Busting biofilms: free-living amoebae disrupt preformed methicillin-resistant Staphylococcus aureus (MRSA) and Mycobacterium bovis biofilms.

Biofilm-associated infections are difficult to eradicate because of their ability to tolerate antibiotics and evade host immune responses. Amoebae and/or their secreted products may provide alternative strategies to inhibit and disperse biofilms on biotic and abiotic surfaces. We evaluated the potential of five predatory amoebae - Acanthamoeba castellanii, Acanthamoeba lenticulata, Acanthamoeba polyphaga, Vermamoeba vermiformis and Dictyostelium discoideum - and their cell-free secretions to disrupt biofilms formed by methicillin-resistant Staphylococcus aureus (MRSA) and Mycobacterium bovis. The biofilm biomass produced by MRSA and M. bovis was significantly reduced when co-incubated with A. castellanii, A. lenticulata and A. polyphaga, and their corresponding cell-free supernatants (CFS). Acanthamoeba spp. generally produced CFS that mediated biofilm dispersal rather than directly killing the bacteria; however, A. polyphaga CFS demonstrated active killing of MRSA planktonic cells when the bacteria were present at low concentrations. The active component(s) of the A. polyphaga CFS is resistant to freezing, but can be inactivated to differing degrees by mechanical disruption and exposure to heat. D. discoideum and its CFS also reduced preformed M. bovis biofilms, whereas V. vermiformis only decreased M. bovis biofilm biomass when amoebae were added. These results highlight the potential of using select amoebae species or their CFS to disrupt preformed bacterial biofilms.

Amoeboid swimming in a compliant channel.

Several prokaryotes and eukaryotic cells swim in the presence of deformable and rigid surfaces that form confinement. The most commonly observed examples from biological systems are motility of leukocytes and pathogens present within the blood suspension through a microvascular network, and locomotion of eukaryotic cells such as immune system cells and cancerous cells through interstices between soft interstitial cells and the extracellular matrix within the interstitial tissue. This motivated us to investigate numerically the flow dynamics of amoeboid swimming in a flexible channel. The effects of wall stiffness and channel confinement on the flow dynamics and swimmer motion are studied. The swimmer motion through the flexible channel is substantially decelerated compared to the rigid channel. The strong confinement in the amply flexible channel imprisons the swimmer by severely restricting its forward motion. The swimmer velocity in a stiff channel displays nonmonotonic variation with the confinement while it shows monotonic reduction in a highly flexible channel. The physical rationale behind such distinct velocity behaviour in flexible and rigid channels is illustrated using an instantaneous flow field and flow history displayed by the swimmer. This behavior follows from a subtle interplay between the shape changes exhibited by the swimmer and the wall compliance. This study may aid in understanding the influence of elasticity of the surrounding environment on cell motility in immunological surveillance and invasiveness of cancer cells.

Eukaryotic organisms of continental hydrothermal systems.

Continental hydrothermal systems are a dynamic component of global thermal and geochemical cycles, exerting a pronounced impact on water chemistry and heat storage. As such, these environments are commonly classified by temperature, thermal fluid ionic concentration, and pH. Terrestrial hydrothermal systems are a refuge for extremophilic organisms, as extremes in temperature, metal concentration, and pH profoundly impact microorganism assemblage composition. While numerous studies focus on Bacteria and Archaea in these environments, few focus on Eukarya-likely due to lower temperature tolerances and because they are not model organisms for understanding the evolution of early life. However, where present, eukaryotic organisms are significant members of continental hydrothermal microorganism communities. Thus, this manuscript focuses on the eukaryotic occupants of terrestrial hydrothermal systems and provides a review of the current status of research, including microbe-eukaryote interactions and suggestions for future directions.

Unraveling past impacts of climate change and land management on historic peatland development using proxy-based reconstruction, monitoring data and process modeling.

Peatlands represent globally significant soil carbon stores that have been accumulating for millennia under water-logged conditions. However, deepening water-table depths (WTD) from climate change or human-induced drainage could stimulate decomposition resulting in peatlands turning from carbon sinks to carbon sources. Contemporary WTD ranges of testate amoebae (TA) are commonly used to predict past WTD in peatlands using quantitative transfer function models. Here we present, for the first time, a study comparing TA-based WTD reconstructions to instrumentally monitored WTD and hydrological model predictions using the MILLENNIA peatland model to examine past peatland responses to climate change and land management. Although there was very good agreement between monitored and modeled WTD, TA-reconstructed water table was consistently deeper. Predictions from a larger European TA transfer function data set were wetter, but the overall directional fit to observed WTD was better for a TA transfer function based on data from northern England. We applied a regression-based offset correction to the reconstructed WTD for the validation period (1931-2010). We then predicted WTD using available climate records as MILLENNIA model input and compared the offset-corrected TA reconstruction to MILLENNIA WTD predictions over an extended period (1750-1931) with available climate reconstructions. Although the comparison revealed striking similarities in predicted overall WTD patterns, particularly for a recent drier period (1965-1995), there were clear periods when TA-based WTD predictions underestimated (i.e. drier during 1830-1930) and overestimated (i.e. wetter during 1760-1830) past WTD compared to MILLENNIA model predictions. Importantly, simulated grouse moor management scenarios may explain the drier TA WTD predictions, resulting in considerable model predicted carbon losses and reduced methane emissions, mainly due to drainage. This study demonstrates the value of a site-specific and combined data-model validation step toward using TA-derived moisture conditions to understand past climate-driven peatland development and carbon budgets alongside modeling likely management impacts.

Diversity and distribution of freshwater testate amoebae (protozoa) along latitudinal and trophic gradients in China.

Freshwater microbial diversity is subject to multiple stressors in the Anthropocene epoch. However, the effects of climate changes and human activities on freshwater protozoa remain poorly understood. In this study, the diversity and distribution of testate amoebae from the surface sediments were investigated in 51 Chinese lakes and reservoirs along two gradients, latitude and trophic status. A total of 169 taxa belonging to 24 genera were identified, and the most diverse and dominant genera were Difflugia (78 taxa), Centropyxis (26 taxa) and Arcella (12 taxa). Our analysis revealed that biomass of testate amoebae decreased significantly along the latitudinal gradient, while Shannon-Wiener indices and species richness presented an opposite trend (P < 0.05). The relationship of diversity and latitude is, we suspect, an artifact of the altitudinal distribution of our sites. Furthermore, biomass-based Shannon-Wiener index and species richness of testate amoebae were significantly unimodally related to trophic status (P < 0.05). This is the first large-scale study showing the effects of latitude and trophic status on diversity and distribution of testate amoebae in China. Therefore, our results provide valuable baseline data on testate amoebae and contribute to lake management and our understanding of the large-scale global patterns in microorganism diversity.

Water-related parasitic diseases in China.

Water-related parasitic diseases are directly dependent on water bodies for their spread or as a habitat for indispensable intermediate or final hosts. Along with socioeconomic development and improvement of sanitation, overall prevalence is declining in the China. However, the heterogeneity in economic development and the inequity of access to public services result in considerable burden due to parasitic diseases in certain areas and populations across the country. In this review, we demonstrated three aspects of ten major water-related parasitic diseases, i.e., the biology and pathogenicity, epidemiology and recent advances in research in China. General measures for diseases control and special control strategies are summarized.

'Run-and-tumble' or 'look-and-run'? A mechanical model to explore the behavior of a migrating amoeboid cell.

Single cell migration constitutes a fundamental phenomenon involved in many biological events. Amoeboid cells are single cell organisms that migrate in a cyclic manner like worms. In this paper, we propose a 3D finite element model of an amoeboid cell migrating over a 2D surface. In particular, we focus on the mechanical aspect of the problem. The cell is able to generate cyclic active deformations, such as protrusion and contraction, in any direction. The progression of the cell is governed by a tight synchronization between the adhesion forces, which are alternatively applied at the front and at the rear edges of the cell, and the protrusion-contraction phases of the cell body. Finally, two important aspects have been taken into account: (1) the external stimuli in response to which the cell migrates (e.g. need to feed, morphogenetic events, normal or abnormal environment cues), (2) the heterogeneity of the 2D substrate (e.g. obstacles, rugosity, slippy regions) for which two distinct approaches have been evaluated: the 'run-and-tumble' strategy and the 'look-and-run' strategy. Overall, the results show a good agreement with respect to the experimental observations and the data from the literature (e.g. velocity and strains). Therefore, the present model helps, on one hand, to better understand the intimate relationship between the deformation modes of a cell and the adhesion strength that is required by the cell to crawl over a substrate, and, on the other hand, to put in evidence the crucial role played by mechanics during the migration process.

Evolution and diversity of dictyostelid social amoebae.

Dictyostelid social amoebae are a large and ancient group of soil microbes with an unusual multicellular stage in their life cycle. Taxonomically, they belong to the eukaryotic supergroup Amoebozoa, the sister group to Opisthokonta (animals + fungi). Roughly half of the ~150 known dictyostelid species were discovered during the last five years and probably many more remain to be found. The traditional classification system of Dictyostelia was completely overturned by cladistic analyses and molecular phylogenies of the past six years. As a result, it now appears that, instead of three major divisions there are eight, none of which correspond to traditional higher-level taxa. In addition to the widely studied Dictyostelium discoideum, there are now efforts to develop model organisms and complete genome sequences for each major group. Thus Dictyostelia is becoming an excellent model for both practical, medically related research and for studying basic principles in cell-cell communication and developmental evolution. In this review we summarize the latest information about their life cycle, taxonomy, evolutionary history, genome projects and practical importance.

Sampling gene diversity across the supergroup Amoebozoa: large EST data sets from Acanthamoeba castellanii, Hartmannella vermiformis, Physarum polycephalum, Hyperamoeba dachnaya and Hyperamoeba sp.

From comparative analysis of EST data for five taxa within the eukaryotic supergroup Amoebozoa, including two free-living amoebae (Acanthamoeba castellanii, Hartmannella vermiformis) and three slime molds (Physarum polycephalum, Hyperamoeba dachnaya and Hyperamoeba sp.), we obtained new broad-range perspectives on the evolution and biosynthetic capacity of this assemblage. Together with genome sequences for the amoebozoans Dictyostelium discoideum and Entamoeba histolytica, and including partial genome sequence available for A. castellanii, we used the EST data to identify genes that appear to be exclusive to the supergroup, and to specific clades therein. Many of these genes are likely involved in cell-cell communication or differentiation. In examining on a broad scale a number of characters that previously have been considered in simpler cross-species comparisons, typically between Dictyostelium and Entamoeba, we find that Amoebozoa as a whole exhibits striking variation in the number and distribution of biosynthetic pathways, for example, ones for certain critical stress-response molecules, including trehalose and mannitol. Finally, we report additional compelling cases of lateral gene transfer within Amoebozoa, further emphasizing that although this process has influenced genome evolution in all examined amoebozoan taxa, it has done so to a variable extent.

Transcriptome analyses of amoebic gill disease-affected Atlantic salmon (Salmo salar) tissues reveal localized host gene suppression.

The transcriptome response of Atlantic salmon (Salmo salar) displaying advanced stages of amoebic gill disease (AGD) was investigated. Naïve smolt were challenged with AGD for 19 days, at which time all fish were euthanized and their severity of infection quantified through histopathological scoring. Gene expression profiles were compared between heavily infected and naïve individuals using a 17 K Atlantic salmon cDNA microarray with real-time quantitative RT-PCR (qPCR) verification. Expression profiles were examined in the gill, anterior kidney, and liver. Twenty-seven transcripts were significantly differentially expressed within the gill; 20 of these transcripts were down-regulated in the AGD-affected individuals compared with naïve individuals. In contrast, only nine transcripts were significantly differentially expressed within the anterior kidney and five within the liver. Again the majority of these transcripts were down-regulated within the diseased individuals. A down-regulation of transcripts involved in apoptosis (procathepsin L, cathepsin H precursor, and cystatin B) was observed in AGD-affected Atlantic salmon. Four transcripts encoding genes with antioxidant properties also were down-regulated in AGD-affected gill tissue according to qPCR analysis. The most up-regulated transcript within the gill was an unknown expressed sequence tag (EST) whose expression was 218-fold (+/- SE 66) higher within the AGD affected gill tissue. Our results suggest that Atlantic salmon experiencing advanced stages of AGD demonstrate general down-regulation of gene expression, which is most pronounced within the gill. We propose that this general gene suppression is parasite-mediated, thus allowing the parasite to withstand or ameliorate the host response.

[Structure of a community of testate amoebae in a sphagnum dominated bog in upper sura flow (middle Volga territory)].

Fifty nine species of testate amoebae were found in a sphagnum moss bog located in the upper Sura flow (Volga highland). The active diversity in communities of sphagnum moss biotopes was formed by 24 species. Minimal species diversity (3 species) and maximum density of organisms were noted in the driest habitat. In the habitats with the medium humidity levels, the level of species richness was similar (13-16 species) and the total density was determined by redox characteristics of the environment: under the conditions of oxygen deficit, it was two to three times lower than in an oxidized environment. The species composition specificity in sphagnum moss biotopes was determined by the degree of humidity: in the driest habitats, Arcella arenaria predominated; in the biotopes with medium humidity, Nebella tenella and Hyalosphenia elegans; and in the most humid biotopes, Hyalosphenia papilio and Heleopera sphagni. Communities of testate amoebae differed by species composition and integral characteristics at different sphagnum moss horizons: the abundance and species richness increased with depth. The proportion of living individuals in the total number of tests was 35 to 75%.

Multiple symbiotes in larval black flies (Diptera: Simuliidae): associations of trichomycete fungi with ichthyosporeans, mermithid nematodes, and microsporidia.

Studies of the interactions between two or more species of symbiotic microorganisms in a single host animal have lagged behind those involving interactions between hymenopteran or dipteran parasitoids. We screened the larvae of four species of black flies (Cnephia ornithophilia, Simulium furculatum, Simulium innoxium, and Simulium vandalicum) to determine if the colonization and prevalence of trichomycete fungi were influenced by ichthyosporeans, mermithid nematodes, microsporidia, or other species of trichomycetes. Differences in the layering of the peritrophic matrix of microsporidian-infected larvae, compared with that of uninfected larvae, were associated with greater levels of colonization by the midgut-inhabiting trichomycete Harpella melusinae. Colonization levels of different species of trichomycetes were significantly correlated with one another in only 2 of 11 cases. Aside from the consistent attachment of the trichomycete Simuliomyces microsporus to the ichthyosporean Paramoebidium chattoni, we found little evidence that prevalence and colonization levels of trichomycetes were influenced by other symbiotes, including other trichomycetes. This trend might reflect the physical separation of trichomycetes, which are gut specific, from other symbiotes. In addition, any combinations of symbiotes that were wholly incompatible would not have been observed in our field-collected material.

Free-living amoebae as opportunistic and non-opportunistic pathogens of humans and animals.

Knowledge that free-living amoebae are capable of causing human disease dates back some 50 years, prior to which time they were regarded as harmless soil organisms or, at most, commensals of mammals. First Naegleria fowleri, then Acanthamoeba spp. and Balamuthia mandrillaris, and finally Sappinia diploidea have been recognised as etiologic agents of encephalitis; Acanthamoeba spp. are also responsible for amoebic keratitis. Some of the infections are opportunistic, occurring mainly in immunocompromised hosts (Acanthamoeba and Balamuthia encephalitides), while others are non-opportunistic (Acanthamoeba keratitis, Naegleria meningoencephalitis, and cases of Balamuthia encephalitis occurring in immunocompetent humans). The amoebae have a cosmopolitan distribution in soil and water, providing multiple opportunities for contacts with humans and animals, as evidenced by antibody titers in surveyed human populations. Although, the numbers of infections caused by these amoebae are low in comparison to other protozoal parasitoses (trypanosomiasis, toxoplasmosis, malaria, etc.), the difficulty in diagnosing them, the challenge of finding optimal antimicrobial treatments and the morbidity and relatively high mortality associated with, in particular, the encephalitides have been a cause for concern for clinical and laboratory personnel and parasitologists. This review presents information about the individual amoebae: their morphologies and life-cycles, laboratory cultivation, ecology, epidemiology, nature of the infections and appropriate antimicrobial therapies, the immune response, and molecular diagnostic procedures that have been developed for identification of the amoebae in the environment and in clinical specimens.

Monopylocystis visvesvarai n. gen., n. sp. and Sawyeria marylandensis n. gen., n. sp.: two new amitochondrial heterolobosean amoebae from anoxic environments.

Two new species of heterolobosean amoebae from anoxic environments, Monopylocystis visvesvarai and Sawyeria marylandensis, are described on the basis of light microscopy, electron microscopy, and their phylogenetic affiliation based on analyses of nuclear small-subunit ribosomal RNA gene sequences. Both species lack mitochondria but have organelles provisionally interpreted as hydrogenosomes, and neither can tolerate aerobic conditions. As their conditions of culture do not exclude all oxygen, they may be microaerophiles rather than strict anaerobes. Both species have unusual nucleolar morphologies. Monopylocystis visvesvarai, from a marine sediment, has nucleolar material distributed around the nuclear periphery. It is the first non-aerobic heterolobosean protist for which a cyst is known; the cyst is unmineralized and unornamented except for a single, raised, plugged pore. Sawyeria marylandensis, from an iron-rich freshwater stream, has nucleolar material distributed in one or two parietal masses, which persist during mitosis. In phylogenetic analyses of small-subunit rRNA gene sequences, Monopylocystis visvesvarai, Sawyeria marylandensis and Psalteriomonas lanterna converge to form a single clade of non-aerobic (anaerobic/microaerophilic) heteroloboseans.

Temporal and spatial distribution of paramoebae in the water column--a pilot study.

Amoebic gill disease is the main disease affecting the salmonid industry in Tasmania, but no information on the distribution of the causative pathogen, Neoparamoeba pemaquidensis, in the aquatic environment is available. This pilot study aimed to determine temporal and spatial distributions of paramoebae species in the water column, using an immuno-dot blot technique. Water samples were collected from inside fish cages at various depths (0.5, 5.5 and 11.0 m) in both summer and winter, as well as various distances (0, 0.5, 240, 280, 750 and 1100 m) away from the sea cage and farming site. Paramoebae densities were estimated using the most probable number technique (MPN). Temperature, salinity, dissolved oxygen, turbidity, nitrite and nitrates, and bacterial counts were measured for each water sample. Data were analysed using a residual maximum likelihood test and significant associations between paramoebae densities and environmental factors were analysed. Results showed that densities were significantly higher in summer (P = 0.017), at 5.5 m depth (P = 0.029), and reduced to the lowest density at 1100 m away from the cage sites (P = 0.008). Bacterial counts, turbidity and temperature were found to be significantly associated with paramoebae densities.

The origins of parasitism in the protists.

The origins of parasitism among the protists are, like the group itself, polyphyletic. Probably the majority of present-day parasitic forms evolved from free-living ancestors which were ingested as part of the food of their hosts, though origins from ectoparasitic forms and via a phase of facultative parasitism are possibilities, particularly among the ciliated protozoa and (for ectoparasitism) the Kinetoplasta. Sporozoan parasites most probably developed via a stage which was ingested and became adapted to life in the host's gut. Further developments in parasitism involved deeper penetration into the host's tissues and the adoption of more than one host in the life cycle, thus avoiding entirely the potentially hazardous phase of existence outside the host.