Dynamic interactions within the host-associated microbiota cause tumor formation in the basal metazoan Hydra.

The extent to which disturbances in the resident microbiota can compromise an animal's health is poorly understood. Hydra is one of the evolutionary oldest animals with naturally occurring tumors. Here, we found a causal relationship between an environmental spirochete (Turneriella spec.) and tumorigenesis in Hydra. Unexpectedly, virulence of this pathogen requires the presence of Pseudomonas spec., a member of Hydra´s beneficial microbiome indicating that dynamic interactions between a resident bacterium and a pathogen cause tumor formation. The observation points to the crucial role of commensal bacteria in maintaining tissue homeostasis and adds support to the view that microbial community interactions are essential for disease. These findings in an organism that shares deep evolutionary connections with all animals have implications for our understanding of cancer.

Deciphering the Role of Multiple Thioredoxin Fold Proteins of Leptospirillum sp. in Oxidative Stress Tolerance.

Thioredoxin fold proteins (TFPs) form a family of diverse proteins involved in thiol/disulfide exchange in cells from all domains of life. Leptospirillum spp. are bioleaching bacteria naturally exposed to extreme conditions like acidic pH and high concentrations of metals that can contribute to the generation of reactive oxygen species (ROS) and consequently the induction of thiol oxidative damage. Bioinformatic studies have predicted 13 genes that encode for TFP proteins in Leptospirillum spp. We analyzed the participation of individual tfp genes from Leptospirillum sp. CF-1 in the response to oxidative conditions. Genomic context analysis predicted the involvement of these genes in the general thiol-reducing system, cofactor biosynthesis, carbon fixation, cytochrome c biogenesis, signal transduction, and pilus and fimbria assembly. All tfp genes identified were transcriptionally active, although they responded differentially to ferric sulfate and diamide stress. Some of these genes confer oxidative protection to a thioredoxin-deficient Escherichia coli strain by restoring the wild-type phenotype under oxidative stress conditions. These findings contribute to our understanding of the diversity and complexity of thiol/disulfide systems, and of adaptations that emerge in acidophilic microorganisms that allow them to thrive in highly oxidative environments. These findings also give new insights into the physiology of these microorganisms during industrial bioleaching operations.

The mechanism of two-phase motility in the spirochete Leptospira: Swimming and crawling.

Many species of bacteria are motile, but their migration mechanisms are considerably diverse. Whatever mechanism is used, being motile allows bacteria to search for more optimal environments for growth, and motility is a crucial virulence factor for pathogenic species. The spirochete Leptospira, having two flagella in the periplasmic space, swims in liquid but has also been previously shown to crawl over solid surfaces. The present motility assays show that the spirochete movements both in liquid and on surfaces involve a rotation of the helical cell body. Direct observations of cell-surface movement with amino-specific fluorescent dye and antibody-coated microbeads suggest that the spirochete attaches to the surface via mobile, adhesive outer membrane components, and the cell body rotation propels the cell relative to the anchoring points. Our results provide models of how the spirochete switches its motility mode from swimming to crawling.

Binding of human complement C1 sterase inhibitor to Leptospira spp.

Leptospirosis is an important zoonosis of global importance caused by bacteria Leptospira spp. Pathogenic Leptospira is resistant to Complement System killing while non-pathogenic Leptospira is rapidly killed by exposure to normal human serum (NHS). Pathogenic Leptospira interact with Complement Regulators such as Factor H, C4b binding protein and Vitronectin avoiding Complement activation and killing by Alternative and Classical Pathways. One important regulator is C1-inhibitor (C1INH) that interacts with C1s or MASPs controlling the cleavage of C4 and C2 molecules, thereby inhibiting the activation of the Classical and Lectin Pathways. In this study, we demonstrate that attenuated, saprophytic and pathogenic Leptospira interact with C1INH that maintain its regulatory capacity of interaction with C1s preventing the activation of Complement system. Although the interaction with C1INH is not crucial for pathogenic Leptospira survival, it seems to be important for the survival of attenuated and saprophytic Leptospira in normal human serum.

Effects of pyrite and sphalerite on population compositions, dynamics and copper extraction efficiency in chalcopyrite bioleaching process.

This study used an artificial microbial community with four known moderately thermophilic acidophiles (three bacteria including Acidithiobacillus caldus S1, Sulfobacillus thermosulfidooxidans ST and Leptospirillum ferriphilum YSK, and one archaea, Ferroplasma thermophilum L1) to explore the variation of microbial community structure, composition, dynamics and function (e.g., copper extraction efficiency) in chalcopyrite bioleaching (C) systems with additions of pyrite (CP) or sphalerite (CS). The community compositions and dynamics in the solution and on the ore surface were investigated by real-time quantitative PCR (qPCR). The results showed that the addition of pyrite or sphalerite changed the microbial community composition and dynamics dramatically during the chalcopyrite bioleaching process. For example, A. caldus (above 60%) was the dominant species at the initial stage in three groups, and at the middle stage, still dominated C group (above 70%), but it was replaced by L. ferriphilum (above 60%) in CP and CS groups; at the final stage, L. ferriphilum dominated C group, while F. thermophilum dominated CP group on the ore surface. Furthermore, the additions of pyrite or sphalerite both made the increase of redox potential (ORP) and the concentrations of Fe3+ and H+, which would affect the microbial community compositions and copper extraction efficiency. Additionally, pyrite could enhance copper extraction efficiency (e.g., improving around 13.2% on day 6) during chalcopyrite bioleaching; on the contrary, sphalerite restrained it.

Generation of acid mine drainage around the Karaerik copper mine (Espiye, Giresun, NE Turkey): implications from the bacterial population in the Acisu effluent.

The Karaerik Cu mine is a worked-out deposit with large volumes of tailings and slags which were left around the mine site without any protection. Natural feeding of these material and run-off water from the mineralised zones into the Acisu effluent causes a serious environmental degradation and creation of acid mine drainage (AMD) along its entire length. This research aims at modelling the formation of AMD with a specific attempt on the characterisation of the bacterial population in association with AMD and their role on its occurrence. Based on 16SrRNA analyses of the clones obtained from a composite water sample, the bacterial community was determined to consist of Acidithiobacillus ferrivorans, Ferrovum myxofaciens, Leptospirillum ferrooxidans and Acidithiobacillus ferrooxidans as iron-oxidising bacteria, Acidocella facilis, Acidocella aluminiidurans, Acidiphilium cryptum and Acidiphilium multivorum as iron-reducing bacteria, and Acidithiobacillus ferrivorans, Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans and Acidiphilium cryptum as sulphur-oxidising bacteria. This association of bacteria with varying roles was interpreted as evidence of a concomitant occurrence of sulphur and iron cycles during the generation of AMD along the Acisu effluent draining the Karaerik mine.

Photo-dynamics of photoactivated adenylyl cyclase TpPAC from the spirochete bacterium Turneriella parva strain H(T).

The photoactivated adenylyl cyclase TpPAC from the spirochete bacterium Turneriella parva was synthesized and the purified recombinant protein was characterized by biochemical and optical spectroscopic methods. TpPAC consists of a BLUF domain (BLUF = Blue Light sensor Using Flavin) and an adenylyl cyclase homology domain (CHD). A light induced cAMP cyclase activity of ≈ 53.3 nmolmg(-1)min(-1) was measured while in the dark the cyclase activity was approximately a factor of 240 lower. The photo-cycling dynamics of the BLUF domain of TpPAC was studied by absorption spectra, fluorescence quantum distribution, and fluorescence lifetime measurements. The quantum efficiency of BLUF domain signaling state formation was found to be ϕs ≈ 0.59. A three-component exponential recovery of the signaling state to the receptor state was observed with the time constants τrec,1 = 4.8s, τrec,2 = 34.2s, and τrec,3 = 293s at 21.3 °C. The protein thermal stability was studied by stepwise sample heating and cooling. An apparent TpPAC melting temperature of ϑm ≈ 46 °C was determined. The photo-degradation of TpPAC in the signaling state was studied by prolonged intense light exposure at 455 nm. An irreversible flavin photo-degradation was observed with quantum yield ϕD ≈ 8.7 × 10(-6).

A decade of metaproteomics: where we stand and what the future holds.

We are living through exciting times during which we are able to unravel the "microbial dark matter" in and around us through the application of high-resolution "meta-omics". Metaproteomics offers the ability to resolve the major catalytic units of microbial populations and thereby allows the establishment of genotype-phenotype linkages from in situ samples. A decade has passed since the term "metaproteomics" was first coined and corresponding analyses were carried out on mixed microbial communities. Since then metaproteomics has yielded many important insights into microbial ecosystem function in the various environmental settings where it has been applied. Although initial progress in analytical capacities and resulting numbers of proteins identified was extremely fast, this trend slowed rapidly. Here, we discuss several representative metaproteomic investigations of activated sludge, acid mine drainage biofilms, freshwater and seawater microbial communities, soil, and human gut microbiota. By using these case studies, we highlight current challenges and possible solutions for metaproteomics to realize its full potential, i.e. to enable conclusive links between microbial community composition, physiology, function, interactions, ecology, and evolution in situ.

Effects of Arsenite Resistance on the Growth and Functional Gene Expression of Leptospirillum ferriphilum and Acidithiobacillus thiooxidans in Pure Culture and Coculture.

The response of iron-oxidizing Leptospirillum ferriphilum YSK and sulfur-oxidizing Acidithiobacillus thiooxidans A01 to arsenite under pure culture and coculture was investigated based on biochemical characterization (concentration of iron ion and pH value) and related gene expression. L. ferriphilum YSK and At. thiooxidans A01 in pure culture could adapt up to 400 mM and 800 mM As(III) after domestication, respectively, although arsenite showed a negative effect on both strains. The coculture showed a stronger sulfur and ferrous ion oxidation activity when exposed to arsenite. In coculture, the pH value showed no significant difference when under 500 mM arsenite stress, and the cell number of At. thiooxidans was higher than that in pure culture benefiting from the interaction with L. ferriphilum. The expression profile showed that the arsenic efflux system in the coculture was more active than that in pure culture, indicating that there is a synergetic interaction between At. thiooxidans A01 and L. ferriphilum YSK. In addition, a model was proposed to illustrate the interaction between arsenite and the ars operon in L. ferriphilum YSK and At. thiooxidans A01. This study will facilitate the effective application of coculture in the bioleaching process by taking advantage of strain-strain communication and coordination.

Elevated temperature alters proteomic responses of individual organisms within a biofilm community.

Microbial communities that underpin global biogeochemical cycles will likely be influenced by elevated temperature associated with environmental change. Here, we test an approach to measure how elevated temperature impacts the physiology of individual microbial groups in a community context, using a model microbial-based ecosystem. The study is the first application of tandem mass tag (TMT)-based proteomics to a microbial community. We accurately, precisely and reproducibly quantified thousands of proteins in biofilms growing at 40, 43 and 46 °C. Elevated temperature led to upregulation of proteins involved in amino-acid metabolism at the level of individual organisms and the entire community. Proteins from related organisms differed in their relative abundance and functional responses to temperature. Elevated temperature repressed carbon fixation proteins from two Leptospirillum genotypes, whereas carbon fixation proteins were significantly upregulated at higher temperature by a third member of this genus. Leptospirillum group III bacteria may have been subject to viral stress at elevated temperature, which could lead to greater carbon turnover in the microbial food web through the release of viral lysate. Overall, these findings highlight the utility of proteomics-enabled community-based physiology studies, and provide a methodological framework for possible extension to additional mixed culture and environmental sample analyses.

Systematics of leptospiraceae.

Leptospires are spirochetes that may be free-living saprophytes found in freshwater or may cause acute or chronic infection of animals. The family Leptospiraceae comprises three genera: Leptospira Leptospira Leptonema Leptonema, and Turneriella Turneriella. Within the genus Leptospira, three clades can be distinguished, of pathogens, nonpathogens, and an intermediate group. Leptospires are further divided into serovars; antigenically related serovars are clustered into serogroups for convenience.

Leptospirose bovina no Estado da Paraíba: prevalência e fatores de risco associados à ocorrência de propriedades positivas / Bovine leptospirosis in Paraíba State: prevalence and risk factors associated with the occurrence of positive herds

Foram determinadas as prevalências de propriedades positivas e de animais positivos e identificados fatores de risco associados à leptospirose em vacas no Estado da Paraíba, Nordeste do Brasil. Foram aleatoriamente selecionadas 2.317vacas com idade ≥ 24 meses, procedentes de 450propriedades. Para o diagnóstico sorológico da infecção por Leptospira spp. foi empregado o teste de soroaglutinação microscópica (SAM), utilizando-se 24 sorovares como antígenos. Uma propriedade foi considerada positiva quando apresentou pelo menos um animal soropositivo. Das 450 propriedades investigadas 398 (89,7 por cento; IC 95 por cento = 86,6-92,2 por cento) apresentaram pelo menos um animal reagente na SAM para qualquer sorovar, e 1.349 (61,1 por cento; IC por cento = 56,6-65,4 por cento) animais foram soropositivos. O sorovar Hardjo foi o mais prevalente nas propriedades e nos animais, com frequências de 58,17 por cento e 54,69 por cento, respectivamente. Propriedade ser localizada no Sertão (odds ratio = 3,20; p = 0,003), presença de animais silvestres (odds ratio =2,89; p=0,005), não resfriar o leite (odds ratio =3,83; p=0,034) e presença de pastos alagados (odds ratio =2,36; p<0,001) foram identificados como fatores de riscos associados à prevalência de propriedades positivas. Conclui-se que a leptospirose encontra-se amplamente difundida em bovinos do Estado da Paraíba, o que reforça a necessidade de intensificação de medidas de prevenção e controle, como a vacinação dos rebanhos. De acordo com os resultados da análise de fatores de risco, sugere-se que o controle sanitário antes da introdução de animais, drenagem de áreas alagadas e melhora nas condições de manejo são importantes medidas para a prevenção da infecção.

Herd-level and animal-level prevalences were determined and risk factors associated with leptospirosis were identified in cows in the State of Paraíba, Northeastern Brazil. A total of 2,317 cows with ≥ 24 months of age from 450 herds were randomly sampled. For the serological diagnosis of Leptospira spp. infection, the microscopic agglutination test (MAT) was carried out using 24 serovars as antigens. A herd was considered positive when presented at least one seropositive animal. Of the 450 investigated herds, 398 (89.7 percent; 95 percent CI = 86.6-92.2 percent) presented at least one reactant animal at MAT to any serovar, and 1,349 (61.1 percent; 95 percent CI = 56.6-65.4 percent) animals were seropositive. Serovar Hardjo was the most prevalent in herds and animals, with frequencies of 58.17 percent and 54.69 percent respectively. Location of the herd in the Sertão (odds ratio = 3.20; p=0.003), presence of wildlife (odds ratio =2.89; p=0.005), not cooling milk (odds ratio =3.83; p=0.034) and presence of flooded pastures (odds ratio =2.36; p<0.001) were identified as risk factors for herd-level prevalence. It is concluded that leptospirosis is widely spread in cattle in State of Paraíba, which reinforces the need for increased prevention and control measures, such as vaccination of herds. According to the results of risk factors analysis it is suggested that the sanitary control before the introduction of animals, drainage of wetlands and improvement in management conditions are important measures to preventing the infection.

The microbial desulfurization of coal.

The chemical structure of coal macerals is usually characterized by the presence of inorganic and organic sulfur. Inorganic sulfur consists mostly of iron sulfides, the so-called "pyritic sulfur," whereas organic sulfur is covalently bound to the carbon atoms of the coal macromolecule. Comminution of coal to sizes that liberate the iron sulfide grains makes their removal with mineral beneficiation processes theoretically possible, but practically profitless. Microbial removal of pyritic sulfur has been extensively investigated over the last 50 years and the very promising results obtained have encouraged the design and construction of a semi-commercial pilot plant in the framework of Project JOULE 0039 funded by the European Commission. The results of the 1-year operation of this plant are reported here, the most significant being the 90 % pyrite removal achieved in five stirred tank bioreactors operating with a 40 % solids suspension and the pyritic iron solubilization rate of 36 mg dm(-3) h(-1). Taking into account the very high price of the kWh in Italy, a rough estimate of the overall costs is in the range from 25 to 30 per tonne of dry coal. So far the development of a microbial process for organic sulfur removal has shown to be much more difficult and less successful, although significant progress in laboratory research is reported.

Unifying vertical and nonvertical evolution: a stochastic ARG-based framework.

Evolutionary biologists have introduced numerous statistical approaches to explore nonvertical evolution, such as horizontal gene transfer, recombination, and genomic reassortment, through collections of Markov-dependent gene trees. These tree collections allow for inference of nonvertical evolution, but only indirectly, making findings difficult to interpret and models difficult to generalize. An alternative approach to explore nonvertical evolution relies on phylogenetic networks. These networks provide a framework to model nonvertical evolution but leave unanswered questions such as the statistical significance of specific nonvertical events. In this paper, we begin to correct the shortcomings of both approaches by introducing the "stochastic model for reassortment and transfer events" (SMARTIE) drawing upon ancestral recombination graphs (ARGs). ARGs are directed graphs that allow for formal probabilistic inference on vertical speciation events and nonvertical evolutionary events. We apply SMARTIE to phylogenetic data. Because of this, we can typically infer a single most probable ARG, avoiding coarse population dynamic summary statistics. In addition, a focus on phylogenetic data suggests novel probability distributions on ARGs. To make inference with our model, we develop a reversible jump Markov chain Monte Carlo sampler to approximate the posterior distribution of SMARTIE. Using the BEAST phylogenetic software as a foundation, the sampler employs a parallel computing approach that allows for inference on large-scale data sets. To demonstrate SMARTIE, we explore 2 separate phylogenetic applications, one involving pathogenic Leptospirochete and the other Saccharomyces.

Lymphopenia is observed regularly in the acute (leptospiraemic) phase but not the immune phase of leptospirosis.

Lymphocyte counts in patients with leptospirosis have been shown to be variable. This study retrospectively compared lymphocyte counts from the first blood samples taken following hospital presentation in patients with leptospirosis who were either (i) IgM non-reactive, (ii) IgM reactive and microscopic agglutination test (MAT) non-reactive or (iii) IgM and MAT reactive in an effort to determine whether differences in lymphocyte counts are observed in the acute and immune phase of leptospirosis. Statistical differences in lymphocyte counts were observed between the three groups. In conclusion, this study has shown that the phase of leptospiral infection may affect patient lymphocyte counts.

Culturable and molecular phylogenetic diversity of microorganisms in an open-dumped, extremely acidic Pb/Zn mine tailings.

A combination of cultivation-based and molecular-based approaches was used to reveal the culturable and molecular diversity of the microbes inhabiting an open-dumped Pb/Zn mine tailings that was undergoing intensive acid generation (pH 1.9). Culturable bacteria found in the extremely acidic mine tailings were Acidithiobacillus ferrooxidans, Leptospirillum ferriphilum, Sulfobacillus thermotolerans and Acidiphilium cryptum, where the number of acidophilic heterotrophs was ten times higher than that of the iron- and sulfur-oxidizing bacteria. Cloning and phylogenetic analysis revealed that, in contrast to the adjacent AMD, the mine tailings possessed a low microbial diversity with archaeal sequence types dominating the 16S rRNA gene library. Of the 141 clones examined, 132 were represented by two sequence types phylogenetically affiliated with the iron-oxidizing archaea Ferroplasma acidiphilum and three belonged to two tentative groups within the Thermoplasma lineage so far represented by only a few environmental sequences. Six clones in the library were represented by the only bacterial sequence type and were closely related to the well-described iron-oxidizer L. ferriphilum. The significant differences in the prokaryotic community structures of the extremely acidic mine tailings and the AMD associated with it highlights the importance of studying the microbial communities that are more directly involved in the iron and sulfur cycles of mine tailings.

WC1+ gammadelta T cell memory population is induced by killed bacterial vaccine.

Limited studies have addressed the ability of gammadelta T cells to become memory populations. We previously demonstrated that WC1.1(+) gammadelta T cells from ruminants vaccinated with killed Leptospira borgpetersenii proliferate and produce IFN-gamma in recall responses. Here we show that this response is dependent upon antigen-responsive CD4 T cells, at least across transwell membranes; this requirement cannot be replaced by IL-2. The response was also dependent upon in vivo priming, since gammadelta T cells from leptospira vaccine-naive animals did not respond to antigen even when co-cultured across membranes from antigen-responsive PBMC. Gammadelta T cells were the major antigen-responding T cell population for the first 4 wks following vaccination and replicated more rapidly than CD4 T cells. Primed WC1(+) gammadelta T cells circulated as CD62L(hi)/CD45RO(int)/CD44(lo), characteristics of T(CM) cells. When stimulated with antigen, they decreased CD62L, increased CD44 and CD25, and had no change in CD45RO expression. These changes paralleled those of the leptospira antigen-responsive CD4 T cells but differed from those of gammadelta T cells proliferating to mitogen stimulation. This system for in vivo gammadelta T cell priming is unique, since it relies on a killed antigen to induce memory and may be pertinent to designing vaccines that require type 1 pro-inflammatory cytokines.

The shape and dynamics of the Leptospiraceae.

Most swimming bacteria produce thrust by rotating helical filaments called flagella. Typically, the flagella stick out into the external fluid environment; however, in the spirochetes, a unique group that includes some highly pathogenic species of bacteria, the flagella are internalized, being incased in the periplasmic space; i.e., between the outer membrane and the cell wall. This coupling between the periplasmic flagella and the cell wall allows the flagella to serve a skeletal, as well as a motile, function. In this article, we propose a mathematical model for spirochete morphology based on the elastic interaction between the cell body and the periplasmic flagella. This model describes the mechanics of the composite structure of the cell cylinder and periplasmic flagella and accounts for the morphology of Leptospiraceae. This model predicts that the cell cylinder should be roughly seven times stiffer than the flagellum. In addition, we explore how rotation of the periplasmic flagellum deforms the cell cylinder during motility. We show that the transition between hook-shaped and spiral-shaped ends is purely a consequence of the change in direction of the flagellar motor and does not require flagellar polymorphism.