changes in the metabolic status of main and secondary nodules within the plant. The relevance of producing a different pattern of photosynthetic and photoprotective pigments, flavonoids, organic acids, and carbohydrates are discussed. Finally, we propose that JD2 could be used together with bradyrhizobia to manipulate the chemical composition of plant tissues, promoting the nutritional benefits and health of soybean.

Ultraviolet (UV) light irradiation has serious consequences for cell survival, including DNA damage by formation of cyclobutane pyrimidine dimers (CPD) and pyrimidine (6,4) pyrimidone photoproducts. In general, the Nucleotide Excision Repair pathway repairs these lesions; however, all living forms, except placental mammals and some marsupials, produce a flavoprotein known as photolyase that directly reverses these lesions. The aim of this work was the isolation and identification of Antarctic UVC-resistant bacteria, and the search for novel photolyases. Two Antarctic water samples were UVC-irradiated (254 nm; 50–200 J m− 2) and 12 UVC-resistant bacteria were isolated and identified by 16S rDNA amplification/analysis as members of the genera Pseudomonas, Janthinobacterium, Flavobacterium, Hymenobacter and Sphingomonas. The UVC 50% lethal dose and the photo-repair ability of isolates were analyzed. The occurrence of photolyase coding sequences in Pseudomonas, Hymenobacter and Sphingomonas isolates were searched by PCR or by searching in the draft DNA genome. Results suggest that Pseudomonas and Hymenobacter isolates produce CDP-photolyases, and Sphingomonas produces two CPD-photolyases and a 6,4-photolyase. Results suggest that the Antarctic environment is an important source of genetic material for the identification of novel photolyase genes with potential biotechnological applications.

Delftia sp. JD2 is a chromium-resistant bacterium that reduces Cr(VI) to Cr(III), accumulates Pb(II), produces the phytohormone indole-3-acetic acid and siderophores, and increases the plant growth performance of rhizobia in co-inoculation experiments. We aimed to analyze the biotechnological potential of JD2 using a genomic approach. JD2 has a genome of 6.76Mb, with 6,051 predicted protein coding sequences and 93 RNA genes (tRNA and rRNA). The indole-acetamide pathway was identified as responsible for the synthesis of indole-3-acetic acid. The genetic information involved in chromium resistance (the gene cluster, chrBACF, ) was found. At least 40 putative genes encoding for TonB-dependent receptors, probably involved in the utilization of siderophores and biopolymers, and genes for the synthesis, maturation, exportation and uptake of pyoverdine, and acquisition of Fe-pyochelin and Fe-enterobactin were also identified. The information also suggests that JD2 produce polyhydroxybutyrate, a carbon reserve polymer commonly used for manufacturing petrochemical free bioplastics. In addition, JD2 may degrade lignin-derived aromatic compounds to 2-pyrone-4,6-dicarboxylate, a molecule used in the bio-based polymer industry. Finally, a comparative genomic analysis of JD2, Delftia sp. Cs1-4 and Delftia acidovorans SPH-1 is also discussed. The present work provides insights into the physiology and genetics of a microorganism with many potential uses in biotechnology.

Bacteria of genus Delftia are environmental microorganisms with a wide geographical distribution. They are versatile microbes with diverse metabolic capacities that easily adapt to several environments. This chapter provides an overview of various aspects and potential biotechnological applications of Delftia spp. as microbial model of sustainability, including their use in bioremediation and bioconversion of contaminants, their use in production of bioproducts, and their use as inoculant to increase plant yield. As a few Delftia spp. have been found in clinical samples, their potential role as opportunistic pathogenic agents is also discussed.

Fildes Peninsula, in King George Island, Antarctica, has a great concentration of international facilities, and it has clearly been affected by human activities. The objective of this 5-year study was to assess the impact of anthropogenic activities on the bacterial abundance in water bodies close to Artigas Antarctic Scientific Base（BCAA, in Spanish Base Científica Antártica Artigas）. Water samples from areas under different human influence（Uruguay Lake, nearby ponds, and meltwater from Collins Glacier） were aseptically collected and refrigerated until processed. The number of heterotrophic bacteria and Pseudomonas spp. was analyzed using a culture-dependent approach. Physico-chemical properties of the water samples（temperature, p H, and conductivity） were also determined. Results showed that water from the highly affected area, Uruguay Lake, where the pump that provides water to the BCAA is located, did not suffer significant fluctuations in heterotrophic bacterial abundance（104–105 CFU·m L-1）; however, Pseudomonas abundance increased until becoming the predominant population. In other water samples, the number of heterotrophic bacteria and Pseudomonas gradually increased during this 5-year study, by 2014 reaching similar values to those observed for Uruguay Lake. The implications of human activities on Antarctic bacterial abundance are discussed.

This chapter reviews how some practices commonly used by farmers, mainly biocontrol and biofertilization, affect the structure (abundance and composition) of soil microbial communities. The data show that many factors related to agricultural practices, other than inoculation, play an important role in determining the structure of microbial populations.