Little is known about the viability of eukaryotic microorganisms preserved in icy regions. Here we report on the diversity of microbial eukaryotes in ice samples derived from four Pyrenean glaciers. The species composition of eukaryotic communities in these glaciers is unknown mostly because of the presence of a multi-year ice cap, and it is not clear whether they harbor the same populations. The recent deglaciation of these areas is allowing an easy access to glacial layers that correspond to the “Little Ice Age” although some isolated deposits are attributed to previous glacial cycles. In this study, we use molecular 18S rRNA-based approaches to characterize some of the microbial eukaryotic populations associated with Pyrenean glaciers. Firstly, we performed a chemical and microscopical characterization of ice samples. Secondly, molecular analyses revealed interesting protist genetic diversity in glaciers. In order to understand the microbial composition of the ice samples the eukaryotic communities resident in the glacial samples were examined by amplifying community DNA and constructing clone libraries with 18S rRNA primers. After removal of potential chimeric sequences and dereplication of identical sequences, phylogenetic analysis demonstrated that several different protists could be identified. Protist diversity was more phylum rich in Aneto and Monte Perdido glaciers. The dominant taxonomic groups across all samples (>1% of all sequences) were Viridiplantae and Rhizaria. Significant variations in relative abundances of protist phyla between higher and lower glaciers were observed. At the genus level, significant differences were also recorded for the dominant genera Chloromonas, Raphidonema, Heteromita, Koliella, and Bodomorpha. In addition, protist community structure showed significant differences between glaciers. The relative abundances of protist groups at different taxonomic levels correlated with the altitude and area of glaciers and with pH of ice, but little or no relationships to other chemical characteristics were found.
eukaryotic microorganisms; glaciers; ancient ice; climate change; biodiversity; Pyrenean glaciers
Marine microorganisms are important for the global nitrogen cycle, but marine nitrifiers, especially aerobic nitrite oxidizers, remain largely unexplored. To increase the number of cultured representatives of marine nitrite-oxidizing bacteria (NOB), a bioreactor cultivation approach was adopted to first enrich nitrifiers and ultimately nitrite oxidizers from Dutch coastal North Sea water. With solely ammonia as the substrate an active nitrifying community consisting of novel marine Nitrosomonas aerobic ammonia oxidizers (ammonia-oxidizing bacteria) and Nitrospina and Nitrospira NOB was obtained which converted a maximum of 2 mmol of ammonia per liter per day. Switching the feed of the culture to nitrite as a sole substrate resulted in a Nitrospira NOB dominated community (approximately 80% of the total microbial community based on fluorescence in situ hybridization and metagenomic data) converting a maximum of 3 mmol of nitrite per liter per day. Phylogenetic analyses based on the 16S rRNA gene indicated that the Nitrospira enriched from the North Sea is a novel Nitrospira species with Nitrospira marina as the next taxonomically described relative (94% 16S rRNA sequence identity). Transmission electron microscopy analysis revealed a cell plan typical for Nitrospira species. The cytoplasm contained electron light particles that might represent glycogen storage. A large periplasmic space was present which was filled with electron dense particles. Nitrospira-targeted polymerase chain reaction analyses demonstrated the presence of the enriched Nitrospira species in a time series of North Sea genomic DNA samples. The availability of this new Nitrospira species enrichment culture facilitates further in-depth studies such as determination of physiological constraints, and comparison to other NOB species.
marine nitrification; enrichment; Nitrosomonas, Nitrospira; fluorescence in situ hybridization; transmission electron microscopy; 16S rRNA
Temporary wetlands are short-term alternative ecosystems formed by flooding for irrigation of areas used for rice farming. The goal of this study is to describe the development cycle of rice fields as temporary wetlands in southern Brazil, evaluating how this process affect the gas production (CH4 and CO2) in soil with difference % carbon and organic matter content. Two areas adjacent to Lake Mangueira in southern Brazil were used during a rice-farming cycle. One area had soil containing 1.1% carbon and 2.4% organic matter, and the second area had soil with 2.4% carbon and 4.4% organic matter. The mean rates of gas production were 0.04 ± 0.02 mg CH4 m−2 d−1 and 1.18 ± 0.30 mg CO2 m−2 d−1 in the soil area with the lower carbon content, and 0.02 ± 0.03 mg CH4 m−2 d−1 and 1.38 ± 0.41 mg CO2 m−2 d−1 in the soil area with higher carbon content. Our results showed that mean rates of CO2 production were higher than those of CH4 in both areas. No statistically significant difference was observed for production of CH4 considering different periods and sites. For carbon dioxide (CO2), however, a Two-Way ANOVA showed statistically significant difference (p = 0.05) considering sampling time, but no difference between areas. The results obtained suggest that the carbon and organic matter contents in the soil of irrigated rice cultivation areas may have been used in different ways by soil microorganisms, leading to variations in CH4 and CO2 production.
ecosystem development; % carbon; % organic matter; CH4; CO2
Marine subsurface environments such as deep-sea sediments, house abundant and diverse microbial communities that are believed to influence large-scale geochemical processes. These processes include the biotransformation and mineralization of numerous petroleum constituents. Thus, microbial communities in the Gulf of Mexico are thought to be responsible for the intrinsic bioremediation of crude oil released by the Deepwater Horizon (DWH) oil spill. While hydrocarbon contamination is known to enrich for aerobic, oil-degrading bacteria in deep-seawater habitats, relatively little is known about the response of communities in deep-sea sediments, where low oxygen levels may hinder such a response. Here, we examined the hypothesis that increased hydrocarbon exposure results in an altered sediment microbial community structure that reflects the prospects for oil biodegradation under the prevailing conditions. We explore this hypothesis using metagenomic analysis and metabolite profiling of deep-sea sediment samples following the DWH oil spill. The presence of aerobic microbial communities and associated functional genes was consistent among all samples, whereas, a greater number of Deltaproteobacteria and anaerobic functional genes were found in sediments closest to the DWH blowout site. Metabolite profiling also revealed a greater number of putative metabolites in sediments surrounding the blowout zone relative to a background site located 127 km away. The mass spectral analysis of the putative metabolites revealed that alkylsuccinates remained below detection levels, but a homologous series of benzylsuccinates (with carbon chain lengths from 5 to 10) could be detected. Our findings suggest that increased exposure to hydrocarbons enriches for Deltaproteobacteria, which are known to be capable of anaerobic hydrocarbon metabolism. We also provide evidence for an active microbial community metabolizing aromatic hydrocarbons in deep-sea sediments of the Gulf of Mexico.
Deepwater Horizon; metagenomics; metabolomics; oil-degradation
Understanding the impact of antimicrobial use on the emergence of resistant bacteria is imperative to prevent its emergence. For instance, activation of the AcrAB efflux pumps is responsible for the emergence of antimicrobial-resistant Salmonella strains. Here, we examined the expression levels of acrB and its multiple regulator genes (RamA, SoxS, MarA, and Rob) in 17 field isolates of S. Choleraesuis by using quantitative PCR methods. The expression of acrB increased in eight of the field isolates (P < 0.05). The expression of acrB was associated with that of ramA in one isolate, soxS in one isolate, and both these genes in six isolates. Thereafter, to examine the effect of selected antimicrobials (enrofloxacin, ampicillin, oxytetracycline, kanamycin, and spectinomycin) on the expression of acrB and its regulator genes, mutants derived from five isolates of S. Choleraesuis were selected by culture on antimicrobial-containing plates. The expression of acrB and ramA was higher in the mutants selected using enrofloxacin (3.3–6.3- and 24.5–37.7-fold, respectively), ampicillin (1.8–7.7- and 16.1–55.9-fold, respectively), oxytetracycline (1.7–3.3- and 3.2–31.1-fold, respectively), and kanamycin (1.6–2.2- and 5.6–26.4-fold, respectively), which are AcrAB substrates, than in each of the parental strains (P < 0.05). In contrast, in AcrAB substrate-selected mutants, the expression of soxS, marA, and rob remained similar to that in parental strains. Of the four antimicrobials, the level of ramA expression was significantly higher in the enrofloxacin- and ampicillin-selected mutants than in the oxytetracycline- and kanamycin-selected mutants (P < 0.05), whereas the expression levels of acrB and multiple regulator genes in spectinomycin-selected mutants were similar to those in each parental strain. These data suggest that exposure to antimicrobials that are AcrAB substrates enhance the activation of the AcrAB efflux pump via RamA, but not via SoxS, MarA, or Rob in S. Choleraesuis.
AcrAB efflux pump; antimicrobial resistance; RamA; Salmonella Choleraesuis; SoxS
Carbapenems, once considered the last line of defense against of serious infections with Enterobacteriaceae, are threatened with extinction. The increasing isolation of carbapenem-resistant Gram-negative pathogens is forcing practitioners to rely on uncertain alternatives. As little as 5 years ago, reports of carbapenem resistance in Enterobacteriaceae, common causes of both community and healthcare-associated infections, were sporadic and primarily limited to case reports, tertiary care centers, intensive care units, and outbreak settings. Carbapenem resistance mediated by β-lactamases, or carbapenemases, has become widespread and with the paucity of reliable antimicrobials available or in development, international focus has shifted to early detection and infection control. However, as reports of Klebsiella pneumoniae carbapenemases, New Delhi metallo-β-lactamase-1, and more recently OXA-48 (oxacillinase-48) become more common and with the conveniences of travel, the assumption that infections with highly resistant Gram-negative pathogens are limited to the infirmed and the heavily antibiotic and healthcare exposed are quickly being dispelled. Herein, we provide a status report describing the increasing challenges clinicians are facing and forecast the “stormy waters” ahead.
carbapenemases; NDM-1; KPC; OXA-48; metallo-β-lactamases; CHDL
Antibiotics are chemotherapeutic agents, which have been a very powerful tool in the clinical management of bacterial diseases since the 1940s. However, benefits offered by these magic bullets have been substantially lost in subsequent days following the widespread emergence and dissemination of antibiotic-resistant strains. While it is obvious that excessive and imprudent use of antibiotics significantly contributes to the emergence of resistant strains, antibiotic resistance is also observed in natural bacteria of remote places unlikely to be impacted by human intervention. Both antibiotic biosynthetic genes and resistance-conferring genes have been known to evolve billions of years ago, long before clinical use of antibiotics. Hence it appears that antibiotics and antibiotics resistance determinants have some other roles in nature, which often elude our attention because of overemphasis on the therapeutic importance of antibiotics and the crisis imposed by the antibiotic resistance in pathogens. In the natural milieu, antibiotics are often found to be present in sub-inhibitory concentrations acting as signaling molecules supporting the process of quorum sensing and biofilm formation. They also play an important role in the production of virulence factors and influence host–parasite interactions (e.g., phagocytosis, adherence to the target cell, and so on). The evolutionary and ecological aspects of antibiotics and antibiotic resistance in the naturally occurring microbial community are little understood. Therefore, the actual role of antibiotics in nature warrants in-depth investigations. Studies on such an intriguing behavior of the microorganisms promise insight into the intricacies of the microbial physiology and are likely to provide some lead in controlling the emergence and subsequent dissemination of antibiotic resistance. This article highlights some of the recent findings on the role of antibiotics and the genes that confer resistance to antibiotics in nature.
antibiotics; sub-inhibitory concentration; quorum sensing; virulence; stress response; antibiotic resistance; antibiotic paradox
Bioremediation strategies that depend on bacterial sulfate reduction for heavy metals remediation harness the reactivity of these metals with biogenic aqueous sulfide. Quantitative knowledge of the degree to which specific toxic metals are partitioned into various sulfide, oxide, or other phases is important for predicting the long-term mobility of these metals under environmental conditions. Here we report the quantitative partitioning into sedimentary biogenic sulfides of a suite of metals and metalloids associated with acid mine drainage contamination of a natural estuarine wetland for over a century.
acid mine drainage; heavy metals; metal-sulfides; wetlands; bioremediation; electron microprobe; bacterial sulfate reduction; sulfate-reducing bacteria
The most severe manifestations of malaria (caused by Plasmodium falciparum) occur as a direct result of parasitemia following invasion of erythrocytes by post-liver blood-stage merozoites, and during subsequent cyto-adherence of infected erythrocytes to the vascular endothelium. However, the disproportionate epidemiologic clustering of severe malaria with aggressive forms of endemic diseases such as Kaposi’s sarcoma (KS), a neoplasm that is etiologically linked to infection with KS-associated herpesvirus (KSHV), underscores the significance of previously unexplored co-pathogenetic interactions that have the potential to modify the overall disease burden in co-infected individuals. Based on recent studies of the mechanisms that P. falciparum and KSHV have evolved to interact with their mutual human host, several new perspectives are emerging that highlight a surprising convergence of biological themes potentially underlying their associated co-morbidities. Against this background, ongoing studies are rapidly constructing a fascinating new paradigm in which the major host receptors that control parasite invasion (Basigin/CD147) and cyto-adherence (CD36) are, surprisingly, also important targets for exploitation by KSHV. In this article, we consider the major pathobiological implications of the co-option of Basigin/CD147 and CD36 signaling pathways by both P. falciparum and KSHV, not only as essential host factors for parasite persistence but also as important mediators of the pro-angiogenic phenotype within the virus-infected endothelial microenvironment. Consequently, the triangulation of interactions between P. falciparum, KSHV, and their mutual human host articulates a syndemic relationship that points to a conceptual framework for prevalence of aggressive forms of KS in malaria-endemic areas, with implications for the possibility of dual-use therapies against these debilitating infections in resource-limited parts of the world.
Kaposi’s sarcoma; HHV-8; malaria; PfEMP-1; CD36; Basigin/CD147; PfRh5
The antiviral activity of several cationic compounds – cetyltrimethylammonium bromide (CTAB), chitosan, nisin, and lysozyme – was investigated on the bacteriophage c2 (DNA head and non-contractile tail) infecting Lactococcus strains and the bacteriophage MS2 (F-specific RNA) infecting E. coli. Firstly, these activities were evaluated in a phosphate buffer pH 7 – 10 mM. The CTAB had a virucidal effect on the Lactococcus bacteriophages, but not on the MS2. After 1 min of contact with 0.125 mM CTAB, the c2 population was reduced from 6 to 1.5 log(pfu)/mL and completely deactivated at 1 mM. On the contrary, chitosan inhibited the MS2 more than it did the bacteriophages c2. No antiviral effect was observed for the nisin or the lysozyme on bacteriophages after 1 min of treatment. A 1 and 2.5 log reduction was respectively observed for nisin and lysozyme when the treatment time increased (5 or 10 min). These results showed that the antiviral effect depended both on the virus and structure of the antimicrobial compounds. The antiviral activity of these compounds was also evaluated in different physico-chemical conditions and in complex matrices. The antiviral activity of CTAB was impaired in acid pH and with an increase of the ionic strength. These results might be explained by the electrostatic interactions between cationic compounds and negatively charged particles such as bacteriophages or other compounds in a matrix. Milk proved to be protective suggesting the components of food could interfere with antimicrobial compounds.
bacteriophage; Lactococcus; MS2; chitosan; CTAB; nisin; lysozyme; virucidal activity
In order to identify the biogeochemical parameters controlling pCO2, total chlorophyll a, and dimethyl sulfide (DMS) concentrations during the North East Atlantic Spring Bloom (NASB), we used previously unpublished particulate and dissolved elemental concentrations to construct several linear regression models; first by hypothesis-testing, and then with exhaustive stepwise linear regression followed by leave-one-out cross-validation. The field data was obtained along a latitudinal transect from the Azores Islands to the North Atlantic, and best-fit models (determined by lowest predictive error) of up to three variables are presented. Total chlorophyll a is predicted best by biomass (POC, PON) parameters and by pigments characteristic of picophytoplankton for the southern section of the sampling transect (from the Azores to the Rockhall-Hatton Plateau) and coccolithophores in the northern portion (from the Rockhall-Hatton Plateau to the Denmark Strait). Both the pCO2 and DMS models included variables traditionally associated with the development of the NASB such as mixed-layer depth and with Fe, Si, and P-deplete conditions (dissolved Fe, dissolved and biogenic silica, dissolved PO3−4). However, the regressions for pCO2 and DMS also include intracellular V and Mo concentrations, respectively. Mo is involved in DMS production as a cofactor in dimethylsulfoxide reductase. No significant biological role for V has yet been determined, although intracellular V is significantly correlated (p-value <0.05) with biogenic silica (R2 = 0.72) and total chlorophyll a (R2 = 0.49) while the same is not true for its biogeochemical analogue Mo, suggesting active uptake of V by phytoplankton. Our statistical analysis suggests these two lesser-studied metals may play more important roles in bloom dynamics than previously thought, and highlights a need for studies focused on determining their potential biological requirements and cell quotas.
trace nutrients; North Atlantic Spring Bloom; B-vitamins; vanadium; molybdenum
Human T cell leukemia virus type 1 (HTLV-1) is the etiological agent of adult T cell leukemia/lymphoma (ATLL) and several inflammatory diseases. Tax, the protein encoded by HTLV-1, may be responsible for the development of the diseases caused by this virus. To investigate the pathogenic role of Tax, several transgenic mouse strains expressing Tax have been developed in recent years. These mice develop various tumors including large granular lymphocytic leukemia, as well as inflammatory diseases such as arthritis. These results suggest that Tax expression alone is sufficient to cause both malignant neoplastic diseases and inflammatory diseases. However, until recently, there were no tax transgenic mice that develop T cell leukemia and lymphoma resembling ATLL. The first successful induction of leukemia in T cells was pre-T cell leukemia generated in transgenic mice in which a mouse lymphocyte-specific protein tyrosine kinase p56lck (lck)-proximal promoter was used to express the tax gene in immature T cells. Subsequently, transgenic mice were established in which the lck-distal promoter was used to express Tax in mature T cells; these mice developed mature T cell leukemia and lymphoma that more closely resembled ATLL than did earlier mouse models.
animal model; ATLL; HTLV-1; Tax; transgenic mice
B-vitamins are recognized as essential organic growth factors for many organisms, although little is known about their abundance and distribution in marine ecosystems. Despite their metabolic functions regulating important enzymatic reactions, the methodology to directly measure different B-vitamins in aquatic environments has only recently been developed. Here, we present the first direct measurements of two B-vitamins, thiamin (B1), and pyridoxine (B6), in the Amazon River plume-influenced western tropical North Atlantic (WTNA) Ocean, an area known to have high productivity, carbon (C) and dinitrogen (N2) fixation, and C sequestration. The vitamins B1 and B6 ranged in concentrations from undetectable to 230 and 40 pM, respectively. Significantly higher concentrations were measured in the surface plume water at some stations and variation with salinity was observed, suggesting a possible riverine influence on those B-vitamins. The influences of vitamins B1 and B6 on biogeochemical processes such as C and N2 fixation were investigated using a linear regression model that indicated the availability of those organic factors could affect these rates in the WTNA. In fact, significant increases in C fixation and N2 fixation were observed with increasing vitamin B1 concentrations at some low and mesohaline stations (stations 9.1 and 1; p value <0.017 and <0.03, respectively). N2 fixation was also found to have a significant positive correlation with B1 concentrations at station 1 (p value 0.029), as well as vitamin B6 at station 9.1 (p value <0.017). This work suggests that there can be a dynamic interplay between essential biogeochemical rates (C and N2 fixation) and B-vitamins, drawing attention to potential roles of B-vitamins in ecosystem dynamics, community structure, and global biogeochemistry.
B-vitamin; thiamin; thiamine; pyridoxine; Atlantic; biogeochemical cycles; organic growth factors
The plasmids of the incompatibility (Inc) group IncP-1, also called IncP, as extrachromosomal genetic elements can transfer and replicate virtually in all Gram-negative bacteria. They are composed of backbone genes that encode a variety of essential functions and accessory genes that have implications for human health and environmental bioremediation. Broad-host-range IncP plasmids are known to spread genes between distinct phylogenetic groups of bacteria. These genes often code for resistances to a broad spectrum of antibiotics, heavy metals, and quaternary ammonium compounds used as disinfectants. The backbone of these plasmids carries modules that enable them to effectively replicate, move to a new host via conjugative transfer and to be stably maintained in bacterial cells. The adaptive, resistance, and virulence genes are mainly located on mobile genetic elements integrated between the functional plasmid backbone modules. Environmental studies have demonstrated the wide distribution of IncP-like replicons in manure, soils and wastewater treatment plants. They also are present in strains of pathogenic or opportunistic bacteria, which can be a cause for concern, because they may encode multiresistance. Their broad distribution suggests that IncP plasmids play a crucial role in bacterial adaptation by utilizing horizontal gene transfer. This review summarizes the variety of genetic information and physiological functions carried by IncP plasmids, which can contribute to the spread of antibiotic and heavy metal resistance while also mediating the process of bioremediation of pollutants. Due to the location of the resistance genes on plasmids with a broad-host-range and the presence of transposons carrying these genes it seems that the spread of these genes would be possible and quite hazardous in infection control. Future studies are required to determine the level of risk of the spread of resistance genes located on these plasmids.
IncP plasmid; antibiotic resistance; heavy metals; xenobiotic; catabolism; horizontal gene transfer; bioremediation
Urinary tract infections (UTIs) are among the most common bacterial infections worldwide. Disproportionately affecting women, UTIs exact a substantial public burden each year in terms of direct medical expenses, decreased quality of life, and lost productivity. Increasing antimicrobial resistance among strains of extraintestinal pathogenic Escherichia coli challenges successful treatment of UTIs. Community-acquired UTIs were long considered sporadic infections, typically caused by the patients’ native gastrointestinal microbiota; however, the recent recognition of UTI outbreaks with probable foodborne origins has shifted our understanding of UTI epidemiology. Along with this paradigm shift come new opportunities to disrupt the infection process and possibly quell increasing resistance, including the elimination of non-therapeutic antimicrobial use in food-animal production.
antibiotics; antibiotic resistance; antimicrobial resistance; Escherichia coli; food contamination; poultry products; UPEC; urinary tract infections
Antibiotics have natural functions, mostly involving cell-to-cell signaling networks. The anthropogenic production of antibiotics, and its release in the microbiosphere results in a disturbance of these networks, antibiotic resistance tending to preserve its integrity. The cost of such adaptation is the emergence and dissemination of antibiotic resistance genes, and of all genetic and cellular vehicles in which these genes are located. Selection of the combinations of the different evolutionary units (genes, integrons, transposons, plasmids, cells, communities and microbiomes, hosts) is highly asymmetrical. Each unit of selection is a self-interested entity, exploiting the higher hierarchical unit for its own benefit, but in doing so the higher hierarchical unit might acquire critical traits for its spread because of the exploitation of the lower hierarchical unit. This interactive trade-off shapes the population biology of antibiotic resistance, a composed-complex array of the independent “population biologies.” Antibiotics modify the abundance and the interactive field of each of these units. Antibiotics increase the number and evolvability of “clinical” antibiotic resistance genes, but probably also many other genes with different primary functions but with a resistance phenotype present in the environmental resistome. Antibiotics influence the abundance, modularity, and spread of integrons, transposons, and plasmids, mostly acting on structures present before the antibiotic era. Antibiotics enrich particular bacterial lineages and clones and contribute to local clonalization processes. Antibiotics amplify particular genetic exchange communities sharing antibiotic resistance genes and platforms within microbiomes. In particular human or animal hosts, the microbiomic composition might facilitate the interactions between evolutionary units involved in antibiotic resistance. The understanding of antibiotic resistance implies expanding our knowledge on multi-level population biology of bacteria.
antibiotics; resistance; population biology; multi-level selection; evolution; evolvability; resistome; microbiome
In eukaryotic virus systems, infection leads to induction of membranous compartments in which replication occurs. Virus-encoded subunits of the replication complex mediate its interaction with membranes. As replication platforms, RNA viruses use the cytoplasmic surfaces of different membrane compartments, e.g., endoplasmic reticulum (ER), Golgi, endo/lysosomes, mitochondria, chloroplasts, and peroxisomes. Closterovirus infections are accompanied by formation of multivesicular complexes from cell membranes of ER or mitochondrial origin. So far the mechanisms for vesicles formation have been obscure. In the replication-associated 1a polyprotein of Beet yellows virus (BYV) and other closteroviruses, the region between the methyltransferase and helicase domains (1a central region (CR), 1a CR) is marginally conserved. Computer-assisted analysis predicts several putative membrane-binding domains in the BYV 1a CR. Transient expression of a hydrophobic segment (referred to here as CR-2) of the BYV 1a in Nicotiana benthamiana led to reorganization of the ER and formation of ~1-μm mobile globules. We propose that the CR-2 may be involved in the formation of multivesicular complexes in BYV-infected cells. This provides analogy with membrane-associated proteins mediating the build-up of “virus factories” in cells infected with diverse positive-strand RNA viruses (alpha-like viruses, picorna-like viruses, flaviviruses, and nidoviruses) and negative-strand RNA viruses (bunyaviruses).
RNA virus replication; membrane vesicles; virus replication factory; endoplasmic reticulum modification; intracellular traffic
The Naica Mine in northern Mexico is famous for its giant gypsum crystals, which may reach up to 11 m long and contain fluid inclusions that might have captured microorganisms during their formation. These crystals formed under particularly stable geochemical conditions in cavities filled by low salinity hydrothermal water at 54–58°C. We have explored the microbial diversity associated to these deep, saline hydrothermal waters collected in the deepest (ca. 700–760 m) mineshafts by amplifying, cloning and sequencing small-subunit ribosomal RNA genes using primers specific for archaea, bacteria, and eukaryotes. Eukaryotes were not detectable in the samples and the prokaryotic diversity identified was very low. Two archaeal operational taxonomic units (OTUs) were detected in one sample. They clustered with, respectively, basal Thaumarchaeota lineages and with a large clade of environmental sequences branching at the base of the Thermoplasmatales within the Euryarchaeota. Bacterial sequences belonged to the Candidate Division OP3, Firmicutes and the Alpha- and Beta-proteobacteria. Most of the lineages detected appear autochthonous to the Naica system, since they had as closest representatives environmental sequences retrieved from deep sediments or the deep subsurface. In addition, the high GC content of 16S rRNA gene sequences belonging to the archaea and to some OP3 OTUs suggests that at least these lineages are thermophilic. Attempts to amplify diagnostic functional genes for methanogenesis (mcrA) and sulfate reduction (dsrAB) were unsuccessful, suggesting that those activities, if present, are not important in the aquifer. By contrast, genes encoding archaeal ammonium monooxygenase (AamoA) were amplified, suggesting that Naica Thaumarchaeota are involved in nitrification. These organisms are likely thermophilic chemolithoautotrophs adapted to thrive in an extremely energy-limited environment.
aerobic ammonium oxidation; Candidate Division OP3; GC content; hydrothermal; Thaumarchaeota; thermophile; Thermoplasmatales
Lactobacillus helveticus is one of the species of lactic acid bacteria (LAB) most commonly used in the production of fermented milk beverages and some types of hard cheese. The versatile nature of this bacterium is based on its highly efficient proteolytic system consisting of cell-envelope proteinases (CEPs), transport system and intracellular peptidases. Besides use of L. helveticus in cheese processing, the production of fermented milk preparations with health promoting properties has become an important industrial application. Studies have shown that fermented dairy products are able to decrease blood pressure, stimulate the immune system, promote calcium absorption, and exert an anti-virulent effect against pathogens. These beneficial effects are produced by a variety of peptides released during the hydrolysis of milk proteins by the proteolytic system of L. helveticus, which provides the bacterium with its nutritional requirements for growth. In recent years, studies have focused on understanding the factors that affect the kinetics of milk protein hydrolysis by specific strains and have concentrated on the effect of pH, temperature, growth phase, and matrix composition on the bacterial enzymatic system. This review focuses on the role of the proteolytic system of L. helveticus in the production of bioactive compounds formed during fermentation of dairy products. Taking advantage of the powerful proteolytic system of this bacterium opens up future opportunities to search for novel food-derived compounds with potential health promoting properties.
proteolytic; Lactobacillus; helveticus; milk; proteins
In Hawaii, common green ti plants (Cordyline fruticosa L.) have been shown to harbor Cordyline virus 1 (CoV-1) which, along with Little cherry virus 1 (LChV-1), and Grapevine leafroll-associated virus 7 (GLRaV-7), form a distinct clade within the family Closteroviridae. Preliminary work has indicated that, aside from CoV-1, three additional closteroviruses may infect common green ti plants in Hawaii. In this study, pyrosequencing was used to characterize the genomes of closteroviruses infecting a single common green ti plant. The sequence data confirmed the presence of CoV-1 as well as three additional closteroviruses. Although all four viruses had the same general genome organization, the sequence divergence between the RNA-dependent RNA polymerase, heat shock protein 70 homolog, and coat protein ranged from 22 to 61%, indicating these represent four distinct closterovirus species. The names CoV-2, CoV-3, and CoV-4 are proposed for the three new viruses. Phylogenetic analyses placed CoV-2, CoV-3, and CoV-4 in the same clade as CoV-1, LChV-1, and GLRaV-7.
pyrosequencing; Closteroviridae; Velarivirus, Cordyline; ti ringspot