Novel aromatic ring-hydroxylating dioxygenase genes from coastal marine sediments of Patagonia

<p>Abstract</p> <p>Background</p> <p>Polycyclic aromatic hydrocarbons (PAHs), widespread pollutants in the marine environment, can produce adverse effects in marine organisms and can be transferred to humans through seafood. Our knowledge of PAH-degrading bacterial populations in the marine environment is still very limited, and mainly originates from studies of cultured bacteria. In this work, genes coding catabolic enzymes from PAH-biodegradation pathways were characterized in coastal sediments of Patagonia with different levels of PAH contamination.</p> <p>Results</p> <p>Genes encoding for the catalytic alpha subunit of aromatic ring-hydroxylating dioxygenases (ARHDs) were amplified from intertidal sediment samples using two different primer sets. Products were cloned and screened by restriction fragment length polymorphism analysis. Clones representing each restriction pattern were selected in each library for sequencing. A total of 500 clones were screened in 9 gene libraries, and 193 clones were sequenced. Libraries contained one to five different ARHD gene types, and this number was correlated with the number of PAHs found in the samples above the quantification limit (<it>r </it>= 0.834, <it>p </it>< 0.05). Overall, eight different ARHD gene types were detected in the sediments. In five of them, their deduced amino acid sequences formed deeply rooted branches with previously described ARHD peptide sequences, exhibiting less than 70% identity to them. They contain consensus sequences of the Rieske type [2Fe-2S] cluster binding site, suggesting that these gene fragments encode for ARHDs. On the other hand, three gene types were closely related to previously described ARHDs: archetypical <it>nahAc</it>-like genes, <it>phnAc</it>-like genes as identified in <it>Alcaligenes faecalis </it>AFK2, and <it>phnA1</it>-like genes from marine PAH-degraders from the genus <it>Cycloclasticus</it>.</p> <p>Conclusion</p> <p>These results show the presence of hitherto unidentified ARHD genes in this sub-Antarctic marine environment exposed to anthropogenic contamination. This information can be used to study the geographical distribution and ecological significance of bacterial populations carrying these genes, and to design molecular assays to monitor the progress and effectiveness of remediation technologies.</p

Draft genome sequence of Williamsia sp. strain D3, isolated from the Darwin Mountains, Antarctica

Actinobacteria are the dominant taxa in Antarctic desert soils. Here, we describe the first draft genome of a member of the genus Williamsia (strain D3) isolated from Antarctic soil. The genome of this psychrotolerant bacterium may help to elucidate crucial survival mechanisms for organisms inhabiting cold desert soil systems.The South African National Research Foundation and the Genomics Research Institute of the University of Pretoria (to L.G., T.P.M., and D.A.C.), the Ministry of Business Innovation and Employment, New Zealand (projects C09X0307 and C09X1001, to J.A.), and Antarctica New Zealand.http://genomea.asm.orgam201

Metagenómica y metatranscriptómica aplicadas al estudio de Chloroflexota en sistemas de tratamiento de aguas residuales escala real

El filo Chloroflexota es uno de los grupos predominantes en sistemas de tratamiento de aguas residuales aerobios (lodos activados) y anaerobios (metanogénicos). Dentro de este filo, la clase Anaerolineae representa más del 80%, sin embargo, su rol en estos sistemas aún sigue sin conocerse. Esto se debe principalmente a las dificultades para asilarlos en cultivo puro. Los pocos representantes cultivados son capaces de fermentar, se caracterizan por tener crecimiento lento y morfología filamentosa. Se ha postulado que están involucrados en la formación de gránulos en reactores anaerobios y flóculos en reactores de lodos activados, pero su crecimiento excesivo se ha relacionado problemas de sedimentación de la biomasa (bulking). Las condiciones que favorecen el crecimiento excesivo de estas bacterias siguen siendo desconocidas. Expandir el conocimiento sobre este grupo es esencial para controlar su sobrecrecimiento y prevenir episodios de bulking. Para determinar la morfología, diversidad y expresión génica de organismos del filo Chloroflexota, se aplicaron diversas técnicas de biología molecular como hibridación in situ fluorescente, secuenciación de amplicones, metagenómica y metatranscriptómica en dos reactores de lodos activados y dos reactores metanogénicos que trataban distintas aguas residuales industriales. El filo Chloroflexota fue uno de los 5 filos más abundantes en todos los reactores y presentó diversas morfologías filamentosas. Se ensamblaron 17 genomas de especies nuevas de la clase Anaerolineae y un genoma de la clase Dehalococcoidia. Mediante el análisis de las vías metabólicas obtenidas mediante metagenómica se determinó que todos los genomas presentaron varias vías de fermentación, que incluían la producción de lactato, acetato, formiato y acetoína. Los genomas obtenidos de sistemas aerobios presentaron el potencial de respirar anaeróbicamente utilizando nitrito y nitrato reductasas como aceptores de electrones. Estas funciones metabólicas fueron confirmadas mediante el análisis de los metatranscriptomas. Por lo tanto, las especies del filo Chloroflexota detectadas en estos sistemas de tratamiento juegan un rol fundamental en la remoción de la materia en sistemas aerobios y anaerobios, y particularmente en sistemas de lodos activados, colaboran en la remoción del nitrogeno de las aguas residuales.Agencia Nacional de Investigación e Innovació

Draft genome sequence of the aromatic hydrocarbon-degrading bacterium Sphingobium sp. strain Ant17, isolated from Antarctic soil

Here, we present the draft genome sequence of Sphingobium sp. strain Ant17, an aromatic hydrocarbon-degrading bacterium that was isolated from Antarctic oil-contaminated soil. An analysis of this genome can lead to insights into the mechanisms of xenobiotic degradation processes at low temperatures and potentially aid in bioremediation applications.The South African National Research Foundation, the University of Pretoria Vice- Chancellor’s Postdoctoral Fellowship Program (to E.M.A.), the Genomics Research Institute of the University of Pretoria (to E.M.A., L.D.G., T.P.M., and D.A.C.), the Ministry of Business Innovation and Employment, New Zealand (projects C09X0307 and C09X1001 to J.M.A.), and Antarctica New Zealand.http://genomea.asm.org/am201

Evolutionary and pulsational properties of white dwarf stars

Abridged. White dwarf stars are the final evolutionary stage of the vast majority of stars, including our Sun. The study of white dwarfs has potential applications to different fields of astrophysics. In particular, they can be used as independent reliable cosmic clocks, and can also provide valuable information about the fundamental parameters of a wide variety of stellar populations, like our Galaxy and open and globular clusters. In addition, the high densities and temperatures characterizing white dwarfs allow to use these stars as cosmic laboratories for studying physical processes under extreme conditions that cannot be achieved in terrestrial laboratories. They can be used to constrain fundamental properties of elementary particles such as axions and neutrinos, and to study problems related to the variation of fundamental constants. In this work, we review the essentials of the physics of white dwarf stars. Special emphasis is placed on the physical processes that lead to the formation of white dwarfs as well as on the different energy sources and processes responsible for chemical abundance changes that occur along their evolution. Moreover, in the course of their lives, white dwarfs cross different pulsational instability strips. The existence of these instability strips provides astronomers with an unique opportunity to peer into their internal structure that would otherwise remain hidden from observers. We will show that this allows to measure with unprecedented precision the stellar masses and to infer their envelope thicknesses, to probe the core chemical stratification, and to detect rotation rates and magnetic fields. Consequently, in this work, we also review the pulsational properties of white dwarfs and the most recent applications of white dwarf asteroseismology.Comment: 85 pages, 28 figures. To be published in The Astronomy and Astrophysics Revie

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio

Burnout among surgeons before and during the SARS-CoV-2 pandemic: an international survey

Background: SARS-CoV-2 pandemic has had many significant impacts within the surgical realm, and surgeons have been obligated to reconsider almost every aspect of daily clinical practice. Methods: This is a cross-sectional study reported in compliance with the CHERRIES guidelines and conducted through an online platform from June 14th to July 15th, 2020. The primary outcome was the burden of burnout during the pandemic indicated by the validated Shirom-Melamed Burnout Measure. Results: Nine hundred fifty-four surgeons completed the survey. The median length of practice was 10&nbsp;years; 78.2% included were male with a median age of 37&nbsp;years old, 39.5% were consultants, 68.9% were general surgeons, and 55.7% were affiliated with an academic institution. Overall, there was a significant increase in the mean burnout score during the pandemic; longer years of practice and older age were significantly associated with less burnout. There were significant reductions in the median number of outpatient visits, operated cases, on-call hours, emergency visits, and research work, so, 48.2% of respondents felt that the training resources were insufficient. The majority (81.3%) of respondents reported that their hospitals were included in the management of COVID-19, 66.5% felt their roles had been minimized; 41% were asked to assist in non-surgical medical practices, and 37.6% of respondents were included in COVID-19 management. Conclusions: There was a significant burnout among trainees. Almost all aspects of clinical and research activities were affected with a significant reduction in the volume of research, outpatient clinic visits, surgical procedures, on-call hours, and emergency cases hindering the training. Trial registration: The study was registered on clicaltrials.gov "NCT04433286" on 16/06/2020