Phenotypic variation in Pseudomonas sp. CM10 determines microcolony formation and survival under protozoan grazing

Protozoan predation as a driver of diversity and virulence in bacterial biofilms

Protozoa are eukaryotic organisms that play a crucial role in nutrient cycling and maintaining balance in the food web. Predation, symbiosis and parasitism are three types of interactions between protozoa and bacteria. However, not all bacterial species are equally susceptible to protozoan predation as many are capable of defending against predation in numerous ways and may even establish either a symbiotic or parasitic life-style. Biofilm formation is one such mechanism by which bacteria can survive predation. Structural and chemical components of biofilms enhance resistance to predation compared to their planktonic counterparts. Predation on biofilms gives rise to phenotypic and genetic heterogeneity in prey that leads to trade-offs in virulence in other eukaryotes. Recent advances, using molecular and genomics techniques, allow us to generate new information about the interactions of protozoa and biofilms of prey bacteria. This review presents the current state of the field on impacts of protozoan predation on biofilms. We provide an overview of newly gathered insights into (i) molecular mechanisms of predation resistance in biofilms, (ii) phenotypic and genetic diversification of prey bacteria, and (iii) evolution of virulence as a consequence of protozoan predation on biofilms.

Pseudomonas ability to utilize different carbon substrates and adaptation influenced by protozoan grazing

Bacteria are major utilizers of dissolved organic matter in aquatic systems. In coastal areas bacteria are supplied with a mixture of food sources, spanning from refractive terrestrial dissolved organic matter to labile marine autochthonous organic matter. Modelling scenarios indicate that in northern coastal areas, the inflow of terrestrial organic matter will increase, and autochthonous production will decrease, thus bacteria will experience a change in the food source composition. How bacteria will cope with such changes is not known. Here, we tested the ability of an isolated bacterium from the northern Baltic Sea coast, Pseudomonas sp., to adapt to varying substrates. We performed a 7-months chemostat experiment, where three different substrates were provided: glucose, representing labile autochthonous organic carbon, sodium benzoate representing refractive organic matter, and acetate - a labile but low energy food source. Growth rate has been pointed out as a key factor for fast adaptation, and since protozoan grazers speed-up the growth rate we added a ciliate to half of the incubations. The results show that the isolated Pseudomonas is adapted to utilize both labile and ring-structured refractive substrates. The growth rate was the highest on the benzoate substrate, and the production increased over time indicating that adaptation did occur. Further, our findings indicate that predation can cause Pseudomonas to change their phenotype to resist and promote survival in various carbon substrates. Genome sequencing reveals different mutations in the genome of adapted populations compared to the native populations, suggesting the adaptation of Pseudomonas sp. To changing environment.

Shifts from cooperative to individual-based predation defense determine microbial predator-prey dynamics

Predation defense is an important feature of predator-prey interactions adding complexity to ecosystem dynamics. Prey organisms have developed various strategies to escape predation which differ in mode (elude vs. attack), reversibility (inducible vs. permanent), and scope (individual vs. cooperative defenses). While the mechanisms and controls of many singular defenses are well understood, important ecological and evolutionary facets impacting long-term predator-prey dynamics remain underexplored. This pertains especially to trade-offs and interactions between alternative defenses occurring in prey populations evolving under predation pressure. Here, we explored the dynamics of a microbial predator-prey system consisting of bacterivorous flagellates (Poteriospumella lacustris) feeding on Pseudomonas putida. Within five weeks of co-cultivation corresponding to about 35 predator generations, we observed a consistent succession of bacterial defenses in all replicates (n = 16). Initially, bacteria expressed a highly effective cooperative defense based on toxic metabolites, which brought predators close to extinction. This initial strategy, however, was consistently superseded by a second mechanism of predation defense emerging via de novo mutations. Combining experiments with mathematical modeling, we demonstrate how this succession of defenses is driven by the maximization of individual rather than population benefits, highlighting the role of rapid evolution in the breakdown of social cooperation.

Functional genomics study of Pseudomonas putida to determine traits associated with avoidance of a myxobacterial predator

Predation contributes to the structure and diversity of microbial communities. Predatory myxobacteria are ubiquitous to a variety of microbial habitats and capably consume a broad diversity of microbial prey. Predator-prey experiments utilizing myxobacteria have provided details into predatory mechanisms and features that facilitate consumption of prey. However, prey resistance to myxobacterial predation remains underexplored, and prey resistances have been observed exclusively from predator-prey experiments that included the model myxobacterium Myxococcus xanthus. Utilizing a predator-prey pairing that instead included the myxobacterium, Cystobacter ferrugineus, with Pseudomonas putida as prey, we observed surviving phenotypes capable of eluding predation. Comparative transcriptomics between P. putida unexposed to C. ferrugineus and the survivor phenotype suggested that increased expression of efflux pumps, genes associated with mucoid conversion, and various membrane features contribute to predator avoidance. Unique features observed from the survivor phenotype when compared to the parent P. putida include small colony variation, efflux-mediated antibiotic resistance, phenazine-1-carboxylic acid production, and increased mucoid conversion. These results demonstrate the utility of myxobacterial predator-prey models and provide insight into prey resistances in response to predatory stress that might contribute to the phenotypic diversity and structure of bacterial communities.

Ecology of Fear: Spines, Armor and Noxious Chemicals Deter Predators in Cancer and in Nature

In nature, many multicellular and unicellular organisms use constitutive defenses such as armor, spines, and noxious chemicals to keep predators at bay. These defenses render the prey difficult and/or dangerous to subdue and handle, which confers a strong deterrent for predators. The distinct benefit of this mode of defense is that prey can defend in place and continue activities such as foraging even under imminent threat of predation. The same qualitative types of armor-like, spine-like, and noxious defenses have evolved independently and repeatedly in nature, and we present evidence that cancer is no exception. Cancer cells exist in environments inundated with predator-like immune cells, so the ability of cancer cells to defend in place while foraging and proliferating would clearly be advantageous. We argue that these defenses repeatedly evolve in cancers and may be among the most advanced and important adaptations of cancers. By drawing parallels between several taxa exhibiting armor-like, spine-like, and noxious defenses, we present an overview of different ways these defenses can appear and emphasize how phenotypes that appear vastly different can nevertheless have the same essential functions. This cross-taxa comparison reveals how cancer phenotypes can be interpreted as anti-predator defenses, which can facilitate therapy approaches which aim to give the predators (the immune system) the upper hand. This cross-taxa comparison is also informative for evolutionary ecology. Cancer provides an opportunity to observe how prey evolve in the context of a unique predatory threat (the immune system) and varied environments.

Coming from the Wild: Multidrug Resistant Opportunistic Pathogens Presenting a Primary, Not Human-Linked, Environmental Habitat

The use and misuse of antibiotics have made antibiotic-resistant bacteria widespread nowadays, constituting one of the most relevant challenges for human health at present. Among these bacteria, opportunistic pathogens with an environmental, non-clinical, primary habitat stand as an increasing matter of concern at hospitals. These organisms usually present low susceptibility to antibiotics currently used for therapy. They are also proficient in acquiring increased resistance levels, a situation that limits the therapeutic options for treating the infections they cause. In this article, we analyse the most predominant opportunistic pathogens with an environmental origin, focusing on the mechanisms of antibiotic resistance they present. Further, we discuss the functions, beyond antibiotic resistance, that these determinants may have in the natural ecosystems that these bacteria usually colonize. Given the capacity of these organisms for colonizing different habitats, from clinical settings to natural environments, and for infecting different hosts, from plants to humans, deciphering their population structure, their mechanisms of resistance and the role that these mechanisms may play in natural ecosystems is of relevance for understanding the dissemination of antibiotic resistance under a One-Health point of view.

Picocyanobacteria aggregation as a response to predation pressure: direct contact is not necessary

Picocyanobacteria (cells <2 µm) can be found either as single-cells (Pcy) or embedded in a mucilaginous sheath as microcolonies or colonies (CPcy). It has been demonstrated that phenotypic plasticity in picocyanobacteria (i.e. the capability of single-cells to aggregate into colonies) can be induced as a response to grazing pressure. The effect of the presence of different predators (cladocerans and rotifers) on the morphological composition of picocyanobacteria was studied in a natural community, and it was observed that the abundance of CPcy significantly increased in all treatments with zooplankton compared with the control without zooplankton. The aggregation capability was also evaluated in a single-cell strain by adding a conditioned medium of flagellates, rotifers and cladocerans. The proportion of cells forming colonies was significantly higher in all treatments with conditioned medium regardless of the predator. These results suggest that the aggregation of Pcy can be induced as a response to the predation pressure exerted by protists and different zooplankters, and also that Pcy has the capability to aggregate into CPcy even without direct contact with any predator, most probably due to the presence of an infochemical dissolved in the water that does not come from disrupted Pcy cells.

Bacterial predator-prey coevolution accelerates genome evolution and selects on virulence-associated prey defences

Generalist bacterial predators are likely to strongly shape many important ecological and evolutionary features of microbial communities, for example by altering the character and pace of molecular evolution, but investigations of such effects are scarce. Here we report how predator-prey interactions alter the evolution of fitness, genomes and phenotypic diversity in coevolving bacterial communities composed of Myxococcus xanthus as predator and Escherichia coli as prey, relative to single-species controls. We show evidence of reciprocal adaptation and demonstrate accelerated genomic evolution specific to coevolving communities, including the rapid appearance of mutator genotypes. Strong parallel evolution unique to the predator-prey communities occurs in both parties, with predators driving adaptation at two prey traits associated with virulence in bacterial pathogens—mucoidy and the outer-membrane protease OmpT. Our results suggest that generalist predatory bacteria are important determinants of how complex microbial communities and their interaction networks evolve in natural habitats.

Predator-prey coevolution is expected to hasten evolutionary rates, but this is difficult to test in long-lived species. Here, the authors report consequences of experimental coevolution between bacterial predators and prey, including accelerated molecular evolution and parallel genomic and phenotypic adaptation.

Feeding and growth of the marine heterotrophic nanoflagellates, Procryptobia sorokini and Paraphysomonas imperforata on a bacterium, Pseudoalteromonas sp. with an inducible defence against grazing

Heterotrophic marine nanoflagellates are important grazers on bacteria in the water column. Some marine bacteria appear more resistant to grazing than do others. Marine nanoflagellates can be grown in the laboratory in batch cultures fed specific bacterial isolates. In some cultures, the flagellates appear unable to completely deplete the bacterial prey even when the bacterial strain otherwise is an excellent prey. This may indicate that some marine bacteria are able to induce defence mechanisms if they are grazed by nanoflagellates. Four morphologically distinct marine heterotrophic nanoflagellates, of which 3 were still identified as Procryptobia sorokini (Kinetoplastea) and one as Paraphysomonas imperforata (Chrysophyceae) were isolated from a coastal location along with 3 isolates of the marine bacterium Pseudoalteromonas sp. Flagellate growth and grazing on bacterial prey were analysed in batch cultures. Pseudoalteromonas was a suitable prey for all 4 flagellate isolates. They grazed and grew on Pseudoalteromonas as sole prey with maximal cell-specific growth rates of 0.1–0.25 h^-1 and gross growth efficiencies of 38–61%. Exposure to dense flagellate cultures or their supernatants did, however, cause a fraction of the Pseudoalteromonas cells to aggregate and the bacterium became apparently resistant to grazing. Concentrations of suspended Pseudoalteromonas cells were therefore not decreased below 1,700–7,500 cells μL^-1 by any of the flagellate isolates. These results indicate that Pseudoalteromonas sp. can be an excellent prey to marine nanoflagellates but also that is in possession of inducible mechanisms that protect against flagellate grazing.

Bacterial pathogens: from natural ecosystems to human hosts

The analysis of the genomes of bacterial pathogens indicates that they have acquired their pathogenic capability by incorporating different genetic elements through horizontal gene transfer. The ancestors of virulent bacteria, as well as the origin of virulence determinants, lay most likely in the environmental microbiota. Studying the role that these determinants may have in non-clinical ecosystems is thus of value for understanding in detail the evolution and the ecology of bacterial pathogens. In this article, I propose that classical virulence determinants might be relevant for basic metabolic processes (for instance iron-uptake systems) or in modulating prey/predator relationships (toxins) in natural, non-infective ecosystems. The different role that horizontal gene transfer and mutation may have in the evolution of bacterial pathogens either for their speciation or in short-sighted evolution processes is also discussed.

Minimal increase in genetic diversity enhances predation resistance

The importance of species diversity to emergent, ecological properties of communities is increasingly appreciated, but the importance of within-species genetic diversity for analogous emergent properties of populations is only just becoming apparent. Here, the properties and effects of genetic variation on predation resistance in populations were assessed and the molecular mechanism underlying these emergent effects was investigated. Using biofilms of the ubiquitous bacterium Serratia marcescens, we tested the importance of genetic diversity in defending biofilms against protozoan grazing, a main source of mortality for bacteria in all natural ecosystems. S. marcescens biofilms established from wild-type cells produce heritable, stable variants, which when experimentally combined, persist as a diverse assemblage and are significantly more resistant to grazing than either wild type or variant biofilms grown in monoculture. This diversity effect is biofilm-specific, a result of either facilitation or resource partitioning among variants, with equivalent experiments using planktonic cultures and grazers resulting in dominance by a single resistant strain. The variants studied are all the result of single nucleotide polymorphisms in one regulatory gene suggesting that the benefits of genetic diversity in clonal biofilms can occur through remarkably minimal genetic change. The findings presented here provide a new insight on the integration of genetics and population ecology, in which diversity arising through minimal changes in genotype can have major ecological implications for natural populations.

Predation impact of ciliated and flagellated protozoa during a summer bloom of brown sulfur bacteria in a meromictic coastal lake

Anaerobic phagotrophic protozoa may play an important role in the carbon flux of chemically stratified environments, especially when phototrophic sulfur bacteria account for a high proportion of the primary production. To test this assumption, we investigated the vertical and temporal distribution of microbial heterotrophs and of autotrophic picoplankton throughout the water column of the meromictic coastal lake Faro (Sicily, Italy), in the summer of 2004, coinciding with a bloom of brown-colored green sulfur bacteria. We also assessed the grazing impact of ciliated and flagellated protozoa within the sulfur bacteria plate using a modification of the fluorescently labeled bacteria uptake approach, attempting to minimize the biases intrinsic to the technique and to preserve the in situ anoxic conditions. Significant correlations were observed between ciliate biomass and bacteriochlorophyll e concentration, and between heterotrophic nanoflagellate biomass and chlorophyll a concentration in the water column. The major predators of anaerobic picoplankton were pleuronematine ciliates and cryptomonad flagellates, with clearances of 26.6 and 9.5 nL per cell h(-1), respectively, and a cumulative impact on the picoplankton gross growth rate ranging between 36% and 72%. We concluded that protozoan grazing channels a large proportion of anaerobic picoplankton production to higher trophic levels without restraining photosynthetic bacteria productivity.

Growth of Acanthamoeba castellanii and Hartmannella vermiformis on live, heat-killed and DTAF-stained bacterial prey

The growth responses of two species of amoeba were evaluated in the presence of live, heat-killed and heat-killed/5-(4,6-dichlorotriazin-2-yl) aminofluorescein (DTAF)-stained cells of Escherichia coli, Pseudomonas aeruginosa, Klebsiella aerogenes, Klebsiella ozaenae and Staphylococcus aureus. The specific growth rates of both species were significantly higher with live bacterial prey, the only exception being Hartmannella vermiformis feeding on S. aureus, for which growth rates were equivalent on all prey states. There was no significant difference between growth rates, yield or ingestion rates of amoebae feeding on heat-killed or heat-killed/stained bacterial cells, suggesting that it was the heat-killing process that influenced the amoeba-bacteria interaction. Pretreatment of prey cells had a greater influence on amoebic processing of Gram-negative bacteria compared with the Gram-positive bacterium, which appeared to be as a result of the former cells being more difficult to digest and/or losing their ability to deter amoebic ingestion. These antipredatory mechanisms included microcolony formation in P. aeruginosa, toxin production in K. ozaenae, and the presence of an intact capsule in K. aerogenes. E. coli and S. aureus did not appear to possess an antipredator mechanism, although intact cells of the S. aureus were observed in faecal pellets, suggesting that any antipredatory mechanism was occurring at the digestion stage.

Effects of nutrient availability and Ochromonas sp. predation on size and composition of a simplified aquatic bacterial community

Predation and competition are two main factors that determine the size and composition of aquatic bacterial populations. Using a simplified bacterial community, composed of three strains characterized by different responses to predation, a short-term laboratory experiment was performed to evaluate adaptations and relative success in communities with experimentally controlled levels of predation and nutrient availability. A strain with a short generation time (Pseudomonas putida), one with high plasticity in cell morphology (Flectobacillus sp. GC5), and one that develops microcolonies (Pseudomonas sp. CM10), were selected. The voracious flagellate Ochromonas sp. was chosen as a predator. To describe adaptations against grazing and starvation, abundance, biomass and relative heterogeneity of bacteria were measured. On the whole, the strains in the predation-free cultures exhibited unicellular growth, and P. putida represented the largest group. The presence of Ochromonas strongly reduced bacterial abundance, but not always the total biomass. The activity of grazers changed the morphological composition of the bacterial communities. Under grazing pressure the relative composition of the community depended on the substrate availability. In the presence of predators, P. putida abundance declined in both high and low nutrient treatments, and Pseudomonas CM10 developed colonies. Flectobacillus was only numerically codominant in the nutrient-rich environments.

Prey food quality affects flagellate ingestion rates

Flagellate feeding efficiency appears to depend on morphological characteristics of prey such as cell size and motility, as well as on other characteristics such as digestibility and cell surface characteristics. Bacteria of varying morphological characteristics (cell size) and mineral nutrient characteristics or food quality (as determined by the C:N:P ratio) were obtained by growing Pseudomonas fluorescens in chemostats at four dilution rates (0.03, 0.06, 0.10, and 0.13 h-1) and three temperatures (14 degrees C, 20 degrees C, and 28 degrees C). Cells of a given food quality were heat-killed and used to grow the flagellate Ochromonas danica. Ingestion and digestion rates were determined by using fluorescently labeled bacteria of the same food quality as the bacteria supporting growth. Ingestion rates were affected by both food quality and cell size. Cells of high food quality (low carbon:element ratio) were ingested at higher rates than cells of low food quality. Multiple regression analysis indicated that cell size also influenced ingestion rate but to a much lesser extent than did food quality. Digestion rates were not correlated with either food quality or cell size. Results suggest that flagellates may adjust feeding efficiency based on the quality of food items available.

Microbial exopolymers link predator and prey in a model yeast biofilm system

Protistan grazing on biofilms is potentially an important conduit enabling energy flow between microbial trophic levels. Contrary to the widely held assumption that protistan feeding primarily involves ingestion of biofilm cells, with negative consequences for the biofilm, this study demonstrated preferential grazing on the noncellular biofilm matrix by a ciliate, with selective ingestion of yeast and bacterial cells of planktonic origin over attached and biofilm-derived planktonic cells. Introducing a ciliate to two biofilm-forming Cryptococcus species, as well as two bacterial species in a model biofilm system, fluorescent probes were applied to determine ingestion of cellular and noncellular biofilm fractions. Fluoromicroscopy, as well as photometric quantification, confirmed that protistan grazing enhanced yeast biofilm metabolism, and an increase in biofilm biomass and viability. We propose that the extracellular polymeric matrix of biofilms may act as an interface regulating interaction between predator and prey, while serving as source of nutrients and energy for protists.

The role of quorum sensing mediated developmental traits in the resistance of Serratia marcescens biofilms against protozoan grazing

Resistance against protozoan grazers is a crucial factor that is important for the survival of many bacteria in their natural environment. However, the basis of resistance to protozoans and how resistance factors are regulated is poorly understood. In part, resistance may be due to biofilm formation, which is known to protect bacteria from environmental stress conditions. The ubiquitous organism Serratia marcescens uses quorum sensing (QS) control to regulate virulence factor expression and biofilm formation. We hypothesized that the QS system of S. marcescens also regulates mechanisms that protect biofilms against protozoan grazing. To investigate this hypothesis, we compared the interactions of wild-type and QS mutant strains of S. marcescens biofilms with two protozoans having different feeding types under batch and flow conditions. Under batch conditions, S. marcescens forms microcolony biofilms, and filamentous biofilms are formed under flow conditions. The microcolony-type biofilms were protected from grazing by the suspension feeder, flagellate Bodo saltans, but were not protected from the surface feeder, Acanthamoeba polyphaga. In contrast, the filamentous biofilm provided protection against A. polyphaga. The main findings presented in this study suggest that (i) the QS system is not involved in grazing resistance of S. marcescens microcolony-type biofilms; (ii) QS in S. marcescens regulates antiprotozoan factor(s) that do not interfere with the grazing efficiency of the protozoans; and (iii) QS-controlled, biofilm-specific differentiation of filaments and cell chains in biofilms of S. marcescens provides an efficient mechanism against protozoan grazing.

Direct and indirect effects of protist predation on population size structure of a bacterial strain with high phenotypic plasticity

We studied the impact of grazing and substrate supply on the size structure of a freshwater bacterial strain (Flectobacillus sp.) which showed pronounced morphological plasticity. The cell length varied from 2 to >40 microm and encompassed rods, curved cells, and long filaments. Without grazers and with a sufficient substrate supply, bacteria grew mainly in the form of medium-sized rods (4 to 7 microm), with a smaller proportion (<10%) of filamentous forms. Grazing experiments with the bacterivorous flagellate Ochromonas sp. showed that freely suspended cells of <7 microm were highly vulnerable to grazers, whereas filamentous cells were resistant to grazing and became enriched during predation. A comparison of long-term growth in carbon-limited chemostats with and without grazers revealed that strikingly different bacterial populations developed: treatments with flagellates were composed of >80% filamentous cells. These attained a biomass comparable to that of populations in chemostats without grazers, which were composed of medium-sized rods and c-shaped cells. Carbon starvation resulted in a fast decrease in cell length and a shift towards small rods, which were highly vulnerable to grazing. Dialysis bag experiments in combination with continuous cultivation revealed that filament formation was significantly enhanced even without direct contact of bacteria with bacterivores and was thus probably stimulated by grazer excretory products.

Biofilm formation and phenotypic variation enhance predation-driven persistence of Vibrio cholerae

Persistence of the opportunistic bacterial pathogen Vibrio cholerae in aquatic environments is the principal cause for seasonal occurrence of cholera epidemics. This causality has been explained by postulating that V. cholerae forms biofilms in association with animate and inanimate surfaces. Alternatively, it has been proposed that bacterial pathogens are an integral part of the natural microbial food web and thus their survival is constrained by protozoan predation. Here, we report that both explanations are interrelated. Our data show that biofilms are the protective agent enabling V. cholerae to survive protozoan grazing while their planktonic counterparts are eliminated. Grazing on planktonic V. cholerae was found to select for the biofilm-enhancing rugose phase variant, which is adapted to the surface-associated niche by the production of exopolymers. Interestingly, grazing resistance in V. cholerae biofilms was not attained by exopolymer production alone but was accomplished by the secretion of an antiprotozoal factor that inhibits protozoan feeding activity. We identified that the cell density-dependent regulator hapR controls the production of this factor in biofilms. The inhibitory effect of V. cholerae biofilms was found to be widespread among toxigenic and nontoxigenic isolates. Our results provide a mechanistic explanation for the adaptive advantage of surface-associated growth in the environmental persistence of V. cholerae and suggest an important contribution of protozoan predation in the selective enrichment of biofilm-forming strains in the out-of-host environment.

Off the hook--how bacteria survive protozoan grazing

Bacterial growth and survival in numerous environments are constrained by the action of bacteria-consuming protozoa. Recent findings suggest that bacterial adaptations against protozoan predation might have a significant role in bacterial persistence and diversification. We argue that selective predation has given rise to diverse routes of bacterial defense, including adaptive mechanisms in bacterial biofilms, and has promoted major transitions in bacterial evolution, such as multicellularity and pathogenesis. We propose that studying predation-driven adaptations will provide an exciting frontier for microbial ecology and evolution at the interface of prokaryotes and eukaryotes.

High motility reduces grazing mortality of planktonic bacteria

We tested the impact of bacterial swimming speed on the survival of planktonic bacteria in the presence of protozoan grazers. Grazing experiments with three common bacterivorous nanoflagellates revealed low clearance rates for highly motile bacteria. High-resolution video microscopy demonstrated that the number of predator-prey contacts increased with bacterial swimming speed, but ingestion rates dropped at speeds of >25 microm s(-1) as a result of handling problems with highly motile cells. Comparative studies of a moderately motile strain (<25 microm s(-1)) and a highly motile strain (>45 microm s(-1)) further revealed changes in the bacterial swimming speed distribution due to speed-selective flagellate grazing. Better long-term survival of the highly motile strain was indicated by fourfold-higher bacterial numbers in the presence of grazing compared to the moderately motile strain. Putative constraints of maintaining high swimming speeds were tested at high growth rates and under starvation with the following results: (i) for two out of three strains increased growth rate resulted in larger and slower bacterial cells, and (ii) starved cells became smaller but maintained their swimming speeds. Combined data sets for bacterial swimming speed and cell size revealed highest grazing losses for moderately motile bacteria with a cell size between 0.2 and 0.4 microm(3). Grazing mortality was lowest for cells of >0.5 microm(3) and small, highly motile bacteria. Survival efficiencies of >95% for the ultramicrobacterial isolate CP-1 (< or =0.1 microm(3), >50 microm s(-1)) illustrated the combined protective action of small cell size and high motility. Our findings suggest that motility has an important adaptive function in the survival of planktonic bacteria during protozoan grazing.

Structure-based mutational analysis of the 4'-phosphopantetheinyl transferases Sfp from Bacillus subtilis: carrier protein recognition and reaction mechanism

The activation of apo-peptidyl carrier proteins (PCPs) of nonribosomal peptide synthetases (NRPSs), apo-acyl carrier proteins (ACPs) of polyketide synthases (PKSs), and fatty acid synthases (FASs) to their active holo form is accomplished with dedicated 4'-phosphopantetheinyl transferases (PPTases). They catalyze the transfer of the essential prosthetic group 4'-phosphopantetheine (4'-Ppant) from coenzyme A (CoA) to a highly conserved serine residue in all PCPs and ACPs. PPTases, based on sequence and substrate specifity, have been classified into three types: bacterial holo-acyl carrier protein synthase (AcpS), fatty acid synthase of eukaryotes (FAS2) and Sfp, a PPTase of secondary metabolism. The recently solved crystal structures of AcpS and Sfp-type PPTases with CoA revealed a common alpha + beta-fold with a beta(1)alpha(3)beta(2) motif and similarities in CoA binding and polymerization mode. However, it was not possible to discern neither the PCP binding region of Sfp nor the priming reaction mechanism from the Sfp-CoA cocrystal. In this work, we provide a model for the reaction mechanism based on mutational analysis of Sfp that suggests a reaction mechanism in which the highly conserved E151 deprotonates the hydroxyl group of the invariant serine of PCP. That, in turn, acts as a nucleophile to attack the beta-phosphate of CoA. The Sfp mutants K112, E117, and K120 further revealed that the loop region between beta4 and alpha5 (residues T111-S124) in Sfp is the PCP binding region. Also, residues T44, K75, S89, H90, D107, E109, E151, and K155 that have been shown in the Sfp-CoA cocrystal structure to coordinate CoA are now all confirmed by mutational and biochemical analysis.