Assessing the functional diversity of rhizobacteria from cacao by partitioning root and shoot biomasses.

Plant-microbe interactions are critical for the sustainability of agricultural production. In this study, our aims were to characterize the genetic and functional diversity of the culturable bacterial community associated with the cacao rhizosphere and access their potential for growth promotion of cacao seedling. Culture-dependent and molecular methods were used to characterize the population densities and diversity of bacterial communities from soil and cacao plants at two locations and two plant ages. A total of 63 strains were identified through hsp60 sequencing. Pseudomonas and Enterobacter were the most abundant genera in association with the cacao rhizosphere, whereas Bacillus was more numerous in soil. Parameters of seedling growth promotion were evaluated 60 days after inoculation of seeds, with partition of the assessments into root and shoot weight. Each isolate showed beneficial, neutral or deleterious effects on plant growth, depending on the isolate and on the parts of plant assessed. Interestingly, although an apparent overall decrease in total biomass of seedlings (roots + shoots dry matters) was observed for the majority of isolates (89%), 94% of all isolates, in fact, revealed an increase in plant roots/shoots dry biomass ratio. Despite that part of the isolates (35%) appeared to significantly decrease plant height, and that 65% did not influence plant height (neutral effect), 18 had significantly increased root dry biomass; nevertheless, seven of these root growth-increasing isolates simultaneously decreased shoots-related growth parameters. The results of this study evidentiated the functional diversity of culturable cacao rhizobacteria and how the partitioning of roots and shoots in the assessment of plant growth parameters could reveal the biotechnological potential of these isolates for promoting growth of clones for rehabilitation of commercial cacao plantations. KEY POINTS: • The most common culturable bacteria in cacao roots were Pseudomonas and Enterobacter • Most culturable bacteria from cacao roots increased the root/shoot ratio • Roots and shoots should be examined separately to detect cacao beneficial bacteria.

Burkholderia perseverans sp. nov., a bacterium isolated from the Restinga ecosystem, is a producer of volatile and diffusible compounds that inhibit plant pathogens.

Gram-negative, aerobic, rod-shaped, non-spore-forming, motile bacteria, designated CBAS 719 T, CBAS 732 and CBAS 720 were isolated from leaf litter samples, collected in Espírito Santo State, Brazil, in 2008. Sequences of the 16S rRNA, gyrB, lepA and recA genes showed that these strains grouped with Burkholderia plantarii LMG 9035 T, Burkholderia gladioli LMG 2216 T and Burkholderia glumae LMG 2196 T in a clade of phytopathogenic Burkholderia species. Digital DNA-DNA hybridization experiments and ANI analyses demonstrated that strain CBAS 719 T represents a novel species in this lineage that is very closely related with B. plantarii. The genome sequence of the type strain is 7.57 Mbp and its G + C content is 69.01 mol%. The absence of growth on TSA medium supplemented with 3% (w/v) NaCl, citrate assimilation, ß-galactosidase (PNPG) activity, and of lipase C14 activity differentiated strain CBAS 719 T from B. plantarii LMG 9035 T, its nearest phylogenetic neighbor. Its predominant fatty acid components were C16:0, C18:1 ω7c, cyclo-C17:0 and summed feature 3 (C16:1 ω7c and/or C15:0 iso 2-OH). Based on these genotypic and phenotypic characteristics, the strains CBAS 719 T, CBAS 732 and CBAS 720 are classified in a novel Burkholderia species, for which the name Burkholderia perseverans sp. nov. is proposed. The type strain is CBAS 719 T (= LMG 31557 T = INN12T).

First-tier detection of intragenomic 16S rRNA gene variation in culturable endophytic bacteria from cacao seeds.

BACKGROUND: Intragenomic variability in 16S rDNA is a limiting factor for taxonomic and diversity characterization of Bacteria, and studies on its occurrence in natural/environmental populations are scarce. In this work, direct DNA amplicon sequencing coupled with frequent-cutter restriction analysis allowed detection of intragenomic 16S rDNA variation in culturable endophytic bacteria from cacao seeds in a fast and attractive manner. METHODS: Total genomic DNA from 65 bacterial strains was extracted and the 16S rDNA hyper variable V5-V9 regions were amplified for enzyme digestion and direct Sanger-type sequencing. The resulting electropherograms were visually inspected and compared to the corresponding AluI-restriction profiles, as well as to complete genome sequences in databases. Restriction analysis were employed to substitute the need of amplicon cloning and re-sequencing. A specifically improved polyacrylamide-gradient electrophoresis allowed to resolve 5-bp differences in restriction fragment sizes. Chi-square analysis on 2 × 2 contingency table tested for the independence between the 'number of AluI bands' and 'type of eletropherogram'. RESULTS: Two types of electropherograms were obtained: unique template, with single peaks per base (clean chromatograms), and heterogeneous template, with various levels of multiple peaks per base (mixed chromatograms). Statistics revealed significant interaction between number of restriction fragments and type of electropherogram for the same amplicons: clean or mixed ones associated to ≤5 or ≥6 bands, respectively. The mixed-template pattern combined with the AluI-restriction profiles indicated a high proportion of 49% of the culturable endophytes from a tropical environment showing evidence of intragenomic 16S rDNA heterogeneity. CONCLUSION: The approach presented here was useful for a rapid, first-tier detection of intragenomic variation in culturable isolates, which can be applied in studies of other natural populations; a preliminary view of intragenomic heterogeneity levels can complement culture-dependent and -independent methods. Consequences of these findings in taxonomic and diversity studies in complex bacterial communities are discussed.

A new alkalophilic isolate of Bacillus as a producer of cyclodextrin glycosyltransferase using cassava flour

Abstract Cyclodextrin glycosyltransferase (CGTase) catalyzes the conversion of starch into non-reducing cyclic sugars, cyclodextrins, which have several industrial applications. This study aimed to establish optimal culture conditions for β-CGTase production by Bacillus sp. SM-02, isolated from soil of cassava industries waste water lake. The optimization was performed by Central Composite Design (CCD) 2, using cassava flour and corn steep liquor as substrates. The maximum production of 1087.9 U mL−1 was obtained with 25.0 g L−1 of cassava flour and 3.5 g L−1 of corn steep after 72 h by submerged fermentation. The enzyme showed optimum activity at pH 5.0 and temperature 55 °C, and maintained thermal stability at 55 °C for 3 h. The enzymatic activity was stimulated in the presence of Mg+2, Ca+2, EDTA, K+, Ba+2 and Na+ and inhibited in the presence of Hg+2, Cu+2, Fe+2 and Zn+2. The results showed that Bacillus sp. SM-02 have good potential for β-CGTase production.

A new alkalophilic isolate of Bacillus as a producer of cyclodextrin glycosyltransferase using cassava flour.

Cyclodextrin glycosyltransferase (CGTase) catalyzes the conversion of starch into non-reducing cyclic sugars, cyclodextrins, which have several industrial applications. This study aimed to establish optimal culture conditions for ß-CGTase production by Bacillus sp. SM-02, isolated from soil of cassava industries waste water lake. The optimization was performed by Central Composite Design (CCD) 2, using cassava flour and corn steep liquor as substrates. The maximum production of 1087.9UmL(-1) was obtained with 25.0gL(-1) of cassava flour and 3.5gL(-1) of corn steep after 72h by submerged fermentation. The enzyme showed optimum activity at pH 5.0 and temperature 55°C, and maintained thermal stability at 55°C for 3h. The enzymatic activity was stimulated in the presence of Mg(+2), Ca(+2), EDTA, K(+), Ba(+2) and Na(+) and inhibited in the presence of Hg(+2), Cu(+2), Fe(+2) and Zn(+2). The results showed that Bacillus sp. SM-02 have good potential for ß-CGTase production.

Production and Partial Characterization of Cellulases from Trichoderma sp. IS-05 Isolated from Sandy Coastal Plains of Northeast Brazil.

This study evaluated the production of cellulolytic enzymes by Trichoderma sp. IS-05 strain, isolated from sand dunes, according to its ability to grow on cellulose as carbon source. Wheat bran was tested as the carbon source and peptone tested as the nitrogen source. Different concentrations of carbon and nitrogen were tested using a factorial design to identify optimal cellulase activity production. The results showed that media containing wheat bran 4.0% (w/v) and peptone 0.25% (w/v) lead to the highest production, 564.0 U L(-1) of cellulase, obtained after 2 days of fermentation. The pH and temperature profile showed optimal activity at pH 3.0 and 60°C. As for thermostability, the cellulase was most tolerant at 60°C, retaining more than 59.6% of maximal activity even after 4 hours of incubation. The combination of acid pH, high temperature tolerance, and production of cellulase from agro-industrial residues by Trichoderma sp. IS-05 offers possibilities condition for the biomass hydrolysis process to produce bioethanol.