Environmental microbiology

Escherichia coli, an important indicator of the presence of fecal material, was isolated from indoor and outdoor environments in Mexico City. The heterogeneity of E. coli was represented by 89 serotypes, most of them coming from settled-dust indoor samples; 21% of them presented antibiotic multiresistance. The numbers of plasmids were higher among the antibiotic-resistant strains. The results of this study suggest that intestinal infections produced by environmental strains could be of more epidemiological impact than previously thought.

Acetochlor is a herbicide widely used in corn production, whose frequent use has caused severe persistence in the soil causing alterations in the microbiota populations, which causes low yields and difficulty for the establishment of other crops, as well as generating threats to the ecosystem and people's health. For this reason, the purpose of this study is to isolate and identify bacterial microorganisms associated with soils with the presence of acetochlor in order to open a panorama towards the use of bioremediation as a biotechnology for the partial or total recovery of this resource. The project was carried out within the facilities of the Instituto de Ciencias Agropecuarias (ICAp), a corn producer who has frequently used acetochlor for weed control was located. Soil samples were taken from the plot and the isolation of microorganisms was carried out by dilution technique. Periodic readings were taken every 24 hours of incubation and five visually different colonies were isolated for purification. Morphological identification was carried out, most of which were different in at least one aspect, as well as Gram staining tests in which they were Gram-positive. This study may lay the foundation for the identification of a bacterial consortium that may have bioremedial applicability in the future.

ABSTRACTVancomycin-resistant enterococcci (VRE) in Europe are thought to have emerged partly due to the use of the glycopeptide avoparcin in animal husbandry. We compared the occurrence of VRE in geographical regions of Europe in which until 1997 large amounts of avoparcin were used (Spain, United Kingdom, and Denmark) with the occurrence of VRE in Sweden, where avoparcin was banned in 1986. We also studied the relatedness between VRE strains from different regions and habitats. In total, 2,580 samples were collected from humans, animals, and the environment (soil, sewage, recipient water). VRE resistant to 20 μg/ml vancomycin were identified in 8.2% of the samples and were found most frequently in raw and treated urban sewage samples (means, 71% and 36% of the samples, respectively), pig manure (17%), and hospital sewage (16%). The proportions of VRE-positive sewage samples were similar in Sweden, Spain, and the United Kingdom, whereas pig feces and manure were more often positive ...

En la búsqueda de fomentar nuevas estrategias para el control de vectores transmisores de enfermedades como Aedes aegypti y Ae. albopictus, se resalta el rol de la microbiota en la oviposición, en especial la presencia de bacterias del género Bacillus, los objetivos de este estudio fue comparar la cantidad y el tipo de bacterias cultivables de sumideros de agua lluvia con presencia y ausencia de larvas zancudos en el campus universitario de la Universidad del Valle sede Meléndez y determinar si las bacterias del género Bacillus predominan en sumideros con larvas, de modo que mediante la selección de seis sumideros (tres con larvas y tres sin larvas) en el campus Meléndez de la Universidad del Valle a los cuales se les midieron parámetros fisicoquímicos y se les realizaron análisis microbiológicos mediante recuento en placa, caracterización morfológica, tinción de Gram y pruebas bioquímicas, obteniendo a si que los sumideros con larvas presentaron mayor oxígeno disuelto y carga bacteriana, mientras que los sumideros sin larvas mostraron mayor diversidad bacteriana, predominando bacterias anaerobias facultativas. Se identificaron especies como Bacillus subtilis, B. cereus y B. pumilus, con una distribución diferencial según la presencia de larvas. En conclusión la composición bacteriana y las condiciones fisicoquímicas del agua influyen significativamente en la presencia de larvas de mosquito. Estos hallazgos refuerzan el papel ecológico de la microbiota y su potencial como herramienta en estrategias de control biológico en entornos urbanos.

A lexander and Turenne in their letter (1) almost completely reiterate their previous comments on our earlier article, which was published in Nucleic Acids Research (2), to which we replied; their letter and the rebuttal were subsequently published . In our earlier rebuttal, we clearly addressed all these issues and left no scope for revisiting them, and hence we are quite surprised that they did not even cite our original paper, their comments on this paper, or our earlier response in their latest letter. We are once again responding to their comments with a hope that there will be no further room for discussion on these issues. They state that the name "Mycobacterium indicus pranii" does not figure in the "List of Prokaryotic Names with Standing in Nomenclature" and that the designation M. indicus pranii does not conform to the binomial naming convention. This opinion is, in our view, irrelevant and nonsustainable. While most bacteria follow a binomial naming system, there are several examples of bacteria being named differently. M. avium paratuberculosis, from the mycobacterial family itself, is one such example. The fact that the name M. indicus pranii has three words does not take away its distinct morphological, biochemical, and genomic identity. Alexander's and Turenne's claim that they are unaware of any comparison of M. indicus pranii with a comprehensive panel of M. intracellulare or M. avium complex (MAC) reflects their ignorance (deliberate?) of published literature. We state once again that M. indicus pranii is very different from all known members of the MAC, including M. intracellulare, in various respects that include colony type, growth pattern, biochemical features, chemotaxonomic features, etc. (Table ). M. indicus pranii is a fast grower (6 to 8 days) compared to M. tuberculosis (Ͼ3 weeks) and members of the MAC complex (including M. intracellulare) (Ͼ2 weeks). M. indicus pranii shares several other biochemical characteristics usually associated with a rapid grower (like M. smegmatis and M. vaccae), such as the absence of pigmentation and the presence of nitrate reduction, aryl sulfatase (14 days), and catalase, to name a few. Fatty acid methyl ester (FAME) analysis is a highly sensitive indicator of uniqueness of a species and is used to define the precise taxonomic position (3). Our earlier comprehensive FAME analysis (4) and comparison with profiles in the Microbial Identification System (3) showed the presence of a unique metabolic machinery in M. indicus pranii very different from that in M. intracellulare and the rest of the organisms in the FAME database. Pathway analyses confirmed the presence of unique KEGG pathways in M. indicus pranii compared to M. intracellulare and M. avium, notably the lipopolysaccharide biosyn-

SummaryMessenger RNA can provide valuable insights into the variability of metabolic processes of microorganisms. However, due to uncertainties that include the stability of RNA, its application for activity profiling of environmental samples is questionable. We explored different factors affecting the decay rate of transcripts of three marine bacterial isolates using qPCR and determined mRNA half‐life time of specific bacterial taxa and of functional genes by metatranscriptomics of a coastal environmental prokaryotic community. The half‐life time of transcripts from 11 genes from bacterial isolates ranged from 1 to 46 min. About 80% of the analysed transcripts exhibited half‐live times shorter than 10 min. Significant differences were found in the half‐life time between mRNA and rRNA. The half‐life time of mRNA obtained from a coastal metatranscriptome ranged from 9 to 400 min. The shortest half‐life times of the metatranscriptome corresponded to transcripts from the same clusters ...

Given the growing concerns over human and animal health issues related to confined animal feeding operations, an in-depth examination is required to monitor for airborne bacteria and associated antibiotic resistance genes. Our 16S rRNA-based pyrosequencing revealed that the airborne microbial community skewed towards a higher abundance of Firmicutes (> 59.2%) and Bacteroidetes (4.2-31.4%) within the confinement buildings, while the office environment was predominated by Proteobacteria (55.2%). Furthermore, bioaerosols in the confinement buildings were sporadically associated with genera of potential pathogens, and these genera were more frequently observed in the bioaerosols of pig and layer hen confinement than the turkey confinement buildings and office environment. High abundances of tetracycline resistance genes (9.55 ¥ 10 2 to 1.69 ¥ 10 6 copies ng -1 DNA) were also detected in the bioaerosols sampled from confinement buildings. Bacterial lineages present in the poultry bioaerosols clustered apart from those present in the pig bioaerosols and among the different phases of pig production, suggesting that different livestock as well as production phase were associated with a distinct airborne microbial community. By understanding the diversity of biotic contaminants associated with the different confinement buildings, this study facilitates the implementation of better management strategies to minimize potential health impacts on both livestock and humans working in this environment.

A reciprocal cross-fostering model with an obese typical Chinese piglet breed and a lean Western breed was used to identify genetic and maternal effects on the acquisition and development gut bacteria from birth until after weaning. Pyrosequencing of 16S rRNA genes results revealed an age-and diet-dependent bacterial succession process in piglets. During the first 3 days after birth, the bacterial community was relatively simple and dominated by Firmicutes with 79% and 65% relative abundance for Meishan and Yorkshire piglets, respectively. During the suckling period until day 14, the piglet breed and the nursing mother lead to increasing differentiation of the fecal bacterial community, with specific bacteria taxa associated with breed, and others with the nursing sow most likely due to its milk composition. Although the effect of nursing mother and the breed were evident through the suckling period, the introduction of solid feed and subsequent weaning were the major events occurring that dominated succession of the gut microbiota in the early life of piglets. This piglet crossfostering model is a useful tool for studying the effects of diet, host genetics and the environment on the development and acquisition of the gut microbiota and over longer studies the subsequent impact on growth, health and performance of pigs.

Microbial communities associated with black band disease (BBD) in massive stony corals from the Northern Red Sea (Eilat) were examined for the first time using molecular tools and microscopy. A high microbial diversity was revealed in the affected tissue in comparison with the healthy area of the same colony. Microscopy revealed the penetration of cyanobacteria into the coral mesoglea and adjacent tissues. Cyanobacterial sequences from Red Sea BBD-affected corals formed a cluster with sequences previously identified from black band and red band diseased corals from the Indo-Pacific and Caribbean. In addition, 11 sequences belonging to the genus Vibrio were retrieved. This group was previously documented as pathogenic to corals. Sulfatereducing bacteria, a group known to be associated with BBD and produce toxic sulfide, were studied using specific primers for the amplification of the dissimilatory sulfite reductase gene (dsrA). This technique facilitated and improved the resolution of the study of diversity of this group. All the sequences obtained were closely related to sequences of the genus Desulfovibrio and 46% showed high homology to Desulfovibrio desulfuricans. The complex nature of BBD and the lack of success in isolating a single causative agent suggest that BBD may be considered a polymicrobial disease.

Peptide nucleic acid (PNA)-mediated PCR clamping (H. Ørum, P. E. Nielsen, M. Egholm, R. H. Berg, O. Buchardt, and C. Stanley, Nucleic Acids Res. 21:5332–5336, 1993) was introduced as a novel procedure to selectively amplify ribosomal DNAs (rDNAs) which are not frequently found in clone libraries generated by standard PCR from complex microbial consortia. Three different PNA molecules were used; two of these molecules (PNA-ALF and PNA-EUB353) overlapped with one of the amplification primers, whereas PNA-1114F hybridized to the middle of the amplified region. Thus, PCR clamping was achieved either by competitive binding between the PNA molecules and the forward or reverse primers (competitive clamping) or by hindering polymerase readthrough (elongation arrest). Gene libraries generated from mixed rDNA templates by using PCR clamping are enriched for clones that do not contain sequences homologous to the appropriate PNA oligomer. This effect of PCR clamping was exploited in the followi...

Metapopulation theory developed in terrestrial ecology provides applicable frameworks for interpreting the role of local and regional processes in shaping species distribution patterns. Yet, empirical testing of metapopulation models on microbial communities is essentially lacking. We determined regional bacterioplankton dynamics from monthly transect sampling in the Baltic Sea Proper using 16S rRNA gene sequencing. A strong positive trend was found between local relative abundance and occupancy of populations. Notably, the occupancy-frequency distributions were significantly bimodal with a satellite mode of rare endemic populations and a core mode of abundant cosmopolitan populations (e.g. Synechococcus, SAR11 and SAR86 clade members). Temporal changes in population distributions supported several theoretical frameworks. Still, bimodality was found among bacterioplankton communities across the entire Baltic Sea, and was also frequent in globally distributed datasets. Datasets spanning waters with widely different physicochemical characteristics or environmental gradients typically lacked significant bimodal patterns. When such datasets were divided into subsets with coherent environmental conditions, bimodal patterns emerged, highlighting the importance of positive feedbacks between local abundance and occupancy within specific biomes. Thus, metapopulation theory applied to microbial biogeography can provide novel insights into the mechanisms governing shifts in biodiversity resulting from natural or anthropogenically induced changes in the environment.

SummaryMetapopulation theory developed in terrestrial ecology provides applicable frameworks for interpreting the role of local and regional processes in shaping species distribution patterns. Yet, empirical testing of metapopulation models on microbial communities is essentially lacking. We determined regional bacterioplankton dynamics from monthly transect sampling in the Baltic Sea Proper using 16S rRNA gene sequencing. A strong positive trend was found between local relative abundance and occupancy of populations. Notably, the occupancy‐frequency distributions were significantly bimodal with a satellite mode of rare endemic populations and a core mode of abundant cosmopolitan populations (e.g. Synechococcus, SAR11 and SAR86 clade members). Temporal changes in population distributions supported several theoretical frameworks. Still, bimodality was found among bacterioplankton communities across the entire Baltic Sea, and was also frequent in globally distributed datasets. Dataset...

Metapopulation theory developed in terrestrial ecology provides applicable frameworks for interpreting the role of local and regional processes in shaping species distribution patterns. Yet, empirical testing of metapopulation models on microbial communities is essentially lacking. Here we determined regional bacterioplankton dynamics from monthly transect sampling in the Baltic Sea Proper (16 sites, 11 occasions, 2010-2011) using 16S rRNA gene pyrosequencing. A strong positive correlation was found between local relative abundance and occupancy of populations. Notably, the occupancy-frequency distributions (the number of populations occupying different number of sites) were significantly bimodal with a satellite mode of mostly rare endemic populations and a core mode of abundant cosmopolitan populations (e.g. Synechococcus, SAR11 and SAR86 clade members). Observed temporal changes in population distributions supported theoretical predictions that stochastic variation in local extin...

The methanogenic endosymbionts of anaerobic and micro-aerophilic protists represent the only known occurrence of intracellular archaea. Here, we present the first comparative genomics analysis of an intracellular archaeum. Thus, this analysis is a significant step forward in our understanding of the effects of the intracellular lifestyle on genomic characteristics and gene content in a domain where this otherwise has not been examined.

Here we investigated whether there is evidence of local adaptation in strains of an ancestrally marine dinoflagellate to the lacustrine environment they now inhabit (optimal genotypes) and/or if they have evolved phenotypic plasticity (a range of phenotypes). Eleven strains of Polarella glacialis were isolated and cultured from three different environments: the polar seas, a hyposaline and a hypersaline Antarctic lake. Local adaptation was tested by comparing growth rates of lacustrine and marine strains at their own and reciprocal site conditions. To determine phenotypic plasticity, we measured the reaction norm for salinity. We found evidence of both, limited local adaptation and higher phenotypic plasticity in lacustrine strains when compared with marine ancestors. At extreme high salinities, local lake strains outperformed other strains, and at extreme low salinities, strains from the hyposaline lake outperformed all other strains. The data suggest that lake populations may have evolved higher phenotypic plasticity in the lake habitats compared with the sea, presumably due to the high temporal variability in salinity in the lacustrine systems. Moreover, the interval of salinity tolerance differed between strains from the hyposaline and hypersaline lakes, indicating local adaptation promoted by different salinity.

Hurricanes have the potential to alter the structures of coastal ecosystems and generate pathogenladen floodwaters that threaten public health. To examine the impact of hurricanes on urban systems, we compared microbial community structures in samples collected after Hurricane Katrina and before and after Hurricane Rita. We extracted environmental DNA and sequenced small-subunit ribosomal RNA (SSU rRNA) gene clone libraries to survey microbial communities in floodwater, water and sediment samples collected from Lake Charles, Lake Pontchartrain, the 17th Street and Industrial Canals in New Orleans and raw sewage. Correspondence Analysis showed that microbial communities associated with sediments formed one cluster while communities associated with lake and Industrial Canal water formed a second. Communities associated with water from the 17th Street Canal and floodwaters collected in New Orleans showed similarity to communities in raw sewage and contained a number of sequences associated with possible pathogenic microbes. This suggests that a distinct microbial community developed in floodwaters following Hurricane Katrina and that microbial community structures as a whole might be sensitive indicators of ecosystem health and serve as "sentinels" of water quality in the environment.

Over the last few decades, molecular methods have vastly improved our ability to study the diversity of microbial communities. In molecular diversity surveys, the function of protists is often inferred from phylogeny. Yet these surveys are unable to distinguish between different trophic modes among closely related taxa. Here we present results from a culture-independent study linking bacterivory to the diversity of pelagic protists from 3 depths of a stratified mesotrophic lake. Bacteria were labeled with bromodeoxyuridine (BrdU) and added to lakewater samples; after incubation, total DNA was extracted from filtered samples. Part of the DNA extract was subjected to immunoprecipitation with anti-BrdU antibodies, and then both whole DNA and BrdU-labeled samples were analyzed using 454-pyrosequencing of the v9 region of 18S small subunit rRNA gene amplicons. The results show that a different community of protists exists at each depth, with limited overlap of taxonomic composition between depths. The community of BrdU-labeled protists, deemed putative bacterivores, is largely a subset of the community found in the whole DNA samples. Many of these BrdU-labeled taxa are poorly represented in GenBank and thus are probably rarely isolated and/or uncultured species. Several of the taxa identified as bacterivores are also phototrophs, highlighting the important role of mixotrophy among eukaryotic microbes. Definitive identity of functional traits among taxa requires careful experimentation, yet this method allows a first-pass assay of the trophic role of microbial eukaryotes from environmental samples.

The study of environmental samples requires a preservation system that stabilizes the sample structure, including cells and biomolecules. To address this fundamental issue, we tested the cell alive system (CAS)-freezing technique for subseafloor sediment core samples. In the CAS-freezing technique, an alternating magnetic field is applied during the freezing process to produce vibration of water molecules and achieve a stable, super-cooled liquid phase. Upon further cooling, the temperature decreases further, achieving a uniform freezing of sample with minimal ice crystal formation. In this study, samples were preserved using the CAS and conventional freezing techniques at 4, -20, -80 and -196 (liquid nitrogen) °C. After 6 months of storage, microbial cell counts by conventional freezing significantly decreased (down to 10.7% of initial), whereas that by CAS-freezing resulted in minimal. When Escherichia coli cells were tested under the same freezing conditions and storage for 2.5 m...

Organisms at hydrothermal vents inhabit discontinuous chemical "islands" along mid-ocean ridges, a scenario that may promote genetic divergence among populations. The 2003 discovery of mussels at the Lost City Hydrothermal Field provided a means of evaluating factors that govern the biogeography of symbiotic bacteria in the deep-sea. The unusual chemical composition of vent fluids, the remote location, and paucity of characteristic vent macrofauna at the site, raised the question of whether microbial symbioses existed at the extraordinary Lost City. And if so, how did symbiotic bacteria therein relate to those hosted by invertebrates at the closest known hydrothermal vents along the Mid-Atlantic Ridge (MAR)? To answer these questions, we performed microscopic and molecular analyses on the bacteria found within the gill tissue of Bathymodiolus mussels (Mytilidae, Bathymodiolinae) that were discovered at the Lost City. Here we show that Lost City mussels harbour chemoautotrophic and methanotrophic endosymbionts simultaneously. Furthermore, populations of the chemoautotrophic symbionts from the Lost City and two sites along the MAR are genetically distinct from each other, which suggests spatial isolation of bacteria in the deep-sea. These findings provide new insights into the processes that drive diversification of bacteria and evolution of symbioses at hydrothermal vents.

Between December 2010 and April 2012, intensive care unit (ICU) patients in our hospital were infrequently colonized with extended-spectrum b-lactamase-positive bacteria (ESBLs). We hypothesized that these ESBLs originated from patients' room sinks, and this was prospectively investigated by weekly culturing of patients and sinks during a 20-week period. ESBLs were isolated from all 13 sinks. Four patients became colonized with ESBLs that were genetically identical to ESBLs that had previously been isolated from the sink. One of these patients died of pneumonia caused by the ESBL. Transmission from sinks to patients was stopped by integrating self-disinfecting siphons to all sinks on the ICU.

To evaluate the respective contributions of patient-to-patient transmission and endogenous acquisition of Enterobacter aerogenes isolates, we conducted a prospective epidemiologic study in two intensive care units (ICUs) between May 1994 and April 1995. We collected a total of 185 E. aerogenes isolates: 130 from 51 patients in a surgical ICU (SICU), 45 from 26 patients in a medical ICU (MICU), and 10 from the environments in these two ICUs. All isolates were typed by random amplification of polymorphic DNA and enterobacterial repetitive intergenic consensus PCR. Among the 175 clinical isolate, we observed 40 different profiles by random amplification of polymorphic DNA and 36 different profiles by enterobacterial repetitive intergenic consensus PCR. We identified a ubiquitous and prevalent clone, corresponding to 58% of SICU and 41% of MICU clinical isolates. Three epidemiologically related strains were specific to each ICU and represented 17% of SICU and 24% of MICU clinical isolat...

We used mesocosm experiments to study the bacterioplankton community in a highly dynamic coastal ecosystem during four contrasting periods of the seasonal cycle: winter mixing, spring phytoplankton bloom, summer stratification and autumn upwelling. A correlation approach was used in order to measure the degree of coupling between the dynamics of major bacterial groups, heterotrophic carbon cycling and environmental factors. We used CARD-FISH to follow changes in the relative abundance of the most abundant groups of bacteria (Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes). Bacterial carbon flux-related variables included bacterial standing stock, bacterial production and microbial respiration. The environmental factors included both, biotic variables such as chlorophyll-a concentration, primary production, phytoplankton extracellular release, and abiotic variables such as the concentration of dissolved inorganic and organic nutrients. Rapid shifts in the dominant bacterial groups occurred associated to environmental changes and bacterial bulk functions. An alternation between Alphaproteobacteria and Bacteroidetes was observed associated to different phytoplankton growth phases. The dominance of the group Bacteroidetes was related to high bacterial biomass and production. We found a significant, non-spurious, linkage between the relative abundances of major bacterial groups and bacterial carbon cycling. Our results suggest that bacteria belonging to these major groups could actually share a function in planktonic ecosystems.

The water-borne pathogen Legionella pneumophila serogroup 1 is the most commonly reported etiologic agent of legionellosis. An analysis by sequence based typing using 7 genes, flaA, pilE, asd, mip, momp, proA and neuA of three environmental Legionella pneumophila serogroup 1 strains isolated from hot water network during the period 2009 2011, confirm that these strains were corresponding to L. pneumophila ST1/Paris’s in the region of Ouarzazate in Morocco. A typing method with this level of discriminatory power has great potential for assisting in epidemiological studies. The outcomes of this research that will be helpful to improve surveillance programs for legionellosis and encourage the authorities to take necessary measures of eradication.

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

Irrational antibiotic use contributes to the development of antibiotic resistance in bacteria, which is a major cause of healthcare-associated infections globally. Molecular research has shown that multiple resistance frequently develops from the uptake of pre-existing resistance genes, which are subsequently intensified under selective pressures. Resistant genes spread and are acquired through mobile genetic elements which are essential for facilitating horizontal gene transfer. MGEs have been identified as carriers of genetic material and are a significant player in evolutionary processes. These include insertion sequences, transposons, integrative and conjugative elements, plasmids, and genomic islands, all of which can transfer between and within DNA molecules. With an emphasis on pathogenic bacteria, this review highlights the salient features of the MGEs that contribute to the development and spread of antibiotic resistance. MGEs carry non-essential genes, including AMR and virulence genes, which can enhance the adaptability and fitness of their bacterial hosts. These elements employ evolutionary strategies to facilitate their replication and dissemination, thus enabling survival without positive selection for the harboring of beneficial genes.

Figure 1 : Illustration des produits de B. bruxellensis d'altération des vins. Parmi les altérations microbiennes des vins, la production des phénols volatils par la levure Brettanomyces bruxellensis (B. bruxellensis) est l'une des plus redoutées par le vinificateur et probablement l'une des plus décriées par le consommateur. En outre, les phénols volatils ne sont pas les seuls produits de B. bruxellensis qui peuvent nuire à la qualité du vin (Figure ) et qui font de cette levure l'ennemi numéro un des vinificateurs soucieux de produire un vin fin, fruité et de qualité. Initialement isolée de la bière (Clausen, 1905), la description de la levure B. bruxellensis dans le vin remonte au début de l'oenologie moderne (Agostino, 1950 ; Barret et al. 1950 ; Peynaud et Domercq, 1956). Mais ce n'est que relativement récemment que les microbiologistes du vin, sensibilisés par des consommateurs de plus en plus soucieux de la qualité du produit, se sont penchés sur cette problématique. Les premiers travaux menés sur la production du 4-éthylphénol et du 4-éthylgaïacol se sont focalisés sur B. bruxellensis. Rapidement B. bruxellensis fut décrite comme la seule espèce impliquée et son développement dans le vin comme la conséquence d'une contamination au chai et du non-respect des conditions élémentaires d'hygiène, si bien que les chais victimes de B. bruxellensis étaient aussitôt montrés du doigt. Depuis des études ont démontré que le problème des « Brett » était commun à de nombreux domaines malgré les efforts d'hygiène réalisés. La levure B. bruxellensis fait partie intégrante du consortium microbiologique oenologique (Medawar, 2003) au même titre que l'espèce Saccharomyces cerevisiae par exemple. Les études ont montré que B. bruxellensis était une levure particulièrement résistante aux contraintes oenologiques comme l'alcool, le SO2 et les bas pH. De plus, elle est peu exigeante d'un point de vue nutritionnel (Uscanga et al. 2000 ; Medawar, 2003) et s'adapte aussi bien à la présence d'oxygène qu'à son absence (Ciani et al. 2003 ; Du Toit et al. 2005). Les vinifications où les B. bruxellensis sont totalement absentes sont très rares, si bien que l'objectif n'est plus de n'avoir aucune B. bruxellensis dans son vin mais de limiter sa multiplication. La question de son origine reste toutefois posée. Pour cela plusieurs pistes ont été avancées, et, curieusement une origine au vignoble a longtemps était délaissée au profit du chai, probablement à cause de la difficulté d'étudier la microflore présente sur le raisin.

Petroleum-based plastics commonly and widely used on a daily basis are a threat to ecological health as they do not degrade in an ecologically feasible time frame. A class of natural polymers known as polyhydroxyalkanoates (PHAs) represents an up-and-coming alternative to petroleum-based materials, as they share properties similar to those of commodity plastics, such as polyethylene, polystyrene, among others, with the advantage of being biodegradable. PHAs are naturally produced by microorganisms under stress, and various farming practices have been proposed to be used for the synergistic and sustainable production of PHA for commercial purposes. Aquaculture has demonstrated particular potential for the production of PHA; however, a large struggle in commercializing these polymers is in procuring necessary feedstocks for manufacture outside of the laboratory environment. Through the coupling of PHA production and biofloc technology in aquaculture, the impediments to commercial exploitation can be potentially surmounted, while also providing for higher production efficiency in aquafarms. This mini-review covers the basic aspects of biofloc technology applied to aquaculture for the commercial production of PHA in large scale and offers a brief perspective on the next steps associated with the research and implementation of PHA production with biofloc technology.

Petroleum-based plastics commonly and widely used on a daily basis are a threat to ecological health as they do not degrade in an ecologically feasible time frame. A class of natural polymers known as polyhydroxyalkanoates (PHAs) represents an up-and-coming alternative to petroleum-based materials, as they share properties similar to those of commodity plastics, such as polyethylene, polystyrene, among others, with the advantage of being biodegradable. PHAs are naturally produced by microorganisms under stress, and various farming practices have been proposed to be used for the synergistic and sustainable production of PHA for commercial purposes. Aquaculture has demonstrated particular potential for the production of PHA; however, a large struggle in commercializing these polymers is in procuring necessary feedstocks for manufacture outside of the laboratory environment. Through the coupling of PHA production and biofloc technology in aquaculture, the impediments to commercial exploitation can be potentially surmounted, while also providing for higher production efficiency in aquafarms. This mini-review covers the basic aspects of biofloc technology applied to aquaculture for the commercial production of PHA in large scale and offers a brief perspective on the next steps associated with the research and implementation of PHA production with biofloc technology.

Paints have been used since ancient times and there several paints of varying chemical composition have been in use for domestic and industrial purposes. The effectiveness of the preservative used in the paint samples which is easily available in the market was evaluated against different microorganisms as the consequences of microbial deterioration have serious economic implications on the paint industry. The aim of this study was, therefore, to investigate the microbial quality of paints with a view to improving the shelf life of paint and paint products. This study was carried to evaluate the resistance of emulsion paints in the container against microorganisms such as Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Aspergillus niger and Candida albicans. It can be observed from this study that the concentration of preservative component in the emulsion paint is directly proportional to the inhibition of the bacterial growth irrespective of its pathogenicity.

In damp environments, indoor building materials are among the main proliferation substrates for microorganisms. Photocatalytic coatings, including nanoparticles of titanium dioxide (TiO2), could be a way to prevent microbial proliferation that grow on indoor building materials as titanium dioxide under ultraviolet light produces a strong oxidative effect and may therefore be used as a photocatalytic disinfectant.

Nontuberculous mycobacteria (21 isolates), biochemically similar to those that are recovered from humans, were recovered from rainwater and from natural river waters and their aerosols in the area of Richmond, Virginia. Field experiments have confirmed the existence of a natural mechanism for the transfer of significant numbers of mycobacteria from water to air. These findings support the hypothesis that aerosolization of potentially pathogenic mycobacteria from waters of the southeastern United States may be a major pathway for human infection.

Cracking in concrete structures is an expensive problem, especially common along coastal areas worldwide. There are several causes for this deterioration process, such as aging, ingress of aggressive components into concrete, such as chloride, and biodeterioration. It has been estimated that biodeterioration related structural problems cost 140 billions of dollars a year in infrastructure maintenance and repair. Researchers have shown that green algae, cyanobacteria, and mussels can be associated with microbiologically induced corrosion (MIC) of construction materials and they can all be found in coastal area, including Milwaukee, USA. This paper presents an overview and analysis of the current state-of-knowledge about biodeterioration of concrete, as well as future research needs. On the basis of identified knowledge, a research agenda has also been developed for the identification of critical structures, assessment of the biodeterioration of concrete, and sustainability of concret...

Cryptosporidium hominis and Cryptosporidium parvum are associated with massive disease outbreaks worldwide. Because these two species have different transmission cycles, identification of these parasites to the species level in clinical samples may provide laboratory data of crucial importance in epidemiologic investigations. To date, the most reliable way to differentiate C. hominis and C. parvum is based on DNA sequencing analysis of PCR amplicons. Although this approach is very effective for differentiation of Cryptosporidium species, it is labor-intensive and time-consuming compared with methods that do not require DNA sequencing analysis as an additional step and that have been successfully used for specific identification of a number of pathogens. In this study, we describe a novel Luminex-based assay that can differentiate C. hominis from C. parvum in a rapid and cost-effective manner. The assay was validated by testing a total of 143 DNA samples extracted from clinical speci...

We report the draft genome sequence of the Stenotrophomonas maltophilia strain EPM1, found in association with a culture of Giardia duodenalis. The draft genome sequence of S. maltophilia strain EPM1, obtained with Roche 454 GS-FLX Titanium technology, is composed of 19 contigs totaling 4,785,869 bp, with a G؉C content of 66.37%.

According to Bergey's Manual of Systematic Bacteriology, the Rickettsiales are '...bacteria with typical Gram-negative cell walls and no flagella'. The recently sequenced genome of 'Candidatus Midichloria mitochondrii', a divergent lineage within the order Rickettsiales capable of invading mitochondria in ixodid ticks, revealed the presence of 26 putative flagellar genes. Open questions in relation to this observation are whether these genes are expressed and whether they possess the domains expected for the flagellar function. Here we show that: (a) the putative flagellar proteins of 'Ca. M. mitochondrii' actually possess the conserved domains and structural features required for their function in a model bacterium; (b) the seven flagellar genes of 'Ca. M. mitochondrii' that have been tested are expressed at the RNA level; and (c) the putative flagellar cap gene of this bacterium (FliD) is expressed at the protein level, and can be stained within the bacterium and at its surface. Beside the specific questions that we have addressed that relate to the first evidence, to our knowledge, for a flagellar apparatus in a member of the order Rickettsiales, we present here novel tools (recombinant protein and antibodies) that will facilitate the study of 'Ca. M. mitochondrii'.

Summary The tick Ixodes ricinus is responsible for the transmission of a number of bacterial, protozoan and viral diseases to humans and animals in Europe and Northern Africa. Female I. ricinus from England, Switzerland and Italy have been found to harbour an intracellular α‐proteobacterium, designated IricES1, within the cells of the ovary. IricES1 is the only prokaryote known to exist within the mitochondria of any animal or multicellular organism. To further examine the distribution, prevalence and mode of transmission of IricES1, we performed polymerase chain reaction screening of I. ricinus adults from 12 countries across its geographic distribution, including tick colonies that have been maintained in the laboratory for varying periods of time. IricES1 was detected in 100% of field‐collected female ticks from all countries examined (n = 128), while 44% of males were found to be infected (n = 108). Those males that are infected appear to harbour fewer bacteria than females. Seq...

“ Candidatus Midichloria mitochondrii” is an intramitochondrial bacterium of the order Rickettsiales associated with the sheep tick Ixodes ricinus . Bacteria phylogenetically related to “ Ca . Midichloria mitochondrii” (midichloria and like organisms [MALOs]) have been shown to be associated with a wide range of hosts, from amoebae to a variety of animals, including humans. Despite numerous studies focused on specific members of the MALO group, no comprehensive phylogenetic and statistical analyses have so far been performed on the group as a whole. Here, we present a multidisciplinary investigation based on 16S rRNA gene sequences using both phylogenetic and statistical methods, thereby analyzing MALOs in the overall framework of the Rickettsiales . This study revealed that (i) MALOs form a monophyletic group; (ii) the MALO group is structured into distinct subgroups, verifying current genera as significant evolutionary units and identifying several subclades that could represent n...

Coastal ecosystem is susceptible to discharge of untreated sewage waste. The present study is aimed to determine water quality status prevailing along the north-west coast of India by monitoring spatial and temporal variations associated with fecal indicator organisms (FIOs) (namely, total coliforms, fecal coliforms, Escherichia coli and Streptococcus fecalis) along the five designated coastal water sites -Veraval, Hazira, Mumbai, Ratnagiri and Malvan for years (2012-14). Spatial waters illustrated that the concentration of FIOs significantly reduced away from the shoreline. Temporal-based sampling elucidates decreasing trend in fecal loads: Monsoon>post-monsoon>pre-monsoon. Based on the resemblance of water quality characteristics applied by hierarchical cluster analysis, these sites were grouped into three categories: Comparatively less polluted, moderately polluted and highly polluted. Regular trends in coastal FIOs variability, collective information about water quality and environmental factors appear useful for monitoring and management towards pollution encumbered at coastal region.

RESUMO - O Fosforo (P) e um dos principais macronutrientes essenciais para o crescimento e desenvolvimento das plantas, entretanto, apesar de abundante nos solos, tanto na forma orgânica quanto inorgânica, o fosforo e o segundo nutriente limitante ao crescimento de plantas. As bacterias solubilizadoras de fosfato sao capazes de solubilizar formas insoluveis de fosforo, tornando-o disponivel para o crescimento das culturas. Assim, objetivou-se por meio desse trabalho quantificar a solubilizacao de fosfatos inorgânicos por bacterias endofiticas de maracuja amarelo ( Passiflora edulis Sims f. flavicarpa). Foram inoculadas em meio liquido NBRIP, 21 estirpes bacterianas, sendo posteriormente incubadas em plena agitacao por um periodo de 15 dias. Decorrido o tempo de incubacao, 1000 μL de cada amostra foi transferida para microtubos, com a adicao do reagente molibdato-vanadato para leitura em espectrofotometro a 420 nm de densidade otica (D.O.), classificando-as em ausente, baixa, media, ...

Integrated plant nutrient management system (IPNMS) is an approach to optimize the nutrient requirement of plants by managing soil on sustainable basis (Roy et al., 2006). The IPNMS seeks for both, increase in agricultural production and sustaining the resources for the future generations. It is a strategy to utilize and manage the organic and inorganic plant nutrient sources for improving crop productivity and soil quality (Peter et al., 2000; Rajamanickam et al., 2011). Chemical fertilizers are considered as a compulsory component for crop production. The continuous and excess application not only reduces the profitability but deteriorates environment quality. Therefore, to get the maximum economic output, it is imperative to use organic nutrient sources in combination with chemical fertilizers. The use organic nutrient sources (such as farm yard manure, poultry manure, etc.) in combination with chemical fertilizers is helpful for improving soil health and sustaining crop producti...

Denitrification causes loss of available nitrogen from soil systems, thereby reducing crop productivity and increasing reliance on agrochemicals. The dynamics of denitrification and denitrifying communities are thought to be altered by land management practices, which affect the physicochemical properties of the soil. In this study, we look at the effects of long-term tillage and fertilization regimes on arable soils following 16 years of treatment in a factorial field trial. By studying the bacterial community composition based on 16S rRNA amplicons, absolute bacterial abundance and diversity of denitrification functional genes (nirK, nirS and nosZ), under conditions of minimum/conventional tillage and organic/synthetic mineral fertilizer, we tested how specific land management histories affect the diversity and distribution of both bacteria and denitrification genes. Bacterial and denitrifier communities were largely unaffected by land management history and clustered predominantly by spatial location, indicating that the variability in bacterial community composition in these arable soils is governed by innate environmental differences and Euclidean distance rather than agricultural management intervention.

Copyright © 2014 Rodrigo N. Millan et al. This is an open access article distributed under the Creative Commons Attribution Li-cense, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. In accordance of the Creative Commons Attribution License all Copyrights © 2014 are reserved for SCIRP and the owner of the intel-lectual property Rodrigo N. Millan et al. All Copyright © 2014 are guarded by law and by SCIRP as a guardian. Environmental pressure, land utilization, and economic feasibility have resulted in the development of alterna-tives to treatment fish farm wastewater. We examined the influence of two water treatment systems—a con-structed wetland (CW) and a soil filter system (SF)—on the constitution of the phytoplankton community ana-lyzed through the functional grouping of species and nutrients removal of aquaculture farm. The CW provided

Borax is still widely used for food in the community. Borax can attack mitochondria and cytoplasm where cellular energy metabolism occurs. The purpose of this study was to analyze the impact of borax on energy metabolism. Settings and Design of this study used Review article. The writing method was based on scientific phenomena that occurred in the research which was then analyzed deeply based on theories taken from the scientific literature. The Result of this study, Boron ions affect the activity of at least 26 different enzymes that are needed for energy metabolism. Boric acid as active substances of borax can form stable complexes with hydroxyl compounds from glucose, protein and fat which are the raw materials for energy metabolism, and inhibit nicotinamide adenine dinucleotide (NAD + ) activity which is a coenzyme in energy metabolism. Decrease in adenosine triphosphate (ATP) due to boric acid through the binding of NAD + and an increase in thermogenic protein pathways. The ATP reduction which disrupts ion pumps and accumulation of boron ions will damage the composition of ions in the cytoplasm where the process of glycolysis occurs. This ion pump disruption will also cause cell swelling, and disrupt the balance of ions which will lead to mitochondrial dysfunction and damage (the site of the Krebs cycle and oxidative phosphorylation). Conclusions of this study, Borax has a negative effect on energy metabolism, through the macronutrient, NAD + , enzymes, ATP, cytoplasm and mitochondria pathway.

The population structure of 56 Enterococcus faecium isolates selected from a collection of enterococci from humans, animals, and the environment in Portugal (1997 to 2007) was analyzed by multilocus sequence typing. We identified 41 sequence types clustering into CC17, CC5, CC9, CC22 and CC94, all clonal lineages comprising isolates from different hosts. Our findings highlight the role of community-associated hosts as reservoirs of enterococci able to cause human infections.

Objectives: We studied the occurrence of diverse copper (Cu) tolerance genes from Gram-positive bacteria and their co-transfer with antibiotic resistance genes among Enterococcus from diverse sources. Methods: Enterococcus (n¼ 922) of several species and from human, animal, environment and food samples were included. Antimicrobial and CuSO 4 susceptibility and conjugation assays were performed by standard procedures, bacterial screening of Cu and antibiotic resistance genes by PCR, and clonality by PFGE/multilocus sequence typing. Results: tcrB and cueO genes occurred in 15% (n¼ 137/922) and 14% (n¼ 128/922) of isolates, respectively, with the highest occurrence in piggeries (P,0.05). They were more frequent among Enterococcus faecium (tcrB: 23% versus 8% in Enterococcus faecalis and 12% in other species; cueO: 25% versus 5% and 9%, respectively; P,0.05). A correlation between phenotypic and genotypic assays was observed for most E. faecium (CuSO 4 MIC 50 ¼ 24 mM in tcrB/cueO + versus CuSO 4 MIC 50 ¼ 12 mM in tcrB/cueO 2 ), but not for other species. Co-transfer of Cu tolerance (associated with tcrB, cueO or an unknown mechanism) with erythromycin, tetracycline, vancomycin, aminoglycosides or ampicillin resistance was demonstrated. A variety of PFGE types was detected among isolates carrying Cu tolerance mechanisms, some identified in sequence types (STs) often linked to human infections (E. faecium from ST18 and ST78 clonal lineages and E. faecalis clonal complex 2). Conclusions: Cu tolerance might contribute to the selection/maintenance of multidrug-resistant Enterococcus (including resistance to first-line antibiotics used to treat enterococcal infections) due to the use of Cu compounds (e.g. antiseptics/animal feed supplements). The distribution of the multicopper oxidase cueO and the co-transfer of ampicillin resistance along with Cu tolerance genes are described for the first time.

This study investigates prokaryotic communities within sub-Antarctic marine sediments impacted by salmonid aquaculture in southern Chile, employing 16S rRNA gene sequencing to assess alpha and beta diversity, as well as the inferred functional roles of prokaryotes in sediment biogeochemistry, with particular emphasis on rocky seabeds exhibiting varying degrees of giant sulphur-oxidising bacteria (GSOB) mat coverage. Candidatus Isobeggiatoa was identified as the predominant member of the Beggiatoaceae GSOB, consistent with its established ecological role in sulphide-rich marine environments. A novel U-shaped pattern in prokaryotic alpha diversity was observed along the GSOB coverage gradient, characterised by a decline of up to 30 % in transitional zones followed by partial recovery in areas of extensive GSOB mat coverage; beta diversity analysis reflected this trend, confirming significant shifts in community structure across the gradient. Changes in community composition were primarily attributable to fluctuations in the relative abundance of key bacterial taxa, notably Sulfurovum and Sulfurimonas, which predominated in transitional zones but diminished at sites with extensive GSOB coverage. The partial recovery of alpha diversity in highly impacted sites with greater GSOB coverage was accompanied by an increase in anaerobic chemolithotrophic and fermentative groups, indicative of a successional dynamic. Collectively, these findings elucidate a clear relationship between GSOB mat coverage and prokaryotic community composition in aquaculture-affected sediments and support the recommendation of a standardised GSOB coverage scale as a bioindicator for the management of vulnerable sub-Antarctic marine ecosystems.