Isolation and Identification of taxonomically diverse bacterial endophytes from citrus in Punjab Pakistan

<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New"; caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); text-align: justify; line-height: 26.666664123535156px;"> <span style="font-size: 12pt; line-height: 32px; font-family: "Times New Roman", serif;">Citrus is an economically important fruit crop grown in all provinces of Pakistan, while Punjab accounting for 95 percent of total production due to its favorable climate for citrus production. Commercially grown varieties in Pakistan include sweet oranges, grapefruits, Mandarine, Lime, and lemon. The goal of this research was to see how diverse the cultivable bacterial populations are found in citrus cultivars. Out of 90 isolated cultures, 37 endophytic bacterial species and 15 </span><span style="font-size: 12pt; line-height: 32px; font-family: "Times New Roman", serif;">different genera of bacteria were characterized</span><span style="font-size: 12pt; line-height: 32px; font-family: "Times New Roman", serif;"> based on morphological, biochemical, and molecular methods from citrus leaves. All the isolated bacteria were subjected to PCR amplification through 16S rDNA followed by sequencing. </span><span style="font-size: 12pt; line-height: 32px; font-family: "Times New Roman", serif;">RDP base classification revealed that class Bacilli has the largest percentage of isolates, whereas class Alpha, Beta, and Gamma Proteobacteria have the lowest percentage among all genotypes used. According to the findings, the phylum Firmicutes contains a common genus (Brevibacterium, 1%; Enterococcus, 6%; Staphylococcus, 7% and Bacillus, 60%). Alpha (Rhizobium) beta (Burkholderia cepacia; Comamonas terigena) gamma Proteobacteria (Enterobacter hermachei (1%), Klebsiella pneumoniae (1%), Proteus mirabilis (8%), Pseudomonas aeruginosa (5%), Psychrobacter pulmonis and Yersinia molalretti (1%) respectively. </span><span style="font-size: 12pt; line-height: 32px; font-family: "Times New Roman", serif;">These results revealed that cultivars of the plants might contribute to the structure and endophytic bacterial communities associated with citrus. Endophytes extracted from leaf samples of different citrus cultivars in Pakistan are reported for the first time. The idea of employing endophytes bacteria to produce enzymes stimulate plant growth, and its purpose as a biological control agent will be investigated in the future.</span><span style="font-size: 12pt; line-height: 32px; font-family: "Times New Roman", serif;"><o:p></o:p></span></pre>

Horizontal Transmission of Stress Resistance Genes Shape the Ecology of Beta- and Gamma-Proteobacteria

The transmissible locus of stress tolerance (tLST) is found mainly in beta- and gamma-Proteobacteria and confers tolerance to elevated temperature, pressure, and chlorine. This genomic island, previously referred to as transmissible locus of protein quality control or locus of heat resistance likely originates from an environmental bacterium thriving in extreme habitats, but has been widely transmitted by lateral gene transfer. Although highly conserved, the gene content on the island is subject to evolution and gene products such as small heat shock proteins are present in several functionally distinct sequence variants. A number of these genes are xenologs of core genome genes with the gene products to widen the substrate spectrum and to be highly (complementary) expressed thus their functionality to become dominant over core genome genes. In this review, we will present current knowledge of the function of core tLST genes and discuss current knowledge on selection and counter-selection processes that favor maintenance of the tLST island, with frequent acquisition of gene products involved in cyclic di-GMP signaling, in different habitats from the environment to animals and plants, processed animal and plant products, man-made environments, and subsequently humans.

YhcB (DUF1043), a novel cell division protein conserved across gamma-proteobacteria

YhcB, an uncharacterized protein conserved across gamma-proteobacteria, is composed predominantly of a single Domain of Unknown Function (DUF 1043) with an N-terminal transmembrane alpha-helix. Here, we show that E. coli YhcB is a conditionally essential protein that interacts with the proteins of the cell divisome (e.g., FtsI, FtsQ) and elongasome (e.g., RodZ, RodA). We found 7 interactions of YhcB that are conserved in Yersinia pestis and/or Vibrio cholerae. Furthermore, we identified several point mutations that abolished interactions of YhcB with FtsI and RodZ. The YhcB knock-out strain does not grow at 45C and is hypersensitive to cell-wall acting antibiotics even in stationary phase. The deletion of yhcB leads to filamentation, abnormal FtsZ ring formation, and aberrant septa development. The 2.8 angstrom crystal structure for the cytosolic domain from Haemophilus ducreyi YhcB shows a unique tetrameric alpha-helical coiled-coil structure that combines parallel and anti-parallel coiled-coil intersubunit interactions. This structure is likely to organize interprotein oligomeric interactions on the inner surface of the cytoplasmic membrane, possibly involved in regulation of cell division and/or envelope biogenesis/integrity in proteobacteria. In summary, YhcB is a conserved and conditionally essential protein that is predicted to play a role in cell division and consequently or in addition affects envelope biogenesis.

A Proline-Rich Element in the Type III Secretion Protein FlhB Contributes to Flagellar Biogenesis in the Beta- and Gamma-Proteobacteria

Flagella are bacterial organelles of locomotion. Their biogenesis is highly coordinated in time and space and relies on a specialized flagellar type III secretion system (fT3SS) required for the assembly of the extracellular hook, rod, and filament parts of this complex motor device. The fT3SS protein FlhB switches secretion substrate specificity once the growing hook reaches its determined length. Here we present the crystal structure of the cytoplasmic domain of the transmembrane protein FlhB. The structure visualizes a so-far unseen proline-rich region (PRR) at the very C-terminus of the protein. Strains lacking the PRR show a decrease in flagellation as determined by hook- and filament staining, indicating a role of the PRR during assembly of the hook and filament structures. Phylogenetic analysis shows that the PRR is a primary feature of FlhB proteins of flagellated beta- and gamma-proteobacteria. Taken together, our study adds another layer of complexity and organismic diversity to the process of flagella biogenesis.

Temporal and vertical variability of bacterioplankton composition in Chipana bay (21º20’S) in a coastal upwelling system of northern Chile: A fluorescence in situ hybridization approach

The bacterioplankton in the upwelling systems associated with oceanographic condition of the oxygen minimum zone (OMZ) of the Eastern tropical South Pacific was studied through visualization and enumeration with fluorescent in situ hybridization (FISH). Six different taxonomic groups were studied (Alpha, Beta, Gamma-proteobacteria, Cytophaga-flavobacterium and the domains Archaea and Bacteria). The analysis showed a greater predominance of the Bacteria domain (20 to 68% of hybridized cells) over Archaea (2 to 18% of hybridized cells). The specific groups showed that Cytophaga-flavobacterium, Alpha-proteobacteria and Gamma-proteobacteria are more abundant in the surface layer. Gamma-proteobacteria is also most abundant in the deep oxycline and, Beta-proteobacteria is the group with the lowest registered abundances. Changes in the vertical distribution of the bacterial community in the water column between OMZ and on oxycline were observed through NMDS. This change is a product of a shift in the abundances of the specific groups Cytophaga-flavobacterium and Gamma-proteobacteria in the surface layers, due to low concentration of chlorophyll-a caused by periods of relaxation in the upwelling.

BACTERIAL BIODIVERSITY IN MINEROMEDICINAL WATERS OF SPA “URAUCO”. PICHINCHA. ECUADOR

The presence of mineromedicinal water springs in Ecuador is related to the large number of volcanoes that exist in the country, which have been used since ancient times as medicines by the population. However, it is unknown what bacterial biodiversity is present. Therefore, the objective of these work was to determine the bacterial biodi- versity of the mineromedicinal waters of “Urauco” spa located in Pichincha Provinces of Ecuador. Water samples of a volume of 1 liter were taken at two points in each spa studied. Sampling was done 2 times over a period of two year. To take and transport the samples, the Ecuadorian standards INEN 2 176-98 and INEN 2 169-98 were followed. For the determination of bacterial biodiversity, the techniques of planting, selection and identification of bacteria indicated by Barrow and Feltan (2004) and MacFfadin (2004) were used, complemented with the bio- chemical tests contained in the API (BioMérieux) galleries and Microgen (Microgen corp.). The results indicate a population of heterotrophic bacteria in the spa waters of 3.1 x 102 CFU / mL, with the prevalence of Gram negative bacteria of the Gamma Proteobacteria class. It was possible to isolate and identify 64 colonies of bacteria. The genera of bacteria were Acidovorax, Aeromonas, Bacillus, Brevundimonas, Budvicia, Citrobacter, Corynebacterium, Edwardsiella, Enterococcus, Ewingella, Flavobacterium, Kurthia, Micrococcus, Proteus, Pseudomonas, Psychrobacter, Ralstonia, Staphylococcus, Vibrio and Yokonella. The bacterial biodiversity observed was high, although low in number .

Sinorhizobium meliloti YbeY is a zinc-dependent single-strand specific endoribonuclease that plays an important role in 16S ribosomal RNA processing

Single-strand specific endoribonuclease YbeY has been shown to play an important role in the processing of the 3′ end of the 16S rRNA in Escherichia coli. Lack of YbeY results in the accumulation of the 17S rRNA precursor. In contrast to a previous report, we show that Sinorhizobium meliloti YbeY exhibits endoribonuclease activity on single-stranded RNA substrate but not on the double-stranded substrate. This study also identifies the previously unknown metal ion involved in YbeY function to be Zn2+ and shows that the activity of YbeY is enhanced when the occupancy of zinc is increased. We have identified a pre-16S rRNA precursor that accumulates in the S. meliloti ΔybeY strain. We also show that ΔybeY mutant of Brucella abortus, a mammalian pathogen, also accumulates a similar pre-16S rRNA. The pre-16S species is longer in alpha-proteobacteria than in gamma-proteobacteria. We demonstrate that the YbeY from E. coli and S. meliloti can reciprocally complement the rRNA processing defect in a ΔybeY mutant of the other organism. These results establish YbeY as a zinc-dependent single-strand specific endoribonuclease that functions in 16S rRNA processing in both alpha- and gamma-proteobacteria.

Partitioning protein ParP directly links chemotaxis to biofilm dispersal in Pseudomonas aeruginosa

The recent characterization of partitioning proteins in the localization of chemotaxis signal transduction systems was proposed to have broad implications for polarly-flagellated non-enterobacteriaceae gamma-proteobacteria. These studies showed that the loss of either partitioning protein resulted in equivalent reductions in swimming motility and chemotaxis protein localization and inheritance. However, the role of these chemotaxis partitioning proteins outside of Vibrio spp. remains untested. Our studies on the chemotaxis partitioning proteins in Pseudomonas aeruginosa revealed an unexpected role for the partitioning protein ParP. While the P. aeruginosa ParC and ParP homologs are needed for wild type swimming motility, the loss of ParP results in a greater swimming defect compared to the parC mutant. Our studies revealed that the Par-like proteins directly interact with each other and the chemotaxis system, and ParP interacts with DipA. Deletion of dipA results in a similar defect in swimming motility as the parP mutant. ParP has an interdependence for polar cluster formation, but not localization, with both CheA and DipA, and CheA cluster formation is partially dependent on ParP. Due to the direct interactions and interdependence of cluster formation of ParP and DipA, and the similar phenotypes of the parP and dipA mutants, further investigation into the role of ParP in biofilm dispersion is warranted.ImportanceImpaired chemotaxis protein cluster formation or inheritance reduces chemotaxis which can have an impact on of the virulence of a bacterium. In some gamma-proteobacteria there are systems in place to ensure that chemotaxis proteins, like chromosomes and plasmids, are localized for optimal chemotaxis and that daughter cells inherit their own clusters for use after cell division. Par-like proteins have been implicated in the partitioning and localization of chemotaxis proteins and the chemotactic ability of Vibrio spp. and Rhodobacter sphaeroides [1–3]. We propose that Par-like proteins can do more than localize chemotaxis proteins to the poles of the cells. In P. aeruginosa, they bring together other key proteins involved in regulating flagellar-based motility, and we propose they function as a critical link between biofilm dispersal and motility.