Co-evolution with lytic phage selects for the mucoid phenotype of Pseudomonas fluorescens SBW25

The effects of co-evolution with lytic phage on bacterial virulence-related traits are largely unknown. In this study we investigate the incidence of the mucoid phenotype of the bacterium Pseudomonas fluorescens SBW25 in response to co-evolution with the lytic phage phi2 (φ2). The mucoid phenotype of Pseudomonas spp. is due to overproduction of alginate and is a considerable virulence factor contributing to the intractability of infections most notably in cystic fibrosis (CF) lung, but also in pathogenic infections of plants. Our data show that this phenotype can evolve as an adaptive response to phage predation and is favoured under specific abiotic conditions, in particular a homogenous spatial structure and a high rate of nutrient replacement. The mucoid phenotype remains partially sensitive to phage infection, which facilitates ‘apparent competition'' with phage-sensitive competitors, partially offsetting the costs of alginate production. Although P. fluorescens SBW25 is not a pathogen, several key characteristics typical of Pseudomonas aeruginosa clinical isolates from CF lung were noted, including loss of motility on mucoid conversion and a high rate of spontaneous reversion to the wild-type phenotype. Although the genetic mechanisms of this phenotype remain unknown, they do not include mutations at many of the commonly reported loci implicated in mucoid conversion, including mucA and algU. These data not only further our understanding of the potential role phage have in the ecology and evolution of bacteria virulence in both natural and clinical settings, but also highlight the need to consider both biotic and abiotic variables if bacteriophages are to be used therapeutically.     

Shifts in bacterial communities of two caribbean reef-building coral species affected by white plague disease

Coral reefs are deteriorating at an alarming rate mainly as a consequence of the emergence of coral diseases. The white plague disease (WPD) is the most prevalent coral disease in the southwestern Caribbean, affecting dozens of coral species. However, the identification of a single causal agent has proved problematic. This suggests more complex etiological scenarios involving alterations in the dynamic interaction between environmental factors, the coral immune system and the symbiotic microbial communities. Here we compare the microbiome of healthy and WPD-affected corals from the two reef-building species Diploria strigosa and Siderastrea siderea collected at the Tayrona National Park in the Caribbean of Colombia. Microbiomes were analyzed by combining culture-dependent methods and pyrosequencing of 16S ribosomal DNA (rDNA) V5-V6 hypervariable regions. A total of 20 410 classifiable 16S rDNA sequences reads were obtained including all samples. No significant differences in operational taxonomic unit diversity were found between healthy and affected tissues; however, a significant increase of Alphaproteobacteria and a concomitant decrease in the Beta- and Gammaproteobacteria was observed in WPD-affected corals of both species. Significant shifts were also observed in the orders Rhizobiales, Caulobacteriales, Burkholderiales, Rhodobacterales, Aleteromonadales and Xanthomonadales, although they were not consistent between the two coral species. These shifts in the microbiome structure of WPD-affected corals suggest a loss of community-mediated growth control mechanisms on bacterial populations specific for each holobiont system.     

In Vivo Microbial Coevolution Favors Host Protection and Plastic Downregulation of Immunity

Microbiota can protect their hosts from infection. The short timescales in which microbes can evolve presents the possibility that “protective microbes” can take-over from the immune system of longer-lived hosts in the coevolutionary race against pathogens. Here, we found that coevolution between a protective bacterium (Enterococcus faecalis) and a virulent pathogen (Staphylococcus aureus) within an animal population (Caenorhabditis elegans) resulted in more disease suppression than when the protective bacterium adapted to uninfected hosts. At the same time, more protective E. faecalis populations became costlier to harbor and altered the expression of 134 host genes. Many of these genes appear to be related to the mechanism of protection, reactive oxygen species production. Crucially, more protective E. faecalis populations downregulated a key immune gene, , known to be effective against S. aureus infection. These results suggest that a microbial line of defense is favored by microbial coevolution and may cause hosts to plastically divest of their own immunity.     

Effects of Size of Carbohydrate Chain on Protease Digestion of Aspergillus niger Endo-β-1,4-glucanase

Three different carbohydrate-depleted enzymes were prepared from an endo-β-l,4-glucanase of Aspergillus niger IF031125 by treatment with endo-β-N-acetylglucosaminidase or α-mannosidase. They were purified by Concanavalin A-Sepharose affinity and DEAE ion-exchange column chromatographies. The molecular sizes of these enzymes had been decreased from 40 kDa containing 9.0% carbohydrate to 39, 38, and 37kDa with carbohydrate at 4.5, 1.3, and 0.8% (wt/wt), respectively. The native and these carbohydrate-depleted enzymes were compared in their enzymatic properties, and it was found that they were identical in their catalytic activities and both thermal and pH stabilities. However, the 37-kDa enzyme was more susceptible to proteolysis by Savinase, proteinase K, and Pronase E. On the other hand, the specific protease trypsin showed no such effect on activity of all enzymes. These results suggested that the core structure of the asparagine-linked sugar chain, which consisted of three monosaccharide residues, contributed to the high stability of the endo-β-l,4-glucanase against protease digestion.     

Analysis of the community structure of abyssal kinetoplastids revealed similar communities at larger spatial scales

Knowledge of the spatial scales of diversity is necessary to evaluate the mechanisms driving biodiversity and biogeography in the vast but poorly understood deep sea. The community structure of kinetoplastids, an important group of microbial eukaryotes belonging to the Euglenozoa, from all abyssal plains of the South Atlantic and two areas of the eastern Mediterranean was studied using partial small subunit ribosomal DNA gene clone libraries. A total of 1364 clones from 10 different regions were retrieved. The analysis revealed statistically not distinguishable communities from both the South-East Atlantic (Angola and Guinea Basin) and the South-West Atlantic (Angola and Brazil Basin) at spatial scales of 1000–3000 km, whereas all other communities were significantly differentiated from one another. It seems likely that multiple processes operate at the same time to shape communities of deep-sea kinetoplastids. Nevertheless, constant and homogenous environmental conditions over large spatial scales at abyssal depths, together with high dispersal capabilities of microbial eukaryotes, maintain best the results of statistically indistinguishable communities at larger spatial scales.     

Influence of Nutrient Availability on the Interaction Between Spotted Knapweed and Bluebunch Wheatgrass

Centaurea maculosa (Lam.) (spotted knapweed) reduces wildlife and livestock habitat biodiversity and increases erosion. Nutrient availability to plants may be used to accelerate succession away from spotted knapweed. Early‐successional plant communities often have high nutrient availability, whereas late‐successional communities are often found on lower nutrient soils. We hypothesized that removal of nutrients would change the competitive advantage from spotted knapweed to Pseudoroegneria spicatum (bluebunch wheatgrass) (late seral). In two addition series matrices, background densities of Secale cereale (annual rye) and Elymus elimoides (bottlebrush squirreltail) (3,000 seeds/m²) were used to remove nutrients from the soil. In another set of addition series matrices, nitrogen (33 kg/ha) or phosphorus (33 kg/ha) were added to the soil. Nutrient analysis of soil and vegetation indicated that annual rye and bottlebrush squirreltail reduced nutrient availability in soils. In another matrix, neither a background density nor nutrients were added. Data were fit into Watkinson's curvilinear model to determine the competitive relationship between bluebunch wheatgrass and spotted knapweed. This allowed comparison of the equivalence ratios (C) generated from each addition series. The C parameters are the per‐plant equivalent of bluebunch wheatgrass or spotted knapweed and can be interpreted as the ratio of intra‐to‐interspecific competition. The C parameters are also the equivalence ratio of the number of spotted knapweed it takes to have equivalent effect on bluebunch wheatgrass or the number of bluebunch wheatgrass having the equivalent effect on spotted knapweed. Without nutrient manipulation, spotted knapweed was more competitive than bluebunch wheatgrass. The C for bluebunch wheatgrass was 0.17, indicating that 0.17 knapweed plants were competitively equivalent to one wheatgrass. Annual rye changed the competitive balance in favor of bluebunch wheatgrass (C = 9.9). Addition of nitrogen, phosphorus, or the mid‐seral species did not change the competitive relationship between the two species. This preliminary study suggests that succession from spotted knapweed to late‐seral bluebunch wheatgrass community may be accelerated by altering resource availability.     

Geochemical baseline establishment and ecological risk evaluation of heavy metals in greenhouse soils from Dongtai,China

Currently, heavy metal (HM) contamination in greenhouse soils is a significant concern due to the rapid expansion of greenhouse agriculture. However, it is difficult to accurately assess HM pollution in greenhouse soils in China due to the lack of local geochemical baseline concentrations (GBCs) or corresponding background values. In the present study, the GBCs of HMs in Dongtai, a representative greenhouse area of China, were established from subsoils using cumulative frequency distribution (CFD) curves. The pollution levels of HMs and potential ecological risks were investigated using different quantitative indices, such as geo-accumulation index (I_geo), pollution index (PI), pollution load index (PLI) and ecological risk index (RI), based on these regional GBCs. The total concentrations of six metals (Cd, Cr, Cu, Ni, Pb and Zn) in surface soils were determined and shown to be lower than the concentrations reported in other greenhouse regions of China. The GBCs of Cd, Cr, Cu, Ni, Pb and Zn were 0.059–0.092, 39.20–54.50, 12.52–15.57, 20.63–23.26, 13.43–16.62 and 43.02–52.65 mg kg⁻¹, respectively. Based on this baseline criterion, Cd, Pb and Zn accumulated in the surface soils because they were present at concentrations higher than their baseline values. The soils were moderately polluted by Cd according to the I_geo values, and the PI results indicated that moderate Cd contamination was present in this area. The large variation of I_geo value of Cd revealed that Cd in this area was likely influenced by agricultural activities. The PLI showed that most of the study area was moderately polluted. However, an analysis of the RI showed that the investigated HMs had low ecological risks. Correlation analysis and principle component analysis suggested that the Cd, Pb and Zn in the greenhouse soils mainly originated from anthropogenic sources (agricultural activities, atmospheric deposition etc.), while Cr, Cu, and Ni originated from natural sources. The findings of this study illustrated the necessity of GBC establishment at the local scale to facilitate more accurate HM evaluation of greenhouse soils. It is advisable to pay more attention to Cd, which could cause environmental problems in the greenhouse system.     

Biotechnological applications of microbial bioconversions

Modern research has focused on the microbial transformation of a huge variety of organic compounds to obtain compounds of therapeutic and/or industrial interest. Microbial transformation is a useful tool for producing new compounds, as a consequence of the variety of reactions for natural products. This article describes the production of many important compounds by biotransformation. Emphasis is placed on reporting the metabolites that may be of special interest to the pharmaceutical and biotechnological industries, as well as the practical aspects of this work in the field of microbial transformations.