Ecology, Evolution, and Gene Transfer Between Diatoms and Bacteria

Although photosynthetic macro-eukaryotes (i.e., plants) make up the majority of organic biomass on earth, bacteria are the second largest taxonomic group, by biomass. Bacteria are ubiquitous in our environment, living on, and within, man-made surfaces, natural environments, and eukaryotes themselves. The relationship between bacteria and eukaryotes has existed from the very beginning of eukaryotic life in the form of bacterial endosymbioses that resulted in mitochondria and plastids. Other eukaryote–bacteria relationships have evolved since then, ranging from the beneficial (e.g., mutualistic) to harmful (e.g., parasitic or pathogenic). Understanding these eukaryote–bacteria relationships is key to understanding both the evolution of important ecosystem processes and how these interactions affect human endeavors such as agriculture. To better understand how bacterial communities affect and interact with their eukaryotic partners, we have utilized the genomes and transcriptomes of the ubiquitous micro-eukaryotes known as diatoms to analyze their co-occurring bacteria. This dissertation explores the composition, dynamics, and interactions between diatoms and their bacterial partners. We first sequenced the genome and transcriptome of the araphid pennate diatom Psammoneis japonica and examined its associated bacterial metagenome. Repetitive element content in P. japonica, and other existing diatom genomes, were found to have a positive relationship with genome size. The partial metagenome of P. japonica revealed a diverse microbial community of at least 25 associated bacterial taxa, including four near-complete genomes for novel species of Planctomycetota, ɑ-proteobacteria, and Bacteroidota. The P. japonica genome was found to contain genes and intergenic open reading frame sequences which were transferred to the P. japonica lineage from members of the lineages of several cohabiting bacteria. Several of these HGT candidate proteins are located in regions with transposon densities higher than the average for the genic and intergenic regions of the P. japonica genome. Subsequently, we mapped and extracted bacterial 16S sequences from existing transcriptome reads of diatoms. Transcriptomes were sourced from the Alverson Lab and the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) to investigate bacterial diversity, community phylogenetics, and cophylogenetic concordance between diatom-bacteria associations across cultured diatom strains. There was a high degree of dissimilarity in phylogenetic beta-diversity between diatom bacterial communities at all taxonomic levels of the diatom tree of life. Ordination analysis of phylogenetic beta-diversity demonstrated distinct groupings of diatom microbiomes by salinity. Significant cophylogenetic concordance was found between diatoms of the genus Chaetoceros and their bacterial partners. These results support that diatom phycosphere communities are more similar within salinity levels, while still maintaining high diversity within and across genera. Lastly, this research demonstrates that incidentally collected sequence data can be utilized to investigate microbiomes. These experiments highlight that incidentally collected sequence data can be utilized to investigate the algal phycosphere by using bioinformatics methods to extract bacterial sequences from xenic algal cultures, as well as how normally discarded data can be used to examine community dynamics that would otherwise be overlooked. These findings also suggest that diatom–bacteria relationships are stable over evolutionary timescales and can lead to recurrent horizontal gene transfer events from symbiont to host, as well as cophylogenetic concordance between diatoms and their bacterial partners

Ecology, Evolution, and Gene Transfer Between Diatoms and Bacteria

Although photosynthetic macro-eukaryotes (i.e., plants) make up the majority of organic biomass on earth, bacteria are the second largest taxonomic group, by biomass. Bacteria are ubiquitous in our environment, living on, and within, man-made surfaces, natural environments, and eukaryotes themselves. The relationship between bacteria and eukaryotes has existed from the very beginning of eukaryotic life in the form of bacterial endosymbioses that resulted in mitochondria and plastids. Other eukaryote–bacteria relationships have evolved since then, ranging from the beneficial (e.g., mutualistic) to harmful (e.g., parasitic or pathogenic). Understanding these eukaryote–bacteria relationships is key to understanding both the evolution of important ecosystem processes and how these interactions affect human endeavors such as agriculture. To better understand how bacterial communities affect and interact with their eukaryotic partners, we have utilized the genomes and transcriptomes of the ubiquitous micro-eukaryotes known as diatoms to analyze their co-occurring bacteria. This dissertation explores the composition, dynamics, and interactions between diatoms and their bacterial partners. We first sequenced the genome and transcriptome of the araphid pennate diatom Psammoneis japonica and examined its associated bacterial metagenome. Repetitive element content in P. japonica, and other existing diatom genomes, were found to have a positive relationship with genome size. The partial metagenome of P. japonica revealed a diverse microbial community of at least 25 associated bacterial taxa, including four near-complete genomes for novel species of Planctomycetota, ɑ-proteobacteria, and Bacteroidota. The P. japonica genome was found to contain genes and intergenic open reading frame sequences which were transferred to the P. japonica lineage from members of the lineages of several cohabiting bacteria. Several of these HGT candidate proteins are located in regions with transposon densities higher than the average for the genic and intergenic regions of the P. japonica genome. Subsequently, we mapped and extracted bacterial 16S sequences from existing transcriptome reads of diatoms. Transcriptomes were sourced from the Alverson Lab and the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) to investigate bacterial diversity, community phylogenetics, and cophylogenetic concordance between diatom-bacteria associations across cultured diatom strains. There was a high degree of dissimilarity in phylogenetic beta-diversity between diatom bacterial communities at all taxonomic levels of the diatom tree of life. Ordination analysis of phylogenetic beta-diversity demonstrated distinct groupings of diatom microbiomes by salinity. Significant cophylogenetic concordance was found between diatoms of the genus Chaetoceros and their bacterial partners. These results support that diatom phycosphere communities are more similar within salinity levels, while still maintaining high diversity within and across genera. Lastly, this research demonstrates that incidentally collected sequence data can be utilized to investigate microbiomes. These experiments highlight that incidentally collected sequence data can be utilized to investigate the algal phycosphere by using bioinformatics methods to extract bacterial sequences from xenic algal cultures, as well as how normally discarded data can be used to examine community dynamics that would otherwise be overlooked. These findings also suggest that diatom–bacteria relationships are stable over evolutionary timescales and can lead to recurrent horizontal gene transfer events from symbiont to host, as well as cophylogenetic concordance between diatoms and their bacterial partners

Supercritical fluid extraction (SFE) and high performance liquid chromotography (HPLC) analysis of polycyclic aromatic hydrocarbon (PAH) contaminated soil

Methods for the extraction and analysis of polycyclic aromatic hydrocarbons (PAHs) from contaminated soil were evaluated for use in a treatability study. Candidate procedures were selected from EPA SW-846 (Third Edition) methods. Soxhlet extraction (3540B) was selected to determine initial PAH concentrations. Supercritical fluid extraction with carbon dioxide (SFE: 3561) and high performance liquid chromatography (HPLC: 8310) were evaluated for use as the extraction and analysis methods. Experimental soil was obtained from a petroleum product refinery site; a Certified Reference Material (CRM) was also studied. Experiments focused on determining concentrations of anthracene, chrysene, fluoranthene, phenanthrene, and pyrene in untreated experimental soil; recoveries from SFE and Soxhlet extraction were compared. SFE method 3561 uses a 5%, 1/4 (v/v) methanol/water modifier; a 5% methanol modifier was also evaluated. Soxhlet extractions yielded the highest recoveries of the PAHs with the exception of fluoranthene, recovered only after SFE with the pure methanol modifier

Des péripéties de la gestion forestière en forêt méditerranéenne en basse montagne

Christiane d'Izarny, propriétaire forestier dans les Alpes-de-Haute-Provence, nous livre ici son récit de vie d'une propriétaire de forêt en basse montagne méditerranéenne. La forêt de Sylvabelle, domaine de 250 ha près de Revest-des-Brousses porte bien son nom, c'est un domaine magnifique, mais qui illustre aussi les difficultés que rencontrent les propriétaires pour la mise en valeur de leur patrimoine. Passion, motivation et pugnacité y sont nécessaires ... ce dont Mme d'Izarny ne semble pas manquer

Atypowe formy zatrudnienia w Brazylii po przeprowadzeniu reformy pracy

The purpose of this publication is to provide an overview of labor law changes in Brazil that have significantly affected fundamental employment principles. Laws 13.427/17 and 13,467/17, collectively known as the Labor Reform, introduced atypical forms of employment, heavily modifying individual and collective labor laws. In particular, the changes include: employment in the form of intermittent work, telework, outsourcing or hyper-sufficient workers. The labor law reform, which has been carried out, introduces a number of novelties into the Brazilian legal system and raises many questions and doubts. There are concerns about whether the regulation undermines the existing legal order and thus threatens the dignity of workers, their physical and mental health, as well as negatively affects the working environment.Celem niniejszej publikacji jest przybliżenie zmian w prawie pracy w Brazylii, które znacząco wpłynęły na fundamentalne zasady zatrudnienia. Ustawy nr 13.427/17 i 13.467/17, zwane zbiorczo Reformą Pracy, wprowadziły atypowe formy zatrudnienia, mocno modyfikując indywidualne i zbiorowe prawo pracy. Zmiany obejmują w szczególności: zatrudnienie w formie pracy przerywanej, telepracę, outsourcing oraz pracowników hyper-sufficient (typ zatrudnienia występujący w Brazylii). Przeprowadzona reforma wprowadzając szereg nowości do brazylijskiego systemu prawnego wzbudza wiele pytań i wątpliwości. Istnieją obawy czy regulacja nie podważa obowiązującego porządku prawnego i tym samym nie zagraża godności pracowników, ich zdrowiu fizycznemu i psychicznemu, jak i negatywnie wpływa na środowisko pracy

1,3-Butadiene: linking metabolism, dosimetry, and mutation induction.

There is increasing concern for the potential adverse health effects of human exposures to chemical mixtures. To better understand the complex interactions of chemicals within a mixture, it is essential to develop a research strategy which provides the basis for extrapolating data from single chemicals to their behavior within the chemical mixture. 1,3-Butadiene (BD) represents an interesting case study in which new data are emerging that are critical for understanding interspecies differences in carcinogenic/genotoxic response to BD. Knowledge regarding mechanisms of BD-induced carcinogenicity provides the basis for assessing the potential effects of mixtures containing BD. BD is a multisite carcinogen in B6C3F1 mice and Sprague-Dawley rats. Mice exhibit high sensitivity relative to the rat to BD-induced tumorigenesis. Since it is likely that BD requires metabolic activation to mutagenic reactive epoxides that ultimately play a role in carcinogenicity of the chemical, a quantitative understanding of the balance of activation and inactivation is essential for improving our understanding and assessment of human risk following exposure to BD and chemical mixtures containing BD. Transgenic mice exposed to 625 ppm BD for 6 hr/day for 5 days exhibited significant mutagenicity in the lung, a target organ for the carcinogenic effect of BD in mice. In vitro studies designed to assess interspecies differences in the activation of BD and inactivation of BD epoxides reveal that significant differences exist among mice, rats, and humans. In general, the overall activation/detoxication ratio for BD metabolism was approximately 10-fold higher in mice compared to rats or humans.(ABSTRACT TRUNCATED AT 250 WORDS

Evaluating the validity and applicable domain of the toxic load model: Impact of concentration vs. time profile on inhalation lethality of hydrogen cyanide

The ten Berge model (or ‘‘toxic load’’ model) is often used to estimate the acute toxicity for varying combinations of inhaled concentration and duration. Expressed as Cn X t = toxic load (TL), TLs are assumed constant for various combinations of concentration (C) and time (t). Experimental data in a recent acute inhalation study of rats exposed to time-varying concentrations of hydrogen cyanide (HCN) supported the validity of the toxic load model except under very brief, discontinuous, high concentration exposures. In the present investigation, experiments were conducted to extend the evaluation of the applicable domain of the model for acute lethality of HCN in the rat (cumulative exposure range of 2900–11,000 ppm min). The lethality of HCN over very short (\u3c5 min) durations of high concentrations did not conform to the toxic load model. A value of n = 1.57 was determined for uninterrupted exposures P5 min. For 30-min exposures, the presence or absence of a gap between two exposure pulses of different concentrations, the relative duration, relative height, and the ordering of the pulses (low then high, vs. high then low) did not appear to have a meaningful impact on the toxic load required for median lethality

Dynamics of Baltic ecosystems and causes of their variability

Dynamics of Baltic ecosystems and causes of their variability are discussed and special attention is paid to the use of ecological models as a tool for research and management. - The causes of the observed changes in salinity, temperature, and oxygen of the deep water of the Baltic Sea are reviewed and discussed. - The work has led to the formulation of a hypothesis by which it appears possible to explain the oxygen development and the long-term development of other hydrographic components. The analyses indicate that the change of the level of the interface from - 80 m at the beginning of the century to about - 60 m today has increased the quantity of dead organic matter sinking down through the halocline as a consequence of the increased area of contact between the surface water and the deep water. The increased contact area has led to a corresponding increase in all fluxes through the halocline driven by turbulent gradient diffusion including an increase in the upward flux of nutrients. This has led to a fertilization of the surface water which has increased organic production in the surface zone. This in turn increases the amount of dead organic matter supplied to the deep water. At the same time the temperature increase has increased the rate of oxygen consumption. The net result is that oxygen in the deep water is being consumed at a much higher rate today than previously. lt is estimated that the rate of consumption has increased about 110% since the end of the last century. This implies an increase in the primary production of about 40%. - The supply of oxygen to the deep water has increased primarily as a consequence of the increase in the area of contact between the surface water and the deep water, and secondly as a consequence of an increase in the vertical oxygen concentration gradient. However, the rate of increase of supply has been smaller than the rate of increase of the consumption. The relative difference between the consumption and the supply has increased from 0 at equilibrium conditions at the end of the last century to about 10% today. Although this change in the balance between supply and consumption appears to be marginal, it is nevertheless sufficient to bring about the dramatic decrease of the oxygen concentration in the deep water from about 3 ml/l at the end of the last century to close to O ml/l today. - The model introduced represents a preliminary step towards a Baltic model, which necessarily must take the changing position of the halocline and related effects into account

Imaging Single ZnO Vertical Nanowire Laser Cavities using UV-Laser Scanning Confocal Microscopy

We report the fabrication and optical characterization of individual ZnO vertical nanowire laser cavities. Dilute nanowire arrays with interwire spacing>10 ?m were produced by a modified chemical vapor transport (CVT) method yielding an ideal platform for single nanowire imaging and spectroscopy. Lasing characteristics of a single vertical nanowire are presented, as well as high-resolution photoluminescence imaging by UV-laser scanning confocal microscopy. In addition, three-dimensional (3D) mapping of the photoluminescence emission performed in both planar and vertical dimensions demonstrates height-selective imaging useful for vertical nanowires and heteronanostructures emerging in the field of optoelectronics and nanophotonics