29 research outputs found
Two subpopulations of Crocosphaera watsonii have distinct distributions in the North and South Pacific
No full textCrocosphaera 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
Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics
No full textThe facultative symbiont of Riftia pachyptila, named here Candidatus Endoriftia persephone, has evaded culture to date, but much has been learned regarding this symbiosis over the past three decades since its discovery. The symbiont population metagenome was sequenced in order to gain insight into its physiology. The population genome indicates that the symbionts use a partial Calvin–Benson Cycle for carbon fixation and the reverse TCA cycle (an alternative pathway for carbon fixation) that contains an unusual ATP citrate lyase. The presence of all genes necessary for heterotrophic metabolism, a phosphotransferase system, and dicarboxylate and ABC transporters indicate that the symbiont can live mixotrophically. The metagenome has a large suite of signal transduction, defence (both biological and environmental) and chemotaxis mechanisms. The physiology of Candidatus Endoriftia persephone is explored with respect to functionality while associated with a eukaryotic host, versus free-living in the hydrothermal environment
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Comparative genomics and natural distributions of phenotypically distinct strains of the nitrogen-fixing cyanobacterium Crocosphaera watsonii
No full textCrocosphaera watsonii is an ecologically important marine unicellular diazotrophic cyanobacterium. It is often abundant in oligotrophic ocean regions where it provides fixed nitrogen to nutrient-limited phytoplankton communities. Previous genetic studies have observed genetic rearrangements but very little sequence variation among natural populations or cultivated strains of Crocosphaera. Those strains exhibit two phenotypes (large- and small-cell) with characteristics that suggest different ecological roles and niches. Prior to this work, the genetic basis for the phenotypic differences was unknown, and molecular methods for enumerating natural C. watsonii could not differentiate between phenotypes. To address those unanswered scientific questions, these studies compared the genomes of six C. watsonii strains, three of each phenotype, which were isolated over large spatial and temporal distances. A large portion of those genome sequences were shared among all strains with nearly 100% nucleotide identity. However, there were also genes that were specific to each strain, and others were specific to each phenotype, including some which could explain phenotypic differences (e.g. EPS biosynthesis). Relative to small-cell strains, large-cell strains had larger genomes and additional genetic capabilities, including possibly increased adaptations to iron and phosphorus limitation. Clustering based on genome sequences and content showed that strains with a common phenotype were evolutionarily most closely related, regardless of their time and location of isolation. Surprisingly, the genome of the C. watsonii type-strain, WH8501, was quite unusual, even compared to those with the same phenotype, suggesting it may not be appropriately representative of the species. To investigate distributions of Crocosphaera types in the marine environment, molecular assays were developed, based on phenotype-specific genes, and applied to samples from the North and South Pacific. In those samples, small-cells dominated in the upper 75 m where abundance of both types was much greater, while large-cells dominated in samples with lower counts between 100 m and 175 m. There was also more evidence that large-cells form aggregates in the N. Pacific. Future studies will be important to determine which of the initial C. watsonii patterns described here can be generalized, both in genomes, and in natural distributions of the two types
Gene expression patterns in Euglena gracilis: Insights into the cellular response to environmental stress
No full textTo better understand Euglena gracilis gene expression under different stress conditions (Chromium, Streptomycin or darkness), we undertook a survey of the E. gracilis transcriptome by cDNA sequencing and microarray analysis. First, we constructed a non-normalized cDNA library from the E. gracilis UTEX strain and sequenced a total of 1000 cDNAs. Six hundred and ten of these ESTs were similar to either Plantae or Protistae genes (e-value < e- 10). Second, microarrays were built by spotting all the ESTs onto mirror slides. Microarray expression analysis indicated that 90 out of those 610 ESTs changed their expression level in response to different stress treatments (p < 0.05). In addition, we detected 10 ESTs that changed expression levels irrespective of the tested stress. These may be considered as part of a larger set of stress-related genes in E. gracilis. Finally, we identified 23 unknown ESTs (U-ESTs) following the expression profiles of these putative stress-related genes suggesting that they could be related to the cellular mechanism of stress response.Fil: Dos Santos Ferreira, Veronica Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina. Universidad de Buenos Aires; ArgentinaFil: Rocchetta, Iara. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Biodiversidad y Biología Experimental; ArgentinaFil: Conforti, Visitacion Teresa D.. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Biodiversidad y Biología Experimental; ArgentinaFil: Bench, Shellie. University of California; Estados UnidosFil: Feldman, Robert. University of California; Estados Unidos. SymBio Corporation; Estados UnidosFil: Levin, Mariano Jorge. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina. Universidad de Buenos Aires; Argentina. lnstitut Cochin; Franci
Coupling FACS and Genomic Methods for the Characterization of Uncultivated Symbionts
No full textSymbioses between microbes are likely widespread and functionally relevant in diverse biological systems; however, they are difficult to discover. Most microbes remain uncultivated, symbioses can be relatively rare or dynamic, and intercellular connections can be delicate. Thus, traditional methods such as microscopy are inadequate for efficient discovery and precise characterization of novel interactions, their metabolic basis, and the species involved. High-throughput metagenomic sequencing of entire microbial communities has revolutionized the field of microbial ecology; however, genomic signals from symbionts can get buried in sequences from abundant organisms and evidence for direct links between microbial species cannot be gained from bulk samples. Thus, a specialized approach to the characterization of symbioses between naturally occurring microbes is required. This chapter presents methods for combining fluorescence-activated cell sorting to isolate and separate uncultivated symbionts with molecular biology techniques for DNA amplification in order to characterize uncultivated symbionts through genomic and metagenomic techniques
Approaching the uncultured endosymbiont of Riftia pachyptila by physiological proteomics
No full textAuthor Posting. © The Authors, 2006. This is the author's version of the work. It is posted here by permission of AAAS for personal use, not for redistribution. The definitive version was published in Science 315 (2007): 247-250, doi:10.1126/science.1132913.The bacterial endosymbiont of the deep-sea tube worm Riftia pachyptila has
never been successfully cultivated outside its host. In the absence of cultivation data we
have taken a proteomic approach based on the metagenome sequence to study the
metabolism of this peculiar microorganism in detail. As one result, we found that three
major sulfide oxidation proteins constitute ~12% of the total cytosolic proteome,
highlighting the essential role of these enzymes for the symbiont’s energy metabolism.
Unexpectedly, the symbiont uses the reductive tricarboxylic acid (TCA) cycle in addition
to the previously identified Calvin cycle for CO2 fixation.This work was supported by
the DFG, grant Schw595/3-1. Other funding sources were: NSF (OCE 04-52333) and NASA Astrobiology Institute (NNA04CC04A) for SMS, MH: postdoctoral
scholarship from WHOI, HF: Academic Senate (RF811S and RE518S)
Chapter Three Coupling FACS and Genomic Methods for the Characterization of Uncultivated Symbionts
No full textA splice of life (home, laptop, wi-fi)
No full textMetramorphosis is a process of change on borderlines and thresholds between being and absence,
memory and oblivion, 1 and non-I, a process of transgression and fading away. The metramorphic
consciousness has no centre, cannot hold a fixed gaze -or, if it has a centre, it constantly slides to the
borders, to the margins.1
This paper examines Bracha Lichtenberg Ettinger’s matrixial theory in relation to her concept of
Metramorphosis as “a process of change on borderlines and thresholds” 2 when experienced from the
perspective of living at home during the pandemic. It attempts to do this by addressing the
circumstances of the artist/author of this paper, as a way to (re)produce encounters, firstly lived
through the screen, then later developed upon through a palimpsestic process whereby layers and
layers of ‘artworking’ are applied through interdisciplinary virtual, digital and analogue methods, as a
response to working through the pandemic
Two strains of Crocosphaera watsonii with highly conserved genomes are distinguished by strain-specific features
No full textUnicellular nitrogen-fixing cyanobacteria are important components of marine phytoplankton. Although non-nitrogen-fixing marine phytoplankton generally exhibit high gene sequence and genomic diversity, gene sequences of natural populations and isolated strains of Crocosphaera watsonii, one of two most abundant open ocean unicellular cyanobacteria groups, have been shown to be 98-100% identical.. The low sequence diversity in Crocosphaera is a dramatic contrast to sympatric species of Prochlorococcus and Synechococcus, and raises the question of how genome differences can explain observed phenotypic diversity among Crocosphaera strains. Here we show, through whole genome comparisons of two phenotypically different strains, that there are strain-specific sequences in each genome, and numerous genome rearrangements, despite exceptionally low sequence diversity in shared genomic regions. Some of the strain-specific sequences encode functions that explain observed phenotypic differences, such as exopolysaccharide biosynthesis. The pattern of strain-specific sequences distributed throughout the genomes, along with rearrangements in shared sequences is evidence of significant genetic mobility that may be attributed to the hundreds of transposase genes found in both strains. Furthermore, such genetic mobility appears to be the main mechanism of strain divergence in Crocosphaera which do not accumulate DNA microheterogeneity over the vast majority of their genomes. The strain-specific sequences found in this study provide tools for future physiological studies, as well as genetic markers to help determine the relative abundance of phenotypes in natural populations
