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      Crowdfunding the Azolla fern genome project: a grassroots approach

      research-article
      Author(s): 1 , , 1
      Publication date (Electronic):
      Journal: GigaScience
      Publisher: BioMed Central
      Keywords: Azolla, Cyanobacteria, Fern, Genome sequencing, Nitrogen fixation, Nostoc, Op-ed, Social media, Symbiosis, Crowdfunding

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          Abstract

          Much of science progresses within the tight boundaries of what is often seen as a “black box”. Though familiar to funding agencies, researchers and the academic journals they publish in, it is an entity that outsiders rarely get to peek into. Crowdfunding is a novel means that allows the public to participate in, as well as to support and witness advancements in science. Here we describe our recent crowdfunding efforts to sequence the Azolla genome, a little fern with massive green potential. Crowdfunding is a worthy platform not only for obtaining seed money for exploratory research, but also for engaging directly with the general public as a rewarding form of outreach.

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          Episodic fresh surface waters in the Eocene Arctic Ocean

          Henk Brinkhuis, Stefan Schouten, Margaret E Collinson … (2006)
          It has been suggested, on the basis of modern hydrology and fully coupled palaeoclimate simulations, that the warm greenhouse conditions that characterized the early Palaeogene period (55-45 Myr ago) probably induced an intensified hydrological cycle with precipitation exceeding evaporation at high latitudes. Little field evidence, however, has been available to constrain oceanic conditions in the Arctic during this period. Here we analyse Palaeogene sediments obtained during the Arctic Coring Expedition, showing that large quantities of the free-floating fern Azolla grew and reproduced in the Arctic Ocean by the onset of the middle Eocene epoch (approximately 50 Myr ago). The Azolla and accompanying abundant freshwater organic and siliceous microfossils indicate an episodic freshening of Arctic surface waters during an approximately 800,000-year interval. The abundant remains of Azolla that characterize basal middle Eocene marine deposits of all Nordic seas probably represent transported assemblages resulting from freshwater spills from the Arctic Ocean that reached as far south as the North Sea. The termination of the Azolla phase in the Arctic coincides with a local sea surface temperature rise from approximately 10 degrees C to 13 degrees C, pointing to simultaneous increases in salt and heat supply owing to the influx of waters from adjacent oceans. We suggest that onset and termination of the Azolla phase depended on the degree of oceanic exchange between Arctic Ocean and adjacent seas.
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            Genome Erosion in a Nitrogen-Fixing Vertically Transmitted Endosymbiotic Multicellular Cyanobacterium

            Liang Ran, John Larsson, Theoden Vigil-Stenman … (2010)
            Background An ancient cyanobacterial incorporation into a eukaryotic organism led to the evolution of plastids (chloroplasts) and subsequently to the origin of the plant kingdom. The underlying mechanism and the identities of the partners in this monophyletic event remain elusive. Methodology/Principal Findings To shed light on this evolutionary process, we sequenced the genome of a cyanobacterium residing extracellularly in an endosymbiosis with a plant, the water-fern Azolla filiculoides Lam. This symbiosis was selected as it has characters which make it unique among extant cyanobacterial plant symbioses: the cyanobacterium lacks autonomous growth and is vertically transmitted between plant generations. Our results reveal features of evolutionary significance. The genome is in an eroding state, evidenced by a large proportion of pseudogenes (31.2%) and a high frequency of transposable elements (∼600) scattered throughout the genome. Pseudogenization is found in genes such as the replication initiator dnaA and DNA repair genes, considered essential to free-living cyanobacteria. For some functional categories of genes pseudogenes are more prevalent than functional genes. Loss of function is apparent even within the ‘core’ gene categories of bacteria, such as genes involved in glycolysis and nutrient uptake. In contrast, serving as a critical source of nitrogen for the host, genes related to metabolic processes such as cell differentiation and nitrogen-fixation are well preserved. Conclusions/Significance This is the first finding of genome degradation in a plant symbiont and phenotypically complex cyanobacterium and one of only a few extracellular endosymbionts described showing signs of reductive genome evolution. Our findings suggest an ongoing selective streamlining of this cyanobacterial genome which has resulted in an organism devoted to nitrogen fixation and devoid of autonomous growth. The cyanobacterial symbiont of Azolla can thus be considered at the initial phase of a transition from free-living organism to a nitrogen-fixing plant entity, a transition process which may mimic what drove the evolution of chloroplasts from a cyanobacterial ancestor.
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              Azolla: A review of its biology and utilization

              Gregory M. Wagner (1997)
              Article 0 comments Cited 55 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Fay-Wei Li
                Kathleen M Pryer
                Journal
                Journal ID (nlm-ta): Gigascience
                Journal ID (iso-abbrev): Gigascience
                Title: GigaScience
                Publisher: BioMed Central
                ISSN (Electronic): 2047-217X
                Publication date Collection: 2014
                Publication date (Electronic): 26 September 2014
                Volume: 3
                Page: 16
                Affiliations
                [1 ]Department of Biology, Duke University, Durham, North Carolina 27708, USA
                Article
                Publisher ID: 2047-217X-3-16
                DOI: 10.1186/2047-217X-3-16
                PMC ID: 4178311
                PubMed ID: 25276348
                SO-VID: 2799cc86-ffa2-4657-ad35-1515b6a8ca72
                Copyright © Copyright © 2014 Li and Pryer; licensee BioMed Central Ltd.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                Date received : 12 August 2014
                Date accepted : 18 September 2014
                Categories
                Subject: Commentary

                Keywords: azolla,cyanobacteria,fern,genome sequencing,nitrogen fixation,nostoc,op-ed,social media,symbiosis,crowdfunding
                Data availability:
                Keywords: azolla, cyanobacteria, fern, genome sequencing, nitrogen fixation, nostoc, op-ed, social media, symbiosis, crowdfunding

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