Microbial Ecology

Previously published experimental work by other authors has shown that certain motile marine bacteria are able to track free-swimming algae by executing a zigzag path and steering toward the algae at each turn. Here, we propose that the apparent steering behaviour could be a hydrodynamic effect, whereby an algal cell’s vorticity and strain-rate fields rotate a pursuing bacterial cell in the appropriate direction. Using simplified models for the bacterial and algal cells, we numerically compute the trajectory of a bacterial cell and demonstrate the plausibility of this hypothesis.

The plant phyllosphere is intensely colonized by a complex and highly diverse microbial population and shows pronounced plant-species-specific differences. The mechanisms and influencing factors determining whether and in which density microorganisms colonize plant phyllosphere tissues are not yet fully understood. One of the key influencing factors is thought to be phytochemical concentration and composition. Therefore, correlations between various concentrations of individual glucosinolates and carotenoids in four different plant species—Brassica juncea, Brassica campestris, Cichorium endivia, and Spinacea oleracea—and the phyllospheric bacterial population size associated with the aerial parts of the same plants were analyzed. The concentration of various individual glucosinolates and carotenoids were measured using high-performance liquid chromatography. The phyllospheric bacterial population size including both nonculturable and culturable organisms was assessed using quantitative real-time polymerase chain reaction, and the physiological profile of the culturable microbial community was analyzed using the Biolog system. Results show significant differences between plant species in both concentration and composition of secondary metabolites, bacterial population size, and microbial community composition in three consecutively performed experiments. An interesting and underlying trend was that bacterial density was positively correlated to concentrations of β-carotene in the plant phyllosphere of the four plant species examined. Likewise, the alkenyl glucosinolates, 2-propenyl, 3-butenyl, and 4-pentenyl, concentrations were positively correlated to the bacterial population density, whereas the aromatic glucosinolate 2-phenylethyl showed a negative correlation to the phyllospheric bacterial population size. Thus, we report for the first time the relationship between individual glucosinolate and carotenoid concentrations and the phyllospheric bacterial population size of nonculturable and culturable organisms and the phyllospheric microbial physiological profiles.

The fate of immigrant bacterial cells on leaves under stressful conditions was determined as a function of the anatomical features and the local spatial density of resident cells at their landing site. Pantoea agglomerans 299R was established on bean leaves and the survival of immigrant cells of Pseudomonas fluorescens A506 and Pseudomonas syringae B728a, as well as P. agglomerans itself, was determined by epifluorescence microscopy following subsequent exposure of plants to desiccation stress. Resident and immigrant bacterial strains constitutively expressed the cyan and the green fluorescent protein, respectively, and the viability of individual cells was assessed directly on leaf surfaces following propidium iodide staining. Although only a small fraction of the immigrant cells landed on established bacterial aggregates, their fate was usually strongly influenced by the presence of indigenous bacteria at the site at which they landed. Immigrants of P. agglomerans 299R or P. fluorescens A506 that arrived as solitary cells had about double the probability of survival when landing on aggregates formed by P. agglomerans 299R than when landing on uncolonized areas of the leaf surface. In contrast, the survival of P. syringae B728a was similar irrespective of whether it landed on colonized or uncolonized parts of a leaf. The nature of plant anatomical features at which immigrant bacteria landed also strongly influenced the fate of immigrant bacteria. The fraction of immigrant cells of each species tested that landed on veins, glandular trichomes, or epidermal cells altered by P. agglomerans that died was always less than when they landed on normal epidermal cells or at the base of hooked trichomes. Depending on the process by which immigrants arrive at a leaf, only a small fraction of cells may be deposited on existing bacterial aggregates. Although uncolonized sites differed greatly in their ability to influence the survival of immigrant cells, the fate of an immigrant bacterium will depend on the nature of the leaf structure on which it is deposited, and apparently indirectly on the amount of nutrients and water available at that site to support the development of bacterial aggregates.

Several media and techniques were compared for their efficiency to enumerate viable heterotrophs from both a karst and sand aquifer spring. A medium designed to enumerate bacteria from nutrient-poor waters (HCFU) as well as R2A medium proved superior to tryptic soy agar; however, the difference was always less than one order of magnitude. Membrane filtration resulted in lower counts of microbes than the spread plate, multitube turbidity, or drop plate methods from samples of both sand and karst springs. The drop plate technique yielded higher viable counts from the sand spring and basin of the karst spring, with a precision of 21% (coefficient of variation) and a maximum plating efficiency of 3.4% (viable count/direct count × 100). Subsequently, 63% of isolates from drop plates were recovered on HCFU. Microcolonies were visible by epifluorescence microscopy, acridine orange staining, and subsequent examination of excised agar sections containing drops.

Ecosystem-level consequences of biodiversity loss of macroorganisms are well understood, while the repercussions of species extirpation in microbial systems are not. We manipulated species richness and phylogenetic relatedness of saprotrophic fungi in situ in a boreal forest to address this issue. Litter decomposition rates (as total mass loss) after 2 months were significantly higher in the least phylogenetically related fungal assemblages. Likewise, cellulose loss was also highest in the most distantly related treatments after 1 year. There were marginal effects of species richness on mass loss that only affected decomposition after 2 months. At the end of 1 year of decomposition, most fungal communities had collapsed from their original diversity to two species, mainly in the Penicillium or Hypocrea clades. Two concurrent processes may explain these results: competition between closely related fungal taxa and phylogenetic conservation in cellulose decomposition. Our results suggest that phylogenetic relatedness of fungal communities may be a more appropriate metric than species richness or community composition to predict functional responses of fungal communities to global change.

Studies on plant viruses are biased towards crop diseases and little is known about viruses in natural vegetation. We conducted extensive surveys of plant viruses in wild Brassicaceae plants occurring in three local plant communities in central Japan. We applied RNA-Seq with selective depletion of rRNA, which allowed us to detect infections of all genome-reported viruses simultaneously. Infections of Turnip mosaic virus (TuMV), Cucumber mosaic virus (CMV), Brassica yellows virus, Pelargonium zonate spot virus, and Arabidopsis halleri partitivirus 1 were detected from the two perennial species, Arabidopsis halleri subsp. gemmifera and Rorippa indica. De novo assembly further detected partial sequences of a putative novel virus in Arabis fragellosa. Virus species composition and infection rate differed depending on site and plant species. Viruses were most frequently detected from the perennial clonal plant, A. halleri, in which a high clonal transmission rate of viruses across multiple years was confirmed. Phylogenetic analysis of TuMV and CMV showed that virus strains from wild Brassicaceae were included as a major clade of these viruses with other reported strains from crop plants, suggesting that viruses were shared among wild plants and crops. Our studies indicated that distribution of viruses in natural plant populations are determined by the combinations of life histories of viruses and hosts. Revealing viral distribution in the natural plant communities improves our knowledge on the ecology of plant viruses.

Attachment strength and exopolysaccharide (EPS) production of Pseudomonas sp. (bacteria) and the diatom Amphora coffaeformis were studied on six different substrata with surface tensions between 19 and 64.5 mN m−1. Test panels of the materials were exposed to bacterial cultures between 3 and 120 hours, and to diatom cultures between 48 and 72 hours. Exopolysaccharide production by surface-associated cells was measured using the phenol sulfuric acid method. Attachment studies were run by exposing test panels to laminar flow pressure using a radial flow chamber. Highest EPS production by bacteria and diatoms was recorded on substrata with surface tensions above 30 mN m−1. Lowest EPS production occurred on substrata between 20 and 25 mN m−1. Highest EPS production and strongest adhesion was found on polycarbonate (33.5 mN m−1). Both test organisms improved their attachment strength with exposure time on most materials. However, amounts of produced EPS and improvement of attachment indicated that mechanisms other than polysaccharide production are more important on substrata with low surface tensions (<25 mN m−1). Simply producing more polysaccharides is not sufficient to overcome weak attachment on materials with low surface tensions. For example, adhesion of Pseudomonas sp. and A. coffaeformis on polytetrafluorethylene/perfluor-copolymer (PFA; 22 mN m−1). and glass (64.5 mN m−1. was equally strong although EPS production was much higher on glass than on PFA. This is somewhat surprising for A. coffaeformis because polysaccharide production has been considered the most important attachment mechanism of A. coffaeformis.