Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution

We present here the hologenome theory of evolution, which considers the holobiont (the animal or plant with all of its associated microorganisms) as a unit of selection in evolution. The hologenome is defined as the sum of the genetic information of the host and its microbiota. The theory is based on four generalizations: (1) All animals and plants establish symbiotic relationships with microorganisms. (2) Symbiotic microorganisms are transmitted between generations. (3) The association between host and symbionts affects the fitness of the holobiont within its environment. (4) Variation in the hologenome can be brought about by changes in either the host or the microbiota genomes; under environmental stress, the symbiotic microbial community can change rapidly. These points taken together suggest that the genetic wealth of diverse microbial symbionts can play an important role both in adaptation and in evolution of higher organisms. During periods of rapid changes in the environment, the diverse microbial symbiont community can aid the holobiont in surviving, multiplying and buying the time necessary for the host genome to evolve. The distinguishing feature of the hologenome theory is that it considers all of the diverse microbiota associated with the animal or the plant as part of the evolving holobiont. Thus, the hologenome theory fits within the framework of the 'superorganism' proposed by Wilson and Sober.     

Temporal patterns of microbial community structure in the Mid-Atlantic Bight

Although open ocean time-series sites have been areas of microbial research for years, relatively little is known about the population dynamics of bacterioplankton communities in the coastal ocean on kilometer spatial and seasonal temporal scales. To gain a better understanding of microbial community variability, monthly samples of bacterial biomass were collected in 1995-1996 along a 34-km transect near the Long-Term Ecosystem Observatory (LEO-15) off the New Jersey coast. Surface and bottom sampling was performed at seven stations along a transect line with depths ranging from 1 to 35 m (n=178). Microbial populations were fingerprinted using ribosomal 16S rRNA genes and terminal restriction fragment length polymorphism analysis. Results from cluster analysis revealed distinct temporal patterns among the bacterioplankton communities in the Mid-Atlantic Bight rather than grouping by sample location or depth. Principal components analysis models supported the temporal patterns. In addition, partial least squares regression modeling could not discern a significant correlation from traditional oceanographic physical and phytoplankton nutrient parameters on overall bacterial community variability patterns at LEO-15. These results suggest factors not traditionally measured during oceanographic studies are structuring coastal microbial communities.     

Influence of plant developmental stage on microbial community structure and activity in the rhizosphere of three field crops

Seasonal shifts in rhizosphere microbial populations were investigated to follow the influence of plant developmental stage. A field study of indigenous microbial rhizosphere communities was undertaken on pea (Pisum satvium var. quincy), wheat (Triticum aestivum var. pena wawa) and sugar beet (Beta vulgaris var. amythyst). Rhizosphere community diversity and substrate utilization patterns were followed throughout a growing season, by culturing, rRNA gene density gradient gel electrophoresis and BIOLOG. Culturable bacterial and fungal rhizosphere community densities were stable in pea and wheat rhizospheres, with dynamic shifts observed in the sugar beet rhizosphere. Successional shifts in bacterial and fungal diversity as plants mature demonstrated that different plants select and define their own functional rhizosphere communities. Assessment of metabolic activity and resource utilization by bacterial community-level physiological profiling demonstrated greater similarities between different plant species rhizosphere communities at the same than at different developmental stages. Marked temporal shifts in diversity and relative activity were observed in rhizosphere bacterial communities with developmental stage for all plant species studied. Shifts in the diversity of fungal and bacterial communities were more pronounced in maturing pea and sugar beet plants. This detailed study demonstrates that plant species select for specialized microbial communities that change in response to plant growth and plant inputs.     

Endophytic colonization of Vitis vinifera L. by Burkholderia phytofirmans strain PsJN: from the rhizosphere to inflorescence tissues

The colonization pattern of Vitis vinifera L. by Burkholderia phytofirmans strain PsJN was determined using grapevine fruiting cuttings with emphasis on putative inflorescence colonization under nonsterile conditions. Two-week-old rooted plants harbouring flower bud initials, grown in nonsterile soil, were inoculated with PsJN:gfp2x. Plant colonization was subsequently monitored at various times after inoculation with plate counts and epifluorescence and/or confocal microscopy. Strain PsJN was chronologically detected on the root surfaces, in the endorhiza, inside grape inflorescence stalks, not inside preflower buds and flowers but rather as an endophyte inside young berries. Data demonstrated low endophytic populations of strain PsJN in inflorescence organs, i.e. grape stalks and immature berries with inconsistency among plants for bacterial colonization of inflorescences. Nevertheless, endophytic colonization of inflorescences by strain PsJN was substantial for some plants. Microscopic analysis revealed PsJN as a thriving endophyte in inflorescence organs after the colonization process. Strain PsJN was visualized colonizing the root surface, entering the endorhiza and spreading to grape inflorescence stalks, pedicels and then to immature berries through xylem vessels. In parallel to these observations, a natural microbial communities was also detected on and inside plants, demonstrating the colonization of grapevine by strain PsJN in the presence of other microorganisms.     

Light enhanced amino acid uptake by dominant bacterioplankton groups in surface waters of the Atlantic Ocean

(35)S-Methionine and (3)H-leucine bioassay tracer experiments were conducted on two meridional transatlantic cruises to assess whether dominant planktonic microorganisms use visible sunlight to enhance uptake of these organic molecules at ambient concentrations. The two numerically dominant groups of oceanic bacterioplankton were Prochlorococcus cyanobacteria and bacteria with low nucleic acid (LNA) content, comprising 60% SAR11-related cells. The results of flow cytometric sorting of labelled bacterioplankton cells showed that when incubated in the light, Prochlorococcus and LNA bacteria increased their uptake of amino acids on average by 50% and 23%, respectively, compared with those incubated in the dark. Amino acid uptake of Synechococcus cyanobacteria was also enhanced by visible light, but bacteria with high nucleic acid content showed no light stimulation. Additionally, differential uptake of the two amino acids by the Prochlorococcus and LNA cells was observed. The populations of these two types of cells on average completely accounted for the determined 22% light enhancement of amino acid uptake by the total bacterioplankton community, suggesting a plausible way of harnessing light energy for selectively transporting scarce nutrients that could explain the numerical dominance of these groups in situ.     

Uptake of adhesive powders from lure stations by Mediterranean fruit fly (Dipt., Tephritidae)

Powders that are capable of adhering to insect cuticles can act as carrier particles when combined with insecticides, entomopathogens, or pheromones, for targeted insect control. One potential method of delivering the powder to an insect is to lure the insects to stations containing powder using a species‐specific attractant. Here, we report on the uptake of two different powders from lure stations (henceforth called ‘dispensers’) by the Mediterranean fruit fly, Ceratitis capitata, and the transfer of the powders to conspecifics during field studies in Portugal, as part of a research programme to develop lure‐and‐kill technologies based on adhesive powder. Uptake of an electrostatic wax powder, Entostat?, from dispensers was greater than uptake of a proprietary metallic powder, Entomag?, for both wild male C. capitata visiting field‐placed dispensers and laboratory‐reared males confined with dispensers in field cages. In agreement with field data, C. capitata also took up more Entostat than Entomag when artificially dosed on dispenser trays containing powder in the laboratory, and the quantities taken up were shown to be greater than that calculated from field experiments. Increasing the amount of Entostat powder in field‐placed dispensers resulted in greater uptake of powder by visiting male C. capitata. Laboratory‐reared male and female C. capitata were released in field cages in which were hung dispensers containing adhesive powder that were baited with the male attractant trimedlure. After 24 h, the powder was successfully extracted from all males and nearly all females collected, indicating that males probably transferred powder to conspecific females after visiting dispensers. The results underscore that a lure‐and‐kill system based on adhesive powder might have potential for controlling Mediterranean fruit fly and other flying insects.     

A cuticle-degrading protease (CDEP-1) of Beauveria bassiana enhances virulence

In order to investigate virulence enhancement of entomopathogenic fungi, a Beauveria bassiana-sourced Pr1 protease (CDEP-1) was expressed by a methylotrophic yeast Pichia pastoris and then used as an additive to three gradient sprays of B. bassiana strain (Bb0062) onto apterous green peach aphid Myzus persicae adults in six bioassays. The resultant data fit well to a time–concentration–mortality model. Generally, the LC₅₀ estimates of the fungal pathogen against the aphid species decreased with increasing CDEP-1 concentrations from 0 to 100 µg mL^?1. The LC₅₀s on days 5–7 after spray were reduced by 1.5–2.5-fold at the concentrations of 20–100 µg mL^?1. However, sprays of 20–100 µg CDEP-1 mL^?1 aqueous solution alone had no significant effect on aphid mortality compared to water spray only. Neither did inclusion of inactivated CDEP-1 at a concentration of 50 µg mL^?1 affect significantly the fungal virulence to aphids. Our results confirm for the first time that the cuticle-degrading protease CDEP-1 enhanced fungal virulence due to acceleration of conidial germination and cuticle penetration. This suggests a new approach to utilising the protease in microbial control.     

Microbial control of Agrilus planipennis (Coleoptera: Buprestidae) with Beauveria bassiana strain GHA: field applications

The effects of Beauveria bassiana strain GHA, applied as BotaniGard ES, on newly colonised and well-established populations of emerald ash borer, Agrilus planipennis (Coleoptera: Buprestidae) were evaluated in the field using foliar and trunk sprays in Michigan in 2004–2005. Results from field trials at a newly colonised white ash site showed a 41% reduction in A. planipennis population in fungal-treated trees compared with that of untreated controls. In addition, fungal infection was also found in 20% of the larval population within 14 days of incubation under laboratory conditions. At a site with a well-established Agrilus planipennis population in green ash trees, larval density was reduced by 47% for trees treated with the fungus compared with that of the controls; 21% of larvae from the current generation were found infected after 14 days of laboratory incubation. Fungal-treated green ash trees also produced fewer adults emerging in the next generation, with a 63% reduction in adult density observed in treated trees compared to that of controls. As a result, fungal-treated trees sustained 42% less crown dieback than did controls. A. planipennis larval density was negatively correlated with trunk height above the ground, and positively correlated with log diameter. Results of laboratory leaf bioassays on A. planipennis adults showed that fungal conidia persisted well under field conditions, with mortality of 78–100% at 7 – days post – exposure for leaves collected between 2 and 264 h after application. Potential strategies for using B. bassiana strain GHA for managing A. planipennis are discussed.     

Glycerol fermentation by (open) mixed cultures: a chemostat study

Glycerol is an important byproduct of bioethanol and biodiesel production processes. This study aims to evaluate its potential application in mixed culture fermentation processes to produce bulk chemicals. Two chemostat reactors were operated in parallel, one fed with glycerol and the other with glucose. Both reactors operated at a pH of 8 and a dilution rate of 0.1 h(-1). Glycerol was mainly converted into ethanol and formate. When operated under substrate limiting conditions, 60% of the substrate carbon was converted into ethanol and formate in a 1:1 ratio. This product spectrum showed sensitivity to the substrate concentration, which partly shifted towards 1,3-propanediol and acetate in a 2:1 ratio at increasing substrate concentrations. Glucose fermentation mainly generated acetate, ethanol and butyrate. At higher substrate concentrations, acetate and ethanol were the dominant products. Co-fermentations of glucose-glycerol were performed with both mixed cultures, previously cultivated on glucose and on glycerol. The product spectrum of the two experiments was very similar: the main products were ethanol and butyrate (38% and 34% of the COD converted, respectively). The product spectrum obtained for glucose and glycerol fermentation could be explained based on the general metabolic pathways found for fermentative microorganisms and on the metabolic constraints: maximization of the ATP production rate and balancing the reducing equivalents involved.