Showing papers in "Environmental Microbiology Reports in 2013"

The Clermont Escherichia coli phylo‐typing method revisited: improvement of specificity and detection of new phylo‐groups

Abstract: There is extensive genetic substructure within the species Escherichia coli. In 2000 a simple triplex PCR method was described by Clermont and colleagues that enables an E. coli isolate to be assigned to one of the phylo-groups A, B1, B2 or D. The growing body of multi-locus sequence data and genome data for E. coli has refined our understanding of E. coli's phylo-group structure and eight phylo-groups are now recognized: seven (A, B1, B2, C, D, E, F) belong to E. coli sensu stricto, whereas the eighth is the Escherichia cryptic clade I. Here a new PCR-based method is developed that enables an E. coli isolate to be assigned to one of the eight phylo-groups and which allows isolates that are members of the other cryptic clades (II to V) of Escherichia to be identified. The development of the method is described and the method is validated. Over 95% of E. coli isolates can be correctly assigned to a phylo-group. Two collections of human faecal isolates were screened using the new phylo-group assignment method demonstrating that about 13% of E. coli isolates belong to the newly described phylo-groups C, E, F and clade I.

Conceptualizing functional traits and ecological characteristics of methane-oxidizing bacteria as life strategies.

Abstract: Methane-oxidizing bacteria (MOB) possess the ability to use methane for energy generation and growth, thereby, providing a key ecosystem service that is highly relevant to the regulation of the global climate. MOB subgroups have different responses to key environmental controls, reflecting on their functional traits. Their unique features (C1-metabolism, unique lipids and congruence between the 16S rRNA and pmoA gene phylogeny) have facilitated numerous environmental studies, which in combination with the availability of cultured representatives, yield the most comprehensive ecological picture of any known microbial functional guild. Here, we focus on the broad MOB subgroups (type I and type II MOB), and aim to conceptualize MOB functional traits and observational characteristics derived primarily from these environmental studies to be interpreted as microbial life strategies. We focus on the functional traits, and the conditions under which these traits will render different MOB subgroups a selective advantage. We hypothesize that type I and type II MOB generally have distinct life strategies, enabling them to predominate under different conditions and maintain functionality. The ecological characteristics implicated in their adopted life strategies are discussed, and incorporated into the Competitor-Stress tolerator-Ruderal functional classification framework as put forward for plant communities. In this context, type I MOB can broadly be classified as competitor-ruderal while type II MOB fit more within the stress tolerator categories. Finally, we provide an outlook on MOB applications by exemplifying two approaches where their inferred life strategies could be exploited thereby, putting MOB into the context of microbial resource management.

The roles of extracellular DNA in the structural integrity of extracellular polymeric substance and bacterial biofilm development.

Abstract: Bacteria adhere to natural and engineered surfaces and develop into mature biofilms encased in self-produced extracellular polymeric substances (EPSs). EPS consists of polysaccharides, proteins, metabolites and extracellular DNA (eDNA). Extracellular DNA release by bacteria is mediated by both quorum-sensing (QS)-dependent and -independent mechanisms. Quorum-sensing-independent mechanisms are responsible for basal levels of eDNA release, whereas QS-dependent mechanisms control the production of prophages, phenazines and proteins involved in cell lysis and subsequent release of elevated amounts of eDNA. Extracellular DNA binds with other biopolymers such as polysaccharides, proteins or metabolites like phenazines, thereby providing structural integrity to EPS. Extracellular DNA promotes attractive acid-base interactions between bacterial cells and between bacteria and surfaces. It therefore plays an essential structural role in stabilising biofilms and protecting bacterial cells from physical and chemical challenges. Accordingly, with current knowledge, it becomes clear that targeting and destroying eDNA in bacterial EPS is a promising strategy for treatment of bacterial-associated infections in a medical context and biofilm control on surfaces to prevent biocorrison in an engineering context. In contrast, the addition of DNA can be applied to engineering of biofilms for beneficial purposes such as remediation of environmental pollutants and electricity or fuel production in bioelectrochemical systems or bioreactors.

Nosema ceranae (Microsporidia), a controversial 21st century honey bee pathogen

Abstract: Summary The worldwide beekeeping sector has been facing a grave threat, with losses up to 100–1000 times greater than those previously reported. Despite the scale of this honey bee mortality, the causes underlying this phenomenon remain unclear, yet they are thought to be multifactorial processes. Nosema ceranae, a microsporidium recently detected in the European bee all over the world, has been implicated in the global phenomenon of colony loss, although its role remains controversial. A review of the current knowledge about this pathogen is presented focussing on discussion related with divergent results, trying to analyse the differences specially based on different methodologies applied and divisive aspects on pathology while considering a biological or veterinarian point of view. For authors, the disease produced by N. ceranae infection cannot be considered a regional problem but rather a global one, as indicated by the wide prevalence of this parasite in multiple hosts. Not only does this type of nosemosis causes a clear pathology on honeybees at both the individual and colony levels, but it also has significant effects on the production of honeybee products.

Strict vegetarian diet improves the risk factors associated with metabolic diseases by modulating gut microbiota and reducing intestinal inflammation.

Abstract: Low-grade inflammation of the intestine results in metabolic dysfunction, in which dysbiosis of the gut microbiota is intimately involved. Dietary fibre induces prebiotic effects that may restore imbalances in the gut microbiota; however, no clinical trials have been reported in patients with metabolic diseases. Here, six obese subjects with type 2 diabetes and/or hypertension were assigned to a strict vegetarian diet (SVD) for 1 month, and blood biomarkers of glucose and lipid metabolisms, faecal microbiota using 454-pyrosequencing of 16S ribosomal RNA genes, faecal lipocalin-2 and short-chain fatty acids were monitored. An SVD reduced body weight and the concentrations of triglycerides, total cholesterol, low-density lipoprotein cholesterol and haemoglobin A1c, and improved fasting glucose and postprandial glucose levels. An SVD reduced the Firmicutes-to-Bacteroidetes ratio in the gut microbiota, but did not alter enterotypes. An SVD led to a decrease in the pathobionts such as the Enterobacteriaceae and an increase in commensal microbes such as Bacteroides fragilis and Clostridium species belonging to clusters XIVa and IV, resulting in reduced intestinal lipocalin-2 and short-chain fatty acids levels. This study underscores the benefits of dietary fibre for improving the risk factors of metabolic diseases and shows that increased fibre intake reduces gut inflammation by changing the gut microbiota.

Distribution of antibiotic resistance genes in glacier environments.

Abstract: Antibiotic resistance genes are biologically transmitted from microorganism to microorganism in particular micro-environments where dense microbial communities are often exposed to an intensive use of antibiotics, such as intestinal microflora, and the soil microflora of agricultural fields. However, recent studies have detected antibiotic-resistant bacteria and/or antibiotic resistance genes in the natural environment geographically isolated from such areas. Here we sought to examine the prevalence of antibiotic resistance genes in 54 snow and ice samples collected from the Arctic, Antarctic, Central Asia, North and South America and Africa, to evaluate the level of these genes in environments supposedly not affected by anthropogenic factors. We observed a widespread distribution of antibiotic resistance genes in samples from various glaciers in Central Asia, North and South America, Greenland and Africa. In contrast, Antarctic glaciers were virtually free from these genes. Antibiotic resistance genes, of both clinical (i.e. aac(3), blaIMP) and agricultural (i.e. strA and tetW) origin, were detected. Our results show regional geographical distribution of antibiotic resistance genes, with the most plausible modes of transmission through airborne bacteria and migrating birds.

Syntrophic Growth with Direct Interspecies Electron Transfer as the Primary Mechanism for Energy Exchange

Abstract: Direct interspecies electron transfer (DIET) through biological electrical connections is an alternative to interspecies H-2 transfer as a mechanism for electron exchange in syntrophic cultures. However, it has not previously been determined whether electrons received via DIET yield energy to support cell growth. In order to investigate this, co-cultures of Geobacter metallireducens, which can transfer electrons to wild-type G.sulfurreducens via DIET, were established with a citrate synthase-deficient G.sulfurreducens strain that can receive electrons for respiration through DIET only. In a medium with ethanol as the electron donor and fumarate as the electron acceptor, co-cultures with the citrate synthase-deficient G.sulfurreducens strain metabolized ethanol as fast as co-cultures with wild-type, but the acetate that G.metallireducens generated from ethanol oxidation accumulated. The lack of acetate metabolism resulted in less fumarate reduction and lower cell abundance of G.sulfurreducens. RNAseq analysis of transcript abundance was consistent with a lack of acetate metabolism in G.sulfurreducens and revealed gene expression levels for the uptake hydrogenase, formate dehydrogenase, the pilus-associated c-type cytochrome OmcS and pili consistent with electron transfer via DIET. These results suggest that electrons transferred via DIET can serve as the sole energy source to support anaerobic respiration.

Dickeya ecology, environment sensing and regulation of virulence programme.

Abstract: The pectinolytic Dickeya spp are soft-rot Gram-negative bacteria that cause severe disease in a wide range of plant species In recent years, there has been an increase in the damage caused by Dickeya in potato crops in Europe Soft-rot symptoms are due to the production and secretion of degradative enzymes that destroy the plant cell wall However, an efficient colonization of the host plant requires many additional bacterial factors, including elements in the early stages allowing for the adhesion and penetration of the bacteria in the plant and different elements in the intermediate stages, involved in the adaptation to the new growth conditions encountered in the host Dickeya pathogenicity is clearly a multifactorial process, and successful infection by these bacteria requires a temporal coordination of survival and virulence gene expression This involves the ancestral nucleoid-associated proteins, Fis and H-NS, and modifications of DNA topology, as well as various specific regulatory systems, including a new quorum-sensing pathway and regulators that sense the bacterial metabolic status or environmental stresses This review presents new information concerning the ecology of Dickeya and the strategies used by this bacterium to coordinate its survival and virulence programmes during infection

Restructuring of the amphibian gut microbiota through metamorphosis

Abstract: Summary Vertebrates maintain complex symbioses with a diverse community of microbes residing within their guts. The microbial players in these symbioses differ between major taxa of vertebrates, such that fish and amniotes maintain notably different communities. To date, there has not been a culture-independent inventory of an amphibian gut microbial community. Here, we compared gut microbial communities of tadpoles and frogs of the Northern leopard frog (Lithobates pipiens). We utilized Illumina sequencing, which allowed us to inventory more than 450 000 microbial sequences. We found that tadpoles and frogs differ markedly in the composition of their gut microbial communities, with tadpoles maintaining a community more similar to fish, whereas the frog community resembles that of amniotes. Additionally, frogs maintain a community with lower phylogenetic diversity compared with tadpoles. The significant restructuring ofthemicrobiotaislikelyduetochangesindietaswell as the large reorganization of the intestinal organ during metamorphosis. Overall, we propose that amphibians represent an important system in which to study regulation and selection of gut microbial communities.

Bacterial communities associated with Microcystis colonies differ from free-living communities living in the same ecosystem

Abstract: The search for a better understanding of why cyanobacteria often dominate phytoplankton communities in eutrophic freshwater ecosystems has led to a growing interest in the interactions between cyanobacteria and bacteria. Against this background, we studied the location of bacteria within Microcystis colonies, and compared the structural and phylogenetic diversity of Microcystis-attached and free-living bacterial communities living in the same French lake, the Villerest reservoir. Using transmission electron microscopy, we show that most of the bacteria inside the colonies were located close to detrital materials that probably resulted from lysis of Microcystis cells. The 16S rRNA sequencing approach revealed a clear distinction between the attached and free-living communities at the levels of both their general structure and their operational taxonomic unit (OTU) composition. In particular, Microcystis colonies appeared to be depleted of Actinobacteria, but conversely enriched in Gammaproteobacteria, in particular when the bloom was declining. At the OTU level, a clear distinction was also found between attached and free-living bacteria, and new clades were identified among our sequences. All these findings suggest that Microcystis colonies constitute a distinct habitat for bacteria living in freshwater ecosystems, and that direct and indirect interactions (cell lysis, nutrient recycling, etc.) may occur between them inside these colonies.

Consequences of increased temperature and acidification on bacterioplankton community composition during a mesocosm spring bloom in the Baltic Sea.

Abstract: Despite the paramount importance of bacteria for biogeochemical cycling of carbon and nutrients, little is known about the potential effects of climate change on these key organisms. The consequenc ...

Bioenergetics of photoheterotrophic bacteria in the oceans

Abstract: Photoheterotrophic microbes, such as proteorhodopsin (PR)-based phototrophic (PRP) and aerobic anoxygenic phototrophic (AAP) bacteria, are well known to be abundant in the oceans, potentially playing unique roles in biogeochemical cycles. However, the contribution of phototrophy to the energy requirements of these bacteria has not been quantitatively examined to date. To better understand the implications of photoheterophy in the oceans, we calculated energy benefits and costs of phototrophy and compared net benefits with maintenance costs. Benefits depend on the number of photosynthetic units (PSUs), absorption cross-section area of each PSU as function of wavelength, the in situ light quality, and the energy yield per absorbed photon. For costs we considered the energy required for the synthesis of pigments, amino acids and proteins in each PSU. Our calculations indicate that AAP bacteria harvest more light energy than do PRP bacteria, but the costs of phototrophy are much higher for AAP bacteria. Still, the net energy gained by AAP bacteria is often sufficient to meet maintenance costs, while that is not the case for PRP bacteria except with high light intensities and large numbers of proteorhodopsin molecules per cell. The low costs and simplicity of PR-based phototrophy explain the high abundance of proteorhodopsin genes in the oceans. However, even for AAP bacteria, the net energy yield of phototrophy is apparently too low to influence the distribution of photoheterotrophic bacteria among various marine systems.

Temporal stability of the mouse gut microbiota in relation to innate and adaptive immunity.

Abstract: Summary Gut microbial community properties of mammals are thought to be partly shaped by a combination of host immunity and environmental factors, but their relative importance is not firmly established. To address this gap, we first characterized the faecal bacteria of mice with a functioning immune system (wild-type, WT), mice with defective immune responses (CD45), mice lacking an adaptive immune system (RAG), and mice with both immune dysfunctions (45RAG). Using fingerprinting of 16S rRNA genes, we observed significant differences in gut microbiota composition across all mouse strains (P 0.05). Time-series analysis indicated that the communities of cohoused mice changed directionally as opposed to the relatively stable communities of non-cohoused controls. When we considered only taxonomic membership, it was the communities of CD45 non-cohoused mice that experienced the highest rate of change. Rather than be governed by fluctuations in the relative abundance of taxa, we suggest that CD45-regulated immune responses either are stimulated by the presence of bacteria per se or promote temporal stability by selecting for the occurrence of specific taxa.

Evidence of species recruitment and development of hot desert hypolithic communities

Abstract: Innovation Fund UID 71682(PhD. scholarship for TPM), the National Research Fund of South Africa and the University of the Western Cape (T.P.M, A.V, I.M.T, and D.A.C). D.C.L. and S.B.P. were funded by the Hong Kong Research Grants Council (Grant number HKU7733/08HKU7763/10).

Commensal Escherichia coli strains in Guiana reveal a high genetic diversity with host‐dependant population structure

Abstract: Summary We undertook a large-scale epidemiological survey of commensal Escherichia coli in Trois-Sauts, an iso- lated village located in the south of French Guiana where human population exchanges are restricted and source of antibiotics controlled. Stools from 162 Wayampi Amerindians and rectal swabs from 33 human associated and 198 wild animals were col- lected in the close proximity of the village. The preva- lence of E. coli was decreasing from humans (100%) to human associated (64%) and wild (45%) animals. A clear genetic structure between these three E. coli populations was observed with human strains belonging very rarely to B2 phylogroup (3.7%), exhib- iting few virulence genes and bacteriocins but being antibiotic resistant whereas wild animal strains were characterized by 46.1% of B2 phylogroup belonging, with very unique and infrequent sequence types, numerous extraintestinal genes and bacteriocins but no antibiotic resistance; the human-associated animal strains being intermediate. Furthermore, an unexpected genetic diversity was observed among the strains, as the housekeeping gene nucleotide diversity per site of the Trois-Sauts's strains was higher than the one of reference strains representa- tive of the known species diversity. The existence of such E. coli structured phylogenetic diversity within various hosts of a single localization has never been reported.

Live feed is not a major determinant of the microbiota associated with cod larvae (Gadus morhua).

Abstract: The gastrointestinal (GI) tract of newly hatched fish is probably colonized by bacteria present in the water, but how environmental and internal factors affect the development of the GI microbiota is poorly understood. In this study, we investigated the effect of diet and of rearing in separate tanks on the cod larval microbiota. Cod larvae were fed three different live feed diets. For each diet, larvae were reared in three replicate tanks. The microbial communities were investigated for water, live feed and individual larvae using a PCR/DGGE (Denaturing Gradient Gel Electrophoresis) strategy. Statistical tests were applied to investigate differences in the larval microbiota between groups of individuals. We found no differences in the larval microbiota due to diet after 8 dph (days post hatching). Moreover, the larval microbiota was similar at 17 and 32 dph, despite a change in live feed at 18 dph. The larval microbiota was generally more similar to the water microbiota than to live feed microbiota. We further found that rearing of larvae in replicate tanks with identical diet could result in significant differences in larval microbiota. These findings indicate that diet does not entail major changes to the composition of cod larval microbiota.

Enrichment and isolation of acidophilic sulfate‐reducing bacteria from Tinto River sediments

Abstract: Although some acidophilic and alkaliphilic species have been described recently, most of the known sulfate-reducing bacteria (SRB) grow optimally at neutral pH. In this study, sulfate reduction was studied with sediment samples from the extremely acidic Tinto River basin. Stable enrichments of SRB were obtained at pH 4 with glycerol, methanol and hydrogen; at pH 4.5 with lactate and at pH 5.5 with succinate as substrates. Inhibition of sulfate reduction by organic acids below their pKa was observed. Cloning and sequencing of 16S rRNA gene showed that fermentative bacteria (Paludibacter spp., Oscillibacter spp.) and SRB (Thermodesulfobium spp., Desulfosporosinus spp., Desulfitobacterium spp., Desulfotomaculum spp.) were co-enriched. By repeated serial dilutions and streaking on agar plates, four strains of SRB belonging to the Firmicutes phylum were obtained. Two of them show 96% 16S rRNA gene sequence similarity with Desulfosporosinus acidophilus, and a third one with Desulfosporosinus orientis. Another isolate has just 93% rRNA gene sequence similarity with the Desulfosporosinus/Desulfitobacterium cluster and might represent a novel species within a novel genus. One of the Desulfosporosinus strains was further investigated showing maximum growth at pH 5.5, and a pH-dependent inhibitory effect of organic acids and sulfide.

Hyperthermophilic archaea produce membrane vesicles that can transfer DNA

Abstract: Thermococcales are hyperthermophilic archaea found in deep-sea hydrothermal vents. They have been recently reported to produce membrane vesicles (MVs) into their culture medium. Here, we have characterized the mode of production and determined the biochemical composition of MVs from two species of Thermococcales, Thermococcus gammatolerans and Thermococcus kodakaraensis. We observed that MVs are produced by a budding process from the cell membrane reminiscent of ectosome (microparticle) formation in eukaryotes. MVs and cell membranes from the same species have a similar protein and lipid composition, confirming that MVs are produced from cell membranes. The major protein present in cell membranes and MVs of both species is the oligopeptide binding protein OppA. This protein is also abundant in MVs from cells grown in minimal medium, suggesting that OppA could be involved in processes other than peptides scavenging. We have previously shown that MVs from Thermococcales harbour DNA and protect DNA against thermodegradation. Here, we show that T. kodakaraensis cells transformed with the shuttle plasmid pLC70 release MVs harbouring this plasmid. Notably, these MVs can be used to transfer pLC70 into plasmid-free cells, suggesting that MVs could be involved in DNA transfer between cells at high temperature.

Transcriptomic fingerprinting of Pseudomonas putida under alternative physiological regimes

Abstract: Summary Pseudomonas putida KT2440 is a metabolically versatile soil bacterium useful both as a model biodegradative organism and as a host of catalytic activities of biotechnological interest. In this report, we present the high-resolution transcriptome of P. putida cultured on different carbon sources as revealed by deep sequencing of the corresponding RNA pools. Examination of the data from growth on substrates that are processed through distinct pathways (glucose, fructose, succinate and glycerol) revealed that ≥ 20% of the P. putida genome is differentially expressed depending on the ensuing physiological regime. Changes affected not only metabolic genes but also a suite of global regulators, e.g. the rpoS sigma subunit of RNA polymerase, various cold-shock proteins and the three HU histone-like proteins. Specifically, the genes encoding HU subunit variants hupA, hupB and hupN drastically altered their expression levels (and thus their ability to form heterodimeric combinations) under the diverse growth conditions. Furthermore, we found that two small RNAs, crcZ and crcY, known to inhibit the Crc protein that mediates catabolite repression in P. putida, were both down-regulated by glucose. The raw transcriptomic data generated in this work is made available to the community through the Gene Expression Omnibus database.

Depth-discrete profiles of bacterial communities reveal pronounced spatio-temporal dynamics related to lake stratification

Abstract: Summary With this work we intend to stress the importance of considering discrete depth sampling for bacterial community analysis of stratified aquatic systems. Depth is a very important parameter to consider when sampling bacterial communities, as their abundance and composition can change within the distinct water layers. Stratified lakes are good model systems to study these connections since changes in environmental parameters can occur on a cm-scale at the thermo- and/or chemocline. Lake Grosse Fuchskuhle was sampled at discrete fine-scale depths at three time points covering a stage in which the lake was stratified and the beginning of winter mixing. In this paper we present the most abundant bacterial groups at the different depths sampled and also the most abundant operational taxonomic units (OTUs). Overall, oxygen was found to be an important factor shaping the microbial community composition.

Bacteriophages of Staphylococcus aureus efficiently package various bacterial genes and mobile genetic elements including SCCmec with different frequencies

Abstract: Staphylococcus aureus is a serious human and veterinary pathogen in which new strains with increasing virulence and antimicrobial resistance occur due to acquiring new genes by horizontal transfer. It is generally accepted that temperate bacteriophages play a major role in gene transfer. In this study, we proved the presence of various bacterial genes of the S. aureus COL strain directly within the phage particles via qPCR and quantified their packaging frequency. Nonparametric statistical analysis showed that transducing bacteriophages 11, 80 and 80lpha of serogroup B, in contrast to serogroup A bacteriophage 81, efficiently package selected chromosomal genes localized in 4 various loci of the chromosome and 8 genes carried on variable elements like staphylococcal cassette chromosome SCCmec, staphylococcal pathogenicity island SaPI1, genomic islands Saalpha and Sabeta, and plasmids with various frequency. Bacterial gene copy number per ng of DNA isolated from phage particles ranged between 1.05x10E2 for the tetK plasmid gene and 3.86x10E5 for the SaPI1 integrase gene. The new and crucial finding that serogroup B bacteriophages can package concurrently ccrA1 (1.16x10E4) and mecA (1.26x10E4) located at SCCmec type I into their capsids indicates that generalized transduction plays an important role in the evolution and emergence of new methicillin-resistant clones.

Apoptosis in the pathogenesis of Nosema ceranae (Microsporidia: Nosematidae) in honey bees (Apis mellifera).

Abstract: Nosema ceranae is a parasite of the epithelial ventricular cells of the honey bee that belongs to the microsporidian phylum, a biological group of single-cell, spore-forming obligate intracellular parasites found in all major animal lineages. The ability of host cells to accommodate a large parasitic burden for several days suggests that these parasites subvert the normal host cells to ensure optimal environmental conditions for growth and development. Once infected, cells can counteract the invasive pathogen by initiating their own death by apoptosis as a defence strategy. To determine whether N. ceranae blocks apoptosis in infected ventricular cells, cell death was assessed in sections of the ventriculum from experimentally infected honey bees using the TUNEL assay and by immunohistochemistry for caspase-3. Ventricular epithelial cells from infected bees were larger than those in the uninfected control bees, and they contained N. ceranae at both mature and immature stages in the cytoplasm. Apoptotic nuclei were only observed in some restricted areas of the ventriculum, whereas apoptosis was typically observed throughout the epithelium in uninfected bees. Indeed, the apoptotic index was higher in uninfected versus infected ventriculi. Our results suggested that N. ceranae prevents apoptosis in epithelial cells of infected ventriculi, a mechanism possible designed to enhance parasite development.

Arabinogalactan and fructo-oligosaccharides have a different fermentation profile in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®)

Abstract: Current prebiotics, such as fructo-oligosaccharides (FOS), are limited in their persistence in the distal colon and are predominantly fermented in the proximal colon. In order to identify a potential alternative, the differences in the fermentation profile of arabinogalactan (AG) and FOS have been assessed in the Simulator of the Human Intestinal Microbial Ecosystem. The effect of each product on the composition and activity of the microbial community was analysed during a 3-week treatment period at a dose of 5 g day(-1). While FOS indeed was mainly fermented in the simulated proximal colon, AG was still available for fermentation in the simulated distal colon as shown by pH profiles, size exclusion chromatography and analyses of specific enzymatic activities. As a consequence, the main effect of the products (increase in propionate and butyrate and decrease in ammonium production) occurred in different intestinal areas. DGGE and qPCR analyses confirmed that the main modulation of the microbiota by the two products occurred in different areas of the gut. AG was associated with a statistically significant increase in the concentration of total bacteria, Bacteroidetes, Faecalibacterium prausnitzii, a delayed bifidogenic effect and a decrease of the pathogenic Clostridium perfringens. FOS led to a strong lactobacillogenic effect.

Near-future ocean acidification causes differences in microbial associations within diverse coral reef taxa.

Abstract: Summary: Microorganisms form symbiotic partnerships with a diverse range of marine organisms and can be critical to the health and survival of their hosts. Despite the importance of these relationships, the sensitivity of symbiotic microbes to ocean acidification (OA) is largely unknown and this needs to be redressed to adequately predict marine ecosystem resilience in a changing climate. We adopted a profiling approach to explore the sensitivity of microbes associated with coral reef biofilms and representatives of three ecologically important calcifying invertebrate phyla [corals, foraminifera and crustose coralline algae (CCA)] to OA. The experimental design for this study comprised four pHs consistent with current IPCC predictions for the next few centuries (pH 8.1, 7.9, 7.7, 7.5); these pH/pCO conditions were produced in flow-through aquaria using CO bubbling. All reduced pH/increased pCO treatments caused clear differences in the microbial communities associated with coral, foraminifera, CCA and reef biofilms over 6 weeks, while no visible signs of host stress were detected over this period. The microbial communities of coral, foraminifera, CCA and biofilms were significantly different between pH8.1 (pCO=464μatm) and pH7.9 (pCO=822μatm), a concentration likely to be exceeded by the end of the present century. This trend continued at lower pHs/higher pCO. 16S rRNA gene sequencing revealed variable and species-specific changes in the microbial communities with no microbial taxa consistently present or absent from specific pH treatments. The high sensitivity of coral, foraminifera, CCA and biofilm microbes to OA conditions projected to occur by 2100 is a concern for reef ecosystems and highlights the need for urgent research to assess the implications of microbial shifts for host health and coral reef processes.

In situ interactions between photosynthetic picoeukaryotes and bacterioplankton in the Atlantic Ocean: evidence for mixotrophy

Abstract: Heterotrophic bacterioplankton, cyanobacteria and phototrophic picoeukaryotes (< 5 μm in size) numerically dominate planktonic oceanic communities. While feeding on bacterioplankton is often attributed to aplastidic protists, recent evidence suggests that phototrophic picoeukaryotes could be important bacterivores. Here, we present direct visual evidence from the surface mixed layer of the Atlantic Ocean that bacterioplankton are internalized by phototrophic picoeukaryotes. In situ interactions of phototrophic picoeukaryotes and bacterioplankton (specifically Prochlorococcus cyanobacteria and the SAR11 clade) were investigated using a combination of flow cytometric cell sorting and dual tyramide signal amplification fluorescence in situ hybridization. Using this method, we observed plastidic Prymnesiophyceae and Chrysophyceae cells containing Prochlorococcus, and to a lesser extent SAR11 cells. These microscopic observations of in situ microbial trophic interactions demonstrate the frequency and likely selectivity of phototrophic picoeukaryote bacterivory in the surface mixed layer of both the North and South Atlantic subtropical gyres and adjacent equatorial region, broadening our views on the ecological role of the smallest oceanic plastidic protists.

Plant flavonoids target Pseudomonas syringae pv. tomato DC3000 flagella and type III secretion system.

Abstract: Summary Flavonoids are among the most abundant plant sec- ondary metabolites involved in plant protection against pathogens, but micro-organisms have devel- oped resistance mechanisms to those compounds. We previously demonstrated that the MexAB-OprM efflux pump mediates resistance of Pseudomonas syringae pv. tomato (Pto) DC3000 to flavonoids, facili- tating its survival and the colonization of the host. Here, we have shown that tomato plants respond to Pto infection producing flavonoids and other phe- nolic compounds. The effects of flavonoids on key traits of this model plant-pathogen bacterium have also been investigated observing that they reduce Pto swimming and swarming because of the loss of fla- gella, and also inhibited the expression and assembly of a functional type III secretion system. Those effects were more severe in a mutant lacking the MexAB- OprM pump. Our results suggest that flavonoids inhibit the function of the GacS/GacA two-component system, causing a depletion of rsmY RNA, therefore affecting the synthesis of two important virulence factors in Pto DC3000, flagella and the type III secre- tion system. These data provide new insights into the flavonoid role in the molecular dialog between host and pathogen.

Salt deliquescence drives photosynthesis in the hyperarid Atacama Desert

Abstract: Summary Endolithic cyanobacteria are found in halite nodules in the hyperarid core of the Atacama Desert. Using Pulse Amplitude Modulated Fluorometry, we show here that photosynthetic systems of these cyanobacteria become active when the relative humidity rises above 70% and the salt becomes wet by way of deliquescence. This is the first evidence of active metabolism in the hyperarid core of the Atacama, and supports the view of a microbial community sustained by deliquescence. Our results expand the water activity envelope of life on Earth.

The transition from freshwater to marine iron‐oxidizing bacterial lineages along a salinity gradient on the Sheepscot River, Maine, USA

Abstract: Oxygen-dependent, neutrophilic iron-oxidizing bacteria (FeOB) are important drivers of iron transformations in marine and freshwater environments. Despite remarkable similarities in physiology and morphotype, known freshwater and marine FeOB are clustered in different classes of Proteobacteria; freshwater FeOB in the Betaproteobacteria and marine FeOB in the Zetaproteobacteria. To determine effects of salinity on these microbes, we examined the mineral biosignatures and molecular ecology of bacteria in FeOB mats collected along an estuarine salinity gradient. Light microscopy and scanning electron microscopy analyses showed the presence of iron oxide stalk and sheath structures in both freshwater and saline iron mats. Results of tagged pyrosequencing, quantitative PCR and fluorescent in situ hybridization, all based on the small subunit rRNA gene, confirmed Zetaproteobacteria were not present in freshwater mats, but were in saline mats at salinities down to 5‰. Among the Betaproteobacteria, Leptothrix spp. were only found in the freshwater mat. Gallionella spp. were limited to freshwater and low salinity mats (< 5‰). Sideroxydans sp. were salt tolerant; however, their relative abundance decreased with increasing salinity. These results suggest salinity is important in shaping the population biology of iron mat communities, and some coexistence between marine and freshwater populations occurs in brackish waters.

Using stable isotope probing to obtain a targeted metatranscriptome of aerobic methanotrophs in lake sediment

Abstract: In this study, we demonstrate the possibility of obtaining a targeted metatranscriptome from a functional group of microorganisms using a stable isotope probing (SIP) approach. Methanotrophs in lake sediment were labelled using (13)CH4, and both labelled and unlabelled-RNA were isolated and sequenced by 454 pyrosequencing. The unlabelled metatranscriptome had a large diversity of bacterial, archaeal, eukaryotic and viral sequences as expected from a diverse sediment community. In contrast, the labelled-RNA metatranscriptome was dominated by methanotroph sequences, particularly from Methylococcaceae. Transcripts of the methane monooxygenase genes pmoCAB were the most abundant in this metatranscriptome, and the pathway of methane oxidation to CO2 could be traced, as well as many steps in the ribulose monophosphate pathway for carbon assimilation. A high abundance of mRNA transcripts for proteins related to motility was detected, suggesting an importance for methanotrophs in lake sediments. This combination of SIP and metatranscriptomics should be broadly applicable, and will enhance the detection and identification of mRNA from target organisms.

The Gac regulon of Pseudomonas fluorescens SBW25

Abstract: Transcriptome analysis of Pseudomonas fluorescens SBW25 showed that 702 genes were differentially regulated in a gacS::Tn5 mutant, with 300 and 402 genes up- and downregulated respectively. Similar to the Gac regulon of other Pseudomonas species, genes involved in motility, biofilm formation, siderophore biosynthesis and oxidative stress were differentially regulated in the gacS mutant of SBW25. Our analysis also revealed, for the first time, that transcription of 19 rhizosphere-induced genes and of genes involved in type II secretion, (exo)polysaccharide and pectate lyase biosynthesis, twitching motility and an orphan non-ribosomal peptide synthetase (NRPS) were significantly affected in the gacS mutant. Furthermore, the gacS mutant inhibited growth of oomycete, fungal and bacterial pathogens significantly more than wild type SBW25. Since RP-HPLC analysis did not reveal any potential candidate metabolites, we focused on the Gac-regulated orphan NRPS gene cluster that was predicted to encode an eight-amino-acid ornicorrugatin-like peptide. Site-directed mutagenesis indicated that the encoded peptide is not involved in the enhanced antimicrobial activity of the gacS mutant but may function as a siderophore. Collectively, this genome-wide analysis revealed that a mutation in the GacS/A two-component regulatory system causes major transcriptional changes in SBW25 and significantly enhances its antimicrobial activities by yet unknown mechanisms.