1,721,243 research outputs found
Marine microorganisms, biogeochemical cycles, and global climate change
No full textSummary:? Marine microbes drive chemical reactions that contribute to Earth's habitability.? Although molecular techniques are used to monitor oceanic microbial communities, collecting intermittent samples for laboratory analysis limits the usefulness of this approach.? Instruments that collect and analyze microbes in situ can provide unprecedented resolution of biogeochemical cycles over large spatial and temporal scales.? We should combine knowledge of key genes with new instruments to obtain time-series information on key marine microbial biogeochemical transformations.The oceans maintain critical ecosystems that, ultimately, determine the habitability of the planet. Moreover, unicellular eukaryotes, bacteria, and archaea are the most abundant organisms within those ecosystems and thus the dominant biomass within the oceans, situated at the base of the food chain that feeds macroscopic invertebrates, fish, and mammals.We are only beginning to uncover the extent of marine microbial genetic diversity and the complex roles that these microbes play in driving the biogeochemistry of global ocean ecosystems. Molecular biology, genomics, microscopy, mass spectrometry, and high-throughput cultivation are already providing useful information on the diversity and activities of marine microflora, including new biochemical pathways. However, in the face of global environmental change, we need to gain a deeper understanding of the distributions of marine microbes and their activities in maintaining ecosystem functions
Two subpopulations of Crocosphaera watsonii have distinct distributions in the North and South Pacific
Get PDFCrocosphaera watsonii is a unicellular nitrogen (N2)-fixing cyanobacterium with ecological importance in oligotrophic oceans. In cultivated strains there are two phenotypes of C.?watsonii (large and small cells) with differences that could differentially impact biogeochemical processes. Recent work has shown the phenotypes diverged through loss or addition of type-specific genes in a fraction of their genomes, whereas the rest of the genomes were maintained at 99–100% DNA identity. Previous molecular assays for C.?watsonii abundances targeted the conserved regions and therefore could not differentiate between phenotypes, so their relative distributions in natural communities were unknown. To determine phenotype distributions, this study developed and applied type-specific quantitative polymerase chain reaction assays to samples from the North and South Pacific. Abundances of both Crocosphaera types declined sharply with depth between 45 and 75?m in both sites. In surface water small cells were 10–100 times more abundant than large cells in the N. Pacific, whereas in the S. Pacific the two phenotypes were nearly equal. Evidence for large cell aggregation was only found in N. Pacific samples. The differences in C.?watsonii sub-populations in the North and South Pacific have direct implications for biogeochemistry and carbon export in oligotrophic gyres
Dissolved hydrogen and nitrogen fixation in the oligotrophic North Pacific Subtropical Gyre
Get PDFThe production of hydrogen (H2) is an inherent component of biological dinitrogen (N2) fixation, and there have been several studies quantifying H2 production relative to N2 fixation in cultures of diazotrophs. However, conducting the relevant measurements for a field population is more complex as shown by this study of N2 fixation, H2 consumption and dissolved H2 concentrations in the oligotrophic North Pacific Ocean. Measurements of H2 oxidation revealed microbial consumption of H2 was equivalent to 1–7% of ethylene produced during the acetylene reduction assay and 11–63% of 15N2 assimilation on a molar scale. Varying abundances of Crocosphaera and Trichodesmium as revealed by nifH gene abundances broadly corresponded with diel changes observed in both N2 fixation and H2 oxidation. However, no corresponding changes were observed in the dissolved H2 concentrations which remained consistently supersaturated (147–560%) relative to atmospheric equilibrium. The results from this field study allow the efficiency of H2 cycling by natural populations of diazotrophs to be compared to cultured representatives. The findings indicate that dissolved H2 concentrations may depend not only on the community composition of diazotrophs but also upon relevant environmental parameters such as light intensity or the presence of other H2-metabolizing microorganisms
Non-cyanobacterial nifH phylotypes in the North Pacific Subtropical Gyre detected by flow-cytometry cell sorting
No full textIn contrast to cyanobacteria, the significance of bacteria and archaea in oceanic N2 fixation remains unknown, apart from the knowledge that their nitrogenase (nifH) genes are diverse, present in all oceans and at least occasionally expressed. Non-cyanobacterial nifH sequences often occur as contamination from reagents and other sources, complicating the detection and interpretation of environmental phylotypes. We amplified and sequenced partial nifH gene fragments directly from cell populations sorted by fluorescence activated cell sorting from water collected in the North Pacific Subtropical Gyre (NPSG). Sequences recovered (195 total) included presumed heterotrophic or photoheterotrophic non-cyanobacterial nifH phylotypes previously unreported in the NPSG. A nifH sequence previously found in the South Pacific Gyre (HM210397) was exclusively recovered from sorted picoeukaryote populations, and was detected in water column samples using quantitative PCR (qPCR), with 60% of samples detected in the >?10??m size fraction in addition to the 0.2–10??m size fraction. A novel cluster 3-like nifH sequence was also recovered from discrete cell sorts and detected by qPCR in environmental samples. This approach enables the detection of rare nifH phylotypes, identifies possible associations with larger cells or particles and offers a possible solution for distinguishing reagent contaminants from real microbial community components
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Recommended from our members
Ecology and Evolution of Diatom-Associated Cyanobacteria Through Genetic Analyses
Get PDFPrimary production in a large fraction of the surface ocean communities is limited by the availability of nitrogen (N). Heterocyst-forming cyanobacteria associated with diatoms of the genera Hemiaulus, Rhizosolenia, and Chaetoceros can dominate surface communities throughout the global oceans, and are an important source of N to these communities. Additionally, these unique associations are directly linked to a highly efficient carbon export system. In order to study the nature and evolution of these symbioses, the genomes of representatives of symbionts from the three common diatom associations were sequenced. The genomes revealed the evolutionary pressure a symbiont undergoes as a result of long-term associations with unicellular diatoms. The implications of the genome streamlining, specifically in the N metabolism pathways, extend to mechanisms for maintenance of the association as well as possible symbiont regulation mechanisms by the diatom. The genomes could additionally be implemented in an unbiased examination of diatom symbiont transcription through an extensive environmental RNA sequence data set. This revealed significant reduction in photosystem II gene expression and possible regulation on the cyclic electron transport of the most abundant diatom symbiont population. The environmental sequences also showed very low diversity amongst the diatom symbiont populations. Lastly, the examination of interruption elements in heterocyst-forming cyanobacteria expanded the framework for which to study these genetic features. Although the majority of the element sequences proved to be highly dynamic, the recombinase sequences on each interruption element gave insights into the evolutionary paths of these unique genetic features. Additionally, the presence of elements in non-N2 fixation genes and in cyanobacteria not capable of cell differentiation implicate the interruption elements in processes beyond heterocyst formation. The genomic sequences of oceanic diatom symbionts have opened a myriad of approaches for which to study the globally significant diatom-diazotroph associations. These analyses have revealed much about the ecology and evolution of diatom symbionts, and carry implications into global oceanic nutrient cycling, as well as plant-microbe associations, in general
“Omics”-Enabled Microbial Sensors on Ocean Platforms
No full textIn order to assess the diversity and function of microbial communities most effectively, molecular assays need to be designed that target the phylogenetic markers and functional genes that are key to major ecological processes and microorganisms. A streamlined design process is presented here that designs probes for microarray and quantitative PCR (qPCR) assays, for application on the lab bench or on remote instrumentation. These assays can be used for DNA (genome) and RNA (gene transcription) studies. The pipeline described here establishes a database of environmental sequences, which is then used for the design of molecular probes for microarrays and to inform the design of qPCR assays, which is detailed here along with the assay optimization process. Finally, the process for the design of high-density microarrays is described. The qPCR protocol is currently used for assay optimization on the Environmental Sample Processor, a deployable robotic “genosensor” (http://www.mbari.org/esp). The protocols described here should advance applications in microbial oceanography using robotic instrumentation as well as traditional sampling methods
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
- …
