Rhizobium hidalgonense and Rhizobium redzepovicii as faba bean (Vicia faba L.) microsymbionts in Mexican soils.

As a legume crop widely cultured in the world, faba bean (Vicia faba L.) forms root nodules with diverse Rhizobium species in different regions. However, the symbionts associated with this plant in Mexico have not been studied. To investigate the diversity and species/symbiovar affiliations of rhizobia associated with faba bean in Mexico, rhizobia were isolated from this plant grown in two Mexican sites in the present study. Based upon the analysis of recA gene phylogeny, two genotypes were distinguished among a total of 35 isolates, and they were identified as Rhizobium hidalgonense and Rhizobium redzepovicii, respectively, by the whole genomic sequence analysis. Both the species harbored identical nod gene cluster and the same phylogenetic positions of nodC and nifH. So, all of them were identified into the symbiovar viciae. As a minor group, R. hidalgonense was only isolated from slightly acid soil and R. redzepovicii was the dominant group in both the acid and neutral soils. In addition, several genes related to resistance to metals (zinc, copper etc.) and metalloids (arsenic) were detected in genomes of the reference isolates, which might offer them some adaptation benefits. As conclusion, the community composition of faba bean rhizobia in Mexico was different from those reported in other regions. Furthermore, our study identified sv. viciae as the second symbiovar in the species R. redzepovicii. These results added novel evidence about the co-evolution, diversification and biogeographic patterns of rhizobia in association with their host legumes in distinct geographic regions.

Microbacterium plantarum sp. nov. and Microbacterium thalli sp. nov., two endophytic metal-resistant bacteria isolated from Sphaeralcea angustifolia (Cav.) G. Don and Prosopis laevigata (Humb. et Bonpl. ex Willd) M.C. Johnston.

Four Gram-positive, aerobic, catalase- and oxidase-negative, rod-shaped, motile endophytic bacterial strains, designated NM3R9T, NE1TT3, NE2TL11 and NE2HP2T, were isolated from the inner tissues (leaf and stem) of Sphaeralcea angustifolia and roots of Prosopis laevigata. They were characterized using a polyphasic approach, which revealed that they represent two novel Microbacterium species. Phylogenetic analysis based on 16S rRNA gene sequencing showed that the species closest to NE2HP2T was Microbacterium arborescens DSM 20754T (99.6 %) and that closest to NM3R9T, NE2TL11 and NE2TT3 was Microbacterium oleivorans NBRC 103075T (97.4 %). The whole-genome average nucleotide identity value between strain NM3R9T and Microbacterium imperiale DSM 20530T was 90.91 %, and that between strain NE2HP2T and M. arborecens DSM 20754T was 91.03 %. Digital DNA-DNA hybridization showed values of less than 70 % with the type strains of related species. The polar lipids present in both strains included diphosphatidylglycerol, phosphatidylglycerol, glycolipids and unidentified lipids, whereas the major fatty acids included anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0. Whole-cell sugars included mannose, rhamnose and galactose. Strains NM3R9T and NE2HP2T showed physiological characteristics different from those present in closely related Microbacterium species. According to the taxonomic analysis, both strains belong to two novel species. The name Microbacterium plantarum sp. nov. is proposed for strain NE2HP2T (=LMG 30875T=CCBAU 101117T) and Microbacterium thalli sp. nov. for strains NM3R9T (=LMG 30873T=CCBAU 101116T), NE1TT3 (=CCBAU 101114) and NE2TL11 (=CCBAU 101115).

Metallophores production by bacteria isolated from heavy metal-contaminated soil and sediment at Lerma-Chapala Basin.

Environmental pollution as a result of heavy metals (HMs) is a worldwide problem and the implementation of eco-friendly remediation technologies is thus required. Metallophores, low molecular weight compounds, could have important biotechnological applications in the fields of agriculture, medicine, and bioremediation. This study aimed to isolate HM-resistant bacteria from soils and sediments of the Lerma-Chapala Basin and evaluated their abilities to produce metallophores and to promote plant growth. Bacteria from the Lerma-Chapala Basin produced metallophores for all the tested metal ions, presented a greater production of As3+ metallophores, and showed high HM resistance especially to Zn2+, As5+, and Ni2+. A total of 320 bacteria were isolated with 170 strains showing siderophores synthesis. Members of the Delftia and Pseudomonas genera showed above 92 percent siderophore units (psu) during siderophores production and hydroxamate proved to be the most common functional group among the analyzed siderophores. Our results provided evidence that Lerma-Chapala Basin bacteria and their metallophores could potentially be employed in bioremediation processes or may even have potential for applications in other biotechnological fields.

Heavy-metal resistance mechanisms developed by bacteria from Lerma-Chapala basin.

Heavy-metal (HM) contamination is a huge environmental problem in many countries including Mexico. Currently, microorganisms with multiple heavy-metal resistance and/or plant-promoting characteristics have been widely used for bioremediation of HM-contaminated soils. The aim of the study was isolated bacteria with multiple heavy-metal resistance and to determinate the resistance mechanism developed by these organisms. A total of 138 aerobic bacteria were isolated from soil and sediments surrounding the Lerma-Chapala basin located in the boundary of the States of Michoacán and Jalisco states of Mexico. One hundred and eight strains showed at least 1 plant growth-promoting features. The Lerma-Chapala basin bacteria were also resistant to high concentrations of HMs including the metalloid arsenic. Sequence analysis of 16S RNA genes reveled that these bacteria were mainly affiliated to the phyla Proteobacteria (38%), Firmicutes (31%) and Actinobacteria (25%), covering 21 genera with Bacillus as the most abundant one. Among them, at least 27 putative novel species were detected in the genera Acinetobacter, Arthrobacter, Bacillus, Agrobacterium, Dyadobacter, Enterobacter, Exiguobacterium, Kluyvera, Micrococcus, Microbacterium and Psychrobacter. In addition, these bacteria developed various heavy-metal-resistance mechanisms, such as biosorption/bioaccumulation, immobilization and detoxification. Therefore, the bacteria isolated from soils and sediments of Lerma-Chapala basin could be used in bioremediation strategies.

Paenibacillus polymyxa NMA1017 as a potential biocontrol agent of Phytophthora tropicalis, causal agent of cacao black pod rot in Chiapas, Mexico.

Cacao represents an important source of income for farmers in the south of Mexico. However, phytosanitary problems have disrupted the production over the years. The use of antagonistic microorganisms as biocontrol agents might improve the production of cacao. In this study, Paenibacillus polymyxa NMA1017, isolated from the rhizosphere of Opuntia ficus-indica L., was used as a biocontrol agent for black pod rot of Theobroma cacao L. cultivated in Chiapas, Mexico. The experiments were carried in vitro and in vivo using pear fruit (Pyrous communis) as model and cacao pods in the field, respectively. The effect of NMA1017 on the phytopathogen was observed by electron microscopy and the production of enzymes was tested as a potential mechanism of action. The bacterium inhibited the radial growth of Phytophthora tropicalis PtCa-14 by 85.9 ± 0.12%. The strain NMA1017 affected mycelial development, as observed by the damage to the cell wall of the oomycete. In pear fruit, the biocontrol agent controlled the production of mycelium on the pear fruit surface, indicating an inhibitory effect exerted. Cacao pods infected with P. tropicalis in the field resulted in a reduction in disease incidence from 86 to 33% and in infection from 68 to 6%. Moreover, strain NMA1017 produced hydrolytic enzymes such as cellulases, xylanases, chitinases and proteases. The results obtained highlight P. polymyxa NMA1017 as an organism of interest for the biocontrol of P. tropicalis, as a method to rescue this important crop in Mexico.

Cupriavidus agavae sp. nov., a species isolated from Agave L. rhizosphere in northeast Mexico.

During the isolation of bacteria from the Agave L. rhizosphere in northeast Mexico, four strains with similar BOX-PCR patterns were collected. The 16S rRNA gene sequences of all four strains were very similar to each other and that of the type strains of Cupriavidus metallidurans CH34T (98.49 % sequence similarity) and Cupriavidus necator N-1T (98.35 %). The genome of strain ASC-9842T was sequenced and compared to those of other Cupriavidus species. ANIb and ANIm values with the most closely related species were lower than 95%, while the in silico DNA-DNA hybridization values were also much lower than 70 %, consistent with the proposal that they represent a novel species. This conclusion was supported by additional phenotypic and chemotaxonomic analyses. Therefore, the name Cupriavidus agavae sp. nov. is proposed with the type strain ASC-9842T (=LMG 26414T=CIP 110327T).

Broad-spectrum antimicrobial activity by Burkholderia cenocepacia TAtl-371, a strain isolated from the tomato rhizosphere.

The Burkholderia cepacia complex (Bcc) comprises a group of 24 species, many of which are opportunistic pathogens of immunocompromised patients and also are widely distributed in agricultural soils. Several Bcc strains synthesize strain-specific antagonistic compounds. In this study, the broad killing activity of B. cenocepacia TAtl-371, a Bcc strain isolated from the tomato rhizosphere, was characterized. This strain exhibits a remarkable antagonism against bacteria, yeast and fungi including other Bcc strains, multidrug-resistant human pathogens and plant pathogens. Genome analysis of strain TAtl-371 revealed several genes involved in the production of antagonistic compounds: siderophores, bacteriocins and hydrolytic enzymes. In pursuit of these activities, we observed growth inhibition of Candida glabrata and Paraburkholderia phenazinium that was dependent on the iron concentration in the medium, suggesting the involvement of siderophores. This strain also produces a previously described lectin-like bacteriocin (LlpA88) and here this was shown to inhibit only Bcc strains but no other bacteria. Moreover, a compound with an m/z 391.2845 with antagonistic activity against Tatumella terrea SHS 2008T was isolated from the TAtl-371 culture supernatant. This strain also contains a phage-tail-like bacteriocin (tailocin) and two chitinases, but the activity of these compounds was not detected. Nevertheless, the previous activities are not responsible for the whole antimicrobial spectrum of TAtl-371 seen on agar plates, suggesting the presence of other compounds yet to be found. In summary, we observed a diversified antimicrobial activity for strain TAtl-371 and believe it supports the biotechnological potential of this Bcc strain as a source of new antimicrobials.

Mechanism of arsenic resistance in endophytic bacteria isolated from endemic plant of mine tailings and their arsenophore production.

Arsenic contamination is an important environmental problem around the world since its high toxicity, and bacteria resist to this element serve as valuable resource for its bioremediation. Aiming at searching the arsenic-resistant bacteria and determining their resistant mechanism, a total of 27 strains isolated from roots of Prosopis laevigata and Spharealcea angustifolia grown in a heavy metal-contaminated region in Mexico were investigated. The minimum inhibitory concentration (MIC) and transformation abilities of arsenate (As5+) and arsenite (As3+), arsenophore synthesis, arsenate uptake, and cytoplasmatic arsenate reductase (arsC), and arsenite transporter (arsB) genes were studied for these strains. Based on these results and the 16S rDNA sequence analysis, these isolates were identified as arsenic-resistant endophytic bacteria (AREB) belonging to the genera Arthrobacter, Bacillus, Brevibacterium, Kocuria, Microbacterium, Micrococcus, Pseudomonas, and Staphylococcus. They could tolerate high concentrations of arsenic with MIC from 20 to > 100 mM for As5+ and 10-20 mM for As3+. Eleven isolates presented dual abilities of As5+ reduction and As3+ oxidation. As the most effective strains, Micrococcus luteus NE2E1 reduced 94% of the As5+ and Pseudomonas zhaodongensis NM2E7 oxidized 46% of As3+ under aerobic condition. About 70 and 44% of the test strains produced arsenophores to chelate As5+ and As3+, respectively. The AREB may absorb arsenate via the same receptor of phosphate uptake or via other way in some case. The cytoplasmic arsenate reductase and alternative arsenate reduction pathways exist in these AREB. Therefore, these AREB could be candidates for the bioremediation process.

Cultivable endophytic bacteria from heavy metal(loid)-tolerant plants.

To evaluate the interactions among endophytes, plants and heavy metal/arsenic contamination, root endophytic bacteria of Prosopis laevigata (Humb and Bonpl. ex Willd) and Sphaeralcea angustifolia grown in a heavy metal(loid)-contaminated zone in San Luis Potosi, Mexico, were isolated and characterized. Greater abundance and species richness were found in Prosopis than in Sphaeralcea and in the nutrient Pb-Zn-rich hill than in the poor nutrient and As-Cu-rich mine tailing. The 25 species identified among the 60 isolates formed three groups in the correspondence analysis, relating to Prosopis/hill (11 species), Prosopis/mine tailing (4 species) and Sphaeralcea/hill (4 species), with six species ungrouped. Most of the isolates showed high or extremely high resistance to arsenic, such as ≥100 mM for As(V) and ≥20 mM for As(III), in mineral medium. These results demonstrated that the abundance and community composition of root endophytic bacteria were strongly affected by the concentration and type of the heavy metals and metalloids (arsenic), as well as the plant species.

Isolation and characterization of yeasts associated with plants growing in heavy-metal- and arsenic-contaminated soils.

Yeasts were quantified and isolated from the rhizospheres of 5 plant species grown at 2 sites of a Mexican region contaminated with arsenic, lead, and other heavy metals. Yeast abundance was about 10(2) CFU/g of soil and 31 isolates were obtained. On the basis of the phylogenetic analysis of 26S rRNA and internal transcribed spacer fragment, 6 species were identified within the following 5 genera: Cryptococcus (80.64%), Rhodotorula (6.45%), Exophiala (6.45%), Trichosporon (3.22%), and Cystobasidium (3.22%). Cryptococcus spp. was the predominant group. Pectinases (51.6%), proteases (51.6%), and xylanases (41.9%) were the enzymes most common, while poor production of siderophores (16.1%) and indole acetic acid (9.67%) was detected. Isolates of Rhodotorula mucilaginosa and Cystobasidium sloffiae could promote plant growth and seed germination in a bioassay using Brassica juncea. Resistance of isolates by arsenic and heavy metals was as follows: As(3+) ≥ 100 mmol/L, As(5+) ≥ 30 mmol/L, Zn(2+) ≥ 2 mmol/L, Pb(2+) ≥ 1.2 mmol/L, and Cu(2+) ≥ 0.5 mmol/L. Strains of Cryptococcus albidus were able to reduce arsenate (As(5+)) into arsenite (As(3+)), but no isolate was capable of oxidizing As(3+). This is the first study on the abundance and identification of rhizosphere yeasts in a heavy-metal- and arsenic-contaminated soil, and of the reduction of arsenate by the species C. albidus.

Brevibacterium metallicus sp. nov., an endophytic bacterium isolated from roots of Prosopis laegivata grown at the edge of a mine tailing in Mexico.

A Gram-positive, aerobic, nonmotile strain, NM2E3(T) was identified as Brevibacterium based on the 16S rRNA gene sequence analysis and had the highest similarities to Brevibacterium jeotgali SJ5-8(T) (97.3 %). This novel bacterium was isolated from root tissue of Prosopis laegivata grown at the edge of a mine tailing in San Luis Potosí, Mexico. Its cells were non-spore-forming rods, showing catalase and oxidase activities and were able to grow in LB medium added with 40 mM Cu(2+), 72 mM As(5+) and various other toxic elements. Anteiso-C15:0 (41.6 %), anteiso-C17:0 (30 %) and iso-C15:0 (9.5 %) were the major fatty acids. MK-8(H2) (88.4 %) and MK-7(H2) (11.6 %) were the major menaquinones. The DNA G + C content of the strain NM2E3(T) was 70.8 mol % (Tm). DNA-DNA hybridization showed that the strain NM2E3(T) had 39.8, 21.7 and 20.3 % relatedness with B. yomogidense JCM 17779(T), B. jeotgali JCM 18571(T) and B. salitolerans TRM 45(T), respectively. Based on the phenotypic and genotypic analyses, the strain NM2E3(T) (=CCBAU 101093(T) = HAMBI 3627(T) = LMG 8673(T)) is reported as a novel species of the genus Brevibacterium, for which the name Brevibacterium metallicus sp. nov., is proposed.

Cupriavidus plantarum sp. nov., a plant-associated species.

During a survey of plant-associated bacteria in northeast Mexico, a group of 13 bacteria was isolated from agave, maize and sorghum plants rhizosphere. This group of strains was related to Cupriavidus respiraculi (99.4 %), but a polyphasic investigation based on DNA-DNA hybridization analysis, other genotypic studies and phenotypic features showed that this group of strains actually belongs to a new Cupriavidus species. Consequently, taking all the results together, the description of Cupriavidus plantarum sp. nov. is proposed.

Increases in the soil ammonia oxidizing phylotypes and their rechange due to long-term irrigation with wastewater.

Wastewater irrigation is a common practice for agricultural systems in arid and semiarid zones, which can help to overcome water scarcity and contribute with nutrient inputs. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are key in the transformation of NH4+-N in soil and can be affected by variations in soil pH, EC, N and C content, or accumulation of pollutants, derived from wastewater irrigation. The objective of this study was to determine the changes in the ammonia oxidizing communities in agricultural soils irrigated with wastewater for different periods of time (25, 50, and 100 years), and in rainfed soils (never irrigated). The amoA gene encoding for the catalytic subunit of the ammonia monooxygenase was used as molecular reporter; it was quantified by qPCR and sequenced by high throughput sequencing, and changes in the community composition were associated with the soil physicochemical characteristics. Soils irrigated with wastewater showed up to five times more the abundance of ammonia oxidizers (based on 16S rRNA gene relative abundance and amoA gene copies) than those under rainfed agriculture. While the amoA-AOA: amoA-AOB ratio decreased from 9.8 in rainfed soils to 1.6 in soils irrigated for 100 years, indicating a favoring environment for AOB rather than AOA. Further, the community structure of both AOA and AOB changed during wastewater irrigation compared to rainfed soils, mainly due to the abundance variation of certain phylotypes. Finally, the significant correlation between soil pH and the ammonia oxidizing community structure was confirmed, mainly for AOB; being the main environmental driver of the ammonia oxidizer community. Also, a calculated toxicity index based on metals concentrations showed a correlation with AOB communities, while the content of carbon and nitrogen was more associated with AOA communities. The results indicate that wastewater irrigation influence ammonia oxidizers communities, manly by the changes in the physicochemical environment.

Diversity and Biotechnological Potential of Cultivable Halophilic and Halotolerant Bacteria from the "Los Negritos" Geothermal Area.

Soil salinization is negatively affecting soils globally, and the spread of this problem is of great concern due to the loss of functions and benefits offered by the soil resource. In the present study, we explored the diversity of halophilic and halotolerant microorganisms in the arable fraction of a sodic-saline soil without agricultural practices and two soils with agricultural practices (one sodic and one saline) near the geothermal area "Los Negritos" in Villamar, Michoacán state. This was achieved through their isolation and molecular identification, as well as the characterization of their potential for the production of metabolites and enzymes of biotechnological interest under saline conditions. Using culture-dependent techniques, 62 halotolerant and moderately halophilic strains belonging to the genera Bacillus, Brachybacterium, Gracilibacillus, Halobacillus, Halomonas, Kocuria, Marinococcus, Nesterenkonia, Oceanobacillus, Planococcus, Priestia, Salibactetium, Salimicrobium, Salinicoccus, Staphylococcus, Terribacillus, and Virgibacillus were isolated. The different strains synthesized hydrolytic enzymes under 15% (w/v) of salts, as well as metabolites with plant-growth-promoting (PGP) characteristics, such as indole acetic acid (IAA), under saline conditions. Furthermore, the production of biopolymers was detected among the strains; members of Bacillus, Halomonas, Staphylococcus, and Salinicoccus showed extracellular polymeric substance (EPS) production, and the strain Halomonas sp. LNSP3E3-1.2 produced polyhydroxybutyrate (PHB) under 10% (w/v) of total salts.

Burkholderia caballeronis sp. nov., a nitrogen fixing species isolated from tomato (Lycopersicon esculentum) with the ability to effectively nodulate Phaseolus vulgaris.

During a survey of Burkholderia species with potential use in agrobiotechnology, a group of 12 strains was isolated from the rhizosphere and rhizoplane of tomato plants growing in Mexico (Nepantla, Mexico State). A phylogenetic analysis of 16S rRNA gene sequences showed that the strains are related to Burkholderia kururiensis and Burkholderia mimosarum (97.4 and 97.1 %, respectively). However, they induced effective nitrogen-fixing nodules on roots of Phaseolus vulgaris. Based on polyphasic taxonomy, the group of strains represents a novel species for which the name Burkholderia caballeronis sp. nov. is proposed. The type species is TNe-841(T) (= LMG 26416(T) = CIP 110324(T)).

Reduction in Salt Stress Due to the Action of Halophilic Bacteria That Promote Plant Growth in Solanum lycopersicum.

Soil salinity is one of the most important factors reducing agricultural productivity worldwide. Halophilic plant growth-promoting bacteria (H-PGPB) represent an alternative method of alleviating saline stress in crops of agricultural interest. In this study, the following halophilic bacteria were evaluated: Bacillus sp. SVHM1.1, Halomonas sp. SVCN6, Halomonas sp. SVHM8, and a consortium. They were grown under greenhouse conditions in Solanum lycopersicum at different salinity concentrations in irrigation water (0, 20, 60, and 100 mM NaCl) to determine the effects on germination, fruit quality, yield, and concentration of osmoprotectors in plant tissue. Our results demonstrate the influence of halophilic bacteria with the capacity to promote plant growth on the germination and development of Solanum lycopersicum at higher salinity levels. The germination percentage was improved at the highest concentration by the inoculated treatments (from 37 to 47%), as were the length of the radicle (30% at 20 mM) and plumule of the germinated seed, this bacterium also increased the weight of the plumule (97% at 100 mM). They also improved the yield. The dry weight of the plant, in addition to having an influence on the quality of the fruit and the concentration of osmoprotectors (Bacillus sp. SVHM 1.1) had the greatest effect on fruit yield (1.5 kg/plant at 20 mM), by the otherhand, Halomonas sp. SVHM8 provided the best fruit quality characteristics at 100 mM. According to the above results, the efficiency of halophilic PGPB in the attenuation of salt stress in Solanum lycopersicum has been proven.

Identification of Halophilic and Halotolerant Bacteria from the Root Soil of the Halophyte Sesuvium verrucosum Raf.

Soil salinity is a condition that limits crop growth and productivity, and soil-dwelling bacteria from halophytic plant roots may be a viable strategy to cope with low productivity due to salt stress. Halophilic and halotolerant bacteria of the root soil of Sesuvium verrucosum were analyzed in this study as there is little evidence regarding its associated microbiology. Soil was sampled from the roots of Sesuvium verrucosum to obtain the cultivable bacteria. Their morphological characteristics were identified and they were molecularly identified by the 16S sequence. The growth capacity of the bacteria was determined at different levels of pH and salinity, and several growth promotion characteristics were identified, such as phosphorus solubilization, indole acetic acid production by the tryptophan-dependent (AIAt) and tryptophan-independent (IAA) pathways, ammonium production from organic sources, solubilization of carbonates, and zinc and sodium capture capacity. In addition, the bacteria that presented the best characteristics for germination variables of Solanum lycopersicum were evaluated. A total of 20 bacteria from root soil of Sesuvium verrucosum Raf. belonging to the phyla Proteobacteria (50%), Firmicutes (45%) and Actinobacteria (5%) were identified, with each one having different morphological characteristics. Among the bacterial isolates, 45% had the ability to resist different levels of salinity and pH, ranging from 0 to 20% of NaCl, and pH between 5 and 11. Moreover, these bacteria had the capacity to solubilize carbonates, phosphorus and zinc, capture sodium, produce ammonium from organic substrates and IAA (indole acetic acid), and promote enzymatic activity of amylases, proteases, lipases and cellulases. The bacteria evaluated on the germination of Solanum lycopersicum had an influence on germination at different salinity levels, with greater influence at 100 mM NaCl. This demonstrated that halophilic bacteria belonging to the rhizosphere of Sesuvium verrucosum have the ability to promote growth in extreme salinity conditions, making them candidates for the recovery of productivity in saline soils.

Bioactive compounds in tomato (Solanum lycopersicum) variety saladette and their relationship with soil mineral content.

The purpose of this study was to determine the relationship between the mineral composition of soils and the bioactive compound content present in tomatoes grown in three regions of Mexico: the state of San Luis Potosí and Tultitlán and Cuautitlán Izcalli from the State of México: Total phenolic compounds, lycopene, and rutin were higher in the Tultitlán tomatoes and were associated with the thallium and magnesium content in the soil. Chlorogenic acid and quercetin in the fruit from C.IZC were associated with molybdenum and nickel found in the soil. A principal component analysis showed that cupper, iron, sodium, manganese, and lead in the soil had a relationship with the antioxidant activity (AA), resveratrol, and naringin in the fruit from SLP. In the soil from TUL, a relationship between thallium with lycopene and rutin with magnesium was found. Some elements in the soil were related to the bioactivities of the fruit.

Paraburkholderia lycopersici sp. nov., a nitrogen-fixing species isolated from rhizoplane of Lycopersicon esculentum Mill. var. Saladette in Mexico.

A survey of our in-house bacterial collection identified a group of six strains isolated from the tomato rhizoplane that possessed 16S rRNA gene sequences with 98.2% sequence similarity to Paraburkholderia pallida, suggesting that these strains represented a novel species. Multilocus sequence analysis using gltB, lepA and recA gene sequences showed the clustering of the strains and the BOX-PCR patterns were similar among these strains. The average nucleotide identity and the DNA-DNA virtual hybridization of strain TNe-862T was <89% and <34%, respectively, to the genomes of any sequenced Paraburkholderia species. The genome of strain TNe-862T possessed all the genes necessary for nitrogen fixation and biosynthesis of indoleacetic acid and antimicrobials terpenes, phosphonates and bacteriocins. It also contained genes for metal resistance, xenobiotic degradation, and hydrolytic enzymes such as a putative chitinase and isoamylase. Even though the strain contained potential genes for degradation of cellulose and starch, the bacterium was unable to utilize these substrates in culture medium. The genome encoded flagella and pili as well as multiple chemotaxis systems. In addition, genes encoding for the type I, II, IV, V and VI secretion systems were also present. The strains grow up to 42°C and 5% NaCl. The optimum growth pH was 8. The major cellular fatty acids were C16:0 and C18:1 ω7c. Based on this polyphasic analysis, these strains represent a novel species in the genus Paraburkholderia, for which the name Paraburkholderia lycopersici sp. nov. is proposed. The type strain is TNe-862T (=LMG 26415T=CIP 110323T).

Draft genome of five Cupriavidus plantarum strains: agave, maize and sorghum plant-associated bacteria with resistance to metals.

Five strains of Cupriavidus plantarum, a metal-resistant, plant-associated bacterium, were selected for genome sequencing through the Genomic Encyclopedia of Bacteria and Archaea (GEBA) Phase IV project at the Joint Genome Institute (JGI) of the U.S. Department of Energy (DOE). The genome of the strains was in the size range of 6.2-6.4 Mbp and encoded 5605-5834 proteins; 16.9-23.7% of these genes could not be assigned to a COG-associated functional category. The G + C content was 65.83-65.99%, and the genomes encoded 59-67 stable RNAs. The strains were resistant in vitro to arsenite, arsenate, cobalt, chromium, copper, nickel and zinc, and their genomes possessed the resistance genes for these metals. The genomes also encoded the biosynthesis of potential antimicrobial compounds, such as terpenes, phosphonates, bacteriocins, betalactones, nonribosomal peptides, phenazine and siderophores, as well as the biosynthesis of cellulose and enzymes such as chitinase and trehalase. The average nucleotide identity (ANI) and DNA-DNA in silico hybridization of the genomes confirmed that C. plantarum is a single species. Moreover, the strains cluster within a single group upon multilocus sequence analyses with eight genes and a phylogenomic analyses. Noteworthy, the ability of the species to tolerate high concentrations of different metals might prove useful for bioremediation of naturally contaminated environments.