Phenotypic responses to interspecies competition and commensalism in a naturally derived microbial co-culture

The fundamental question of whether different microbial species will co-exist or compete in a given environment depends on context, composition and environmental constraints. Model microbial systems can yield some general principles related to this question. In this study we employed a naturally occurring co-culture composed of heterotrophic bacteria, Halomonas sp. HL-48 and Marinobacter sp. HL- 58, to ask two fundamental scientific questions: 1) how do the phenotypes of two naturally co-existing species respond to partnership as compared to axenic growth? and 2) how do growth and molecular phenotypes of these species change with respect to competitive and commensal interactions? We hypothesized – and confirmed – that co-cultivation under glucose as the sole carbon source would result in competitive interactions. Similarly, when glucose was swapped with xylose, the interactions became commensal because Marinobacter HL-58 was supported by metabolites derived from Halomonas HL- 48. Each species responded to partnership by changing both its growth and molecular phenotype as assayed via batch growth kinetics and global transcriptomics. These phenotypic responses depended on nutrient availability and so the environment ultimately controlled how they responded to each other. This simplified model community revealed that microbial interactions are context-specific and different environmental conditions dictate how interspecies partnerships will unfold

Phenotypic responses to interspecies competition and commensalism in a naturally derived microbial co-culture

The fundamental question of whether different microbial species will co-exist or compete in a given environment depends on context, composition and environmental constraints. Model microbial systems can yield some general principles related to this question. In this study we employed a naturally occurring co-culture composed of heterotrophic bacteria, Halomonas sp. HL-48 and Marinobacter sp. HL- 58, to ask two fundamental scientific questions: 1) how do the phenotypes of two naturally co-existing species respond to partnership as compared to axenic growth? and 2) how do growth and molecular phenotypes of these species change with respect to competitive and commensal interactions? We hypothesized – and confirmed – that co-cultivation under glucose as the sole carbon source would result in competitive interactions. Similarly, when glucose was swapped with xylose, the interactions became commensal because Marinobacter HL-58 was supported by metabolites derived from Halomonas HL- 48. Each species responded to partnership by changing both its growth and molecular phenotype as assayed via batch growth kinetics and global transcriptomics. These phenotypic responses depended on nutrient availability and so the environment ultimately controlled how they responded to each other. This simplified model community revealed that microbial interactions are context-specific and different environmental conditions dictate how interspecies partnerships will unfold

SN 2008S: an electron capture SN from a super-AGB progenitor?

We present comprehensive photometric and spectroscopic observations of the faint transient SN 2008S discovered in NGC 6946. SN 2008S exhibited slow photometric evolution and almost no spectral variability during the first nine months, implying a high density CS medium. The light curve is similar in shape to that of SN 1998S and SN 1979C, although significantly fainter at maximum light. Our quasi-bolometric lightcurve extends to 300 days and shows a tail phase decay rate consistent with that of ^{56}Co. We propose that this is evidence for an explosion and formation of ^{56}Ni (0.0015 +/- 0.0004 M_Sun). The large MIR flux detected shortly after explosion can be explained by a light echo from pre-exisiting dust. The late NIR flux excess is plausibly due to a combination of warm newly-formed ejecta dust together with shock-heated dust in the CS environment. We reassess the progenitor object detected previously in Spitzer archive images, supplementing this discussion with a model of the MIR spectral energy distribution. This supports the idea of a dusty, optically thick shell around SN 2008S with an inner radius of nearly 90AU and outer radius of 450AU, and an inferred heating source of 3000 K and luminosity of L ~ 10^{4.6} L_Sun. The combination of our monitoring data and the evidence from the progenitor analysis leads us to support the scenario of a weak electron capture supernova explosion in a super-AGB progenitor star (of initial mass 6-8 M_sun) embedded within a thick CS gaseous envelope. We suggest that all of main properties of the electron capture SN phenomenon are observed in SN 2008S and future observations may allow a definitive answer.Comment: accepted for publication in MNRAS (2009 May 7

SN 2008S: an electron-capture SN from a super-AGB progenitor?

We present comprehensive photometric and spectroscopic observations of the faint transient SN 2008S discovered in the nearby galaxy NGC 6946. SN 2008S exhibited slow photometric evolution and almost no spectral variability during the first nine months, implying a long photon diffusion time and a high-density circumstellar medium. Its bolometric luminosity (≃1041 erg s−1 at peak) is low with respect to most core-collapse supernovae but is comparable to the faintest Type II-P events. Our quasi-bolometric light curve extends to 300 d and shows a tail phase decay rate consistent with that of 56Co. We propose that this is evidence for an explosion and formation of 56Ni (0.0014 ± 0.0003 M⊙). Spectra of SN 2008S show intense emission lines of Hα, [Ca ii] doublet and Ca ii near-infrared (NIR) triplet, all without obvious P-Cygni absorption troughs. The large mid-infrared (MIR) flux detected shortly after explosion can be explained by a light echo from pre-existing dust. The late NIR flux excess is plausibly due to a combination of warm newly formed ejecta dust together with shock-heated dust in the circumstellar environment. We reassess the progenitor object detected previously in Spitzer archive images, supplementing this discussion with a model of the MIR spectral energy distribution. This supports the idea of a dusty, optically thick shell around SN 2008S with an inner radius of nearly 90 au and outer radius of 450 au, and an inferred heating source of 3000 K. The luminosity of the central star is L≃ 104.6 L⊙. All the nearby progenitor dust was likely evaporated in the explosion leaving only the much older dust lying further out in the circumstellar environment. The combination of our long-term multiwavelength monitoring data and the evidence from the progenitor analysis leads us to support the scenario of a weak electron-capture supernova explosion in a super-asymptotic giant branch progenitor star (of initial mass 6-8 M⊙) embedded within a thick circumstellar gaseous envelope. We suggest that all of main properties of the electron-capture SN phenomenon are observed in SN 2008S and future observations may allow a definitive answe

LKB1 is required for hepatic bile acid transport and canalicular membrane integrity in mice

LKB1 is a ‘master’ protein kinase implicated in the regulation of metabolism, cell proliferation, cell polarity and tumorigenesis. However, the long-term role of LKB1 in hepatic function is unknown. In the present study, it is shown that hepatic LKB1 plays a key role in liver cellular architecture and metabolism. We report that liver-specific deletion of LKB1 in mice leads to defective canaliculi and bile duct formation, causing impaired bile acid clearance and subsequent accumulation of bile acids in serum and liver. Concomitant with this, it was found that the majority of BSEP (bile salt export pump) was retained in intracellular pools rather than localized to the canalicular membrane in hepatocytes from LLKB1KO (liver-specific Lkb1-knockout) mice. Together, these changes resulted in toxic accumulation of bile salts, reduced liver function and failure to thrive. Additionally, circulating LDL (low-density lipoprotein)-cholesterol and non-esterified cholesterol levels were increased in LLKB1KO mice with an associated alteration in red blood cell morphology and development of hyperbilirubinaemia. These results indicate that LKB1 plays a critical role in bile acid homoeostasis and that lack of LKB1 in the liver results in cholestasis. These findings indicate a novel key role for LKB1 in the development of hepatic morphology and membrane targeting of canalicular proteins

Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression

Phage integrase genes often play a role in the establishment of lysogeny in temperate phage by catalyzing the integration of the phage into one of the host's replicons. To investigate temperate phage gene expression, an induced viral metagenome from Tampa Bay was sequenced by 454/Pyrosequencing. The sequencing yielded 294,068 reads with 6.6% identifiable. One hundred-three sequences had significant similarity to integrases by BLASTX analysis (e≤0.001). Four sequences with strongest amino-acid level similarity to integrases were selected and real-time PCR primers and probes were designed. Initial testing with microbial fraction DNA from Tampa Bay revealed 1.9×107, and 1300 gene copies of Vibrio-like integrase and Oceanicola-like integrase L−1 respectively. The other two integrases were not detected. The integrase assay was then tested on microbial fraction RNA extracted from 200 ml of Tampa Bay water sampled biweekly over a 12 month time series. Vibrio-like integrase gene expression was detected in three samples, with estimated copy numbers of 2.4-1280 L−1. Clostridium-like integrase gene expression was detected in 6 samples, with estimated copy numbers of 37 to 265 L−1. In all cases, detection of integrase gene expression corresponded to the occurrence of lysogeny as detected by prophage induction. Investigation of the environmental distribution of the two expressed integrases in the Global Ocean Survey Database found the Vibrio-like integrase was present in genome equivalents of 3.14% of microbial libraries and all four viral metagenomes. There were two similar genes in the library from British Columbia and one similar gene was detected in both the Gulf of Mexico and Sargasso Sea libraries. In contrast, in the Arctic library eleven similar genes were observed. The Clostridium-like integrase was less prevalent, being found in 0.58% of the microbial and none of the viral libraries. These results underscore the value of metagenomic data in discovering signature genes that play important roles in the environment through their expression, as demonstrated by integrases in lysogeny

Prokaryotic and Eukaryotic Community Structure in Field and Cultured Microbialites from the Alkaline Lake Alchichica (Mexico)

The geomicrobiology of crater lake microbialites remains largely unknown despite their evolutionary interest due to their resemblance to some Archaean analogs in the dominance of in situ carbonate precipitation over accretion. Here, we studied the diversity of archaea, bacteria and protists in microbialites of the alkaline Lake Alchichica from both field samples collected along a depth gradient (0–14 m depth) and long-term-maintained laboratory aquaria. Using small subunit (SSU) rRNA gene libraries and fingerprinting methods, we detected a wide diversity of bacteria and protists contrasting with a minor fraction of archaea. Oxygenic photosynthesizers were dominated by cyanobacteria, green algae and diatoms. Cyanobacterial diversity varied with depth, Oscillatoriales dominating shallow and intermediate microbialites and Pleurocapsales the deepest samples. The early-branching Gloeobacterales represented significant proportions in aquaria microbialites. Anoxygenic photosynthesizers were also diverse, comprising members of Alphaproteobacteria and Chloroflexi. Although photosynthetic microorganisms dominated in biomass, heterotrophic lineages were more diverse. We detected members of up to 21 bacterial phyla or candidate divisions, including lineages possibly involved in microbialite formation, such as sulfate-reducing Deltaproteobacteria but also Firmicutes and very diverse taxa likely able to degrade complex polymeric substances, such as Planctomycetales, Bacteroidetes and Verrucomicrobia. Heterotrophic eukaryotes were dominated by Fungi (including members of the basal Rozellida or Cryptomycota), Choanoflagellida, Nucleariida, Amoebozoa, Alveolata and Stramenopiles. The diversity and relative abundance of many eukaryotic lineages suggest an unforeseen role for protists in microbialite ecology. Many lineages from lake microbialites were successfully maintained in aquaria. Interestingly, the diversity detected in aquarium microbialites was higher than in field samples, possibly due to more stable and favorable laboratory conditions. The maintenance of highly diverse natural microbialites in laboratory aquaria holds promise to study the role of different metabolisms in the formation of these structures under controlled conditions

Habilidades funcionais, nível de actividade, integração na comunidade e saúde em idosos institucionalizados em lar: resultados preliminares

São escassos os estudos portugueses que avaliam o nível de funcionalidade, o nível de actividade e a saúde em idosos institucionalizados em lar. Objectivos: Estimar os meses de institucionalização dos idosos e as causas que conduziram à institucionalização em lar, bem como o número de idosos que partilha o seu quarto com outros. Estimar as Habilidades Funcionais dos idosos, o tipo de actividades relatadas, dentro e fora da instituição (Nível de Actividade e Integração na Comunidade) e o grau de saúde (objectiva e subjectiva). Analisar a relação entre estas quatro dimensões e analisar a relação destas com algumas variáveis demográficas (idade, género). Métodos: 35 idosos institucionalizados em lar (idade média=80.20 anos; DP=6.263) completaram o Questionário de Informação Pessoal (QIP; Fernándes-Ballesteros, 1995; Maia et al., 2013). Para a análise dos dados recorremos ao SPSS 21. Resultados: A grande generalidade dos idosos está institucionalizada há mais de 16 meses, por motivos maioritariamente de saúde (65,7%), partilha o quarto com terceiros (71.4%) e é autónoma, não necessitando de ajuda (56.7%) em actividades como o cuidado pessoal, comer, vestir/despir, andar, levantar/deitar. Quando se trata das actividades mais complexas, como a administração de dinheiro, uso do telefone ou ida às compras, o grau de dependência aumenta (27.6% dos sujeitos necessitam de muita ajuda e 35.2% de alguma ajuda). Verifica-se que 72.9% da população está inactiva, visto limitar-se a ver televisão ou a ouvir rádio e apenas 14.3% dos idosos se dedicam a actividades fora da Instituição. Os actos religiosos têm uma larga adesão (88.6%). 79.4% dos idosos reporta problemas de mobilidade e 35.3% problemas de foro psicológico. Verifica-se que 45.7% percepcionam a saúde como má, com as mulheres a percepcionarem a sua saúde mais negativamente do que os homens. Nenhum dos idosos, de ambos os géneros, percepciona a sua saúde como boa ou excelente (0%). A dimensão Nível de Actividade apresenta uma correlação positiva com a dimensão Integração na Comunidade (r=.448*). O género apresenta uma correlação significativa com a dimensão Habilidades Funcionais (rho=.383*) e com a dimensão Saúde (r=.414*). O estado civil apresentou uma correlação positiva com as Habilidades Funcionais (rho=.419*) e o grau de escolaridade apresentou uma correlação negativa e com a dimensão Saúde (r=-.446*). Conclusões: Na nossa amostra a institucionalização é causada maioritariamente devido a problemas de saúde. A maioria dos idosos partilha o seu quarto o que pode afectar a sua intimidade e bem-estar. Apesar da maioria dos idosos ser funcionalmente autónoma, a grande generalidade apresenta uma vida pautada pela inactividade e por fracos laços com o exterior. As mulheres percepcionam a sua saúde mais negativamente do que os homens. Importa assim, desenvolver estratégias que conduzam a um envelhecimento activo destes idosos