Crowdfunding the Azolla fern genome project: a grassroots approach

Pollutant removal from dairy wastewater using live Azolla filiculoides in batch and continuous bioreactors

Fast and proper treatment of dairy wastewater is necessary before discharging it to the environment. In this study, healthy Azolla filiculoides was used to remove pollutants, including phosphorus (P), sodium (Na), chemical oxygen demand (COD), biological oxygen demand (BOD), and total dissolved solids (TDS) of dairy effluent in batch, continuous system, as well as continuous with the slow stirring system. These systems were handmade. The maximum removal efficiency was related to the P, which obtained 66.25% after 12 h in the batch bioreactor system. The highest removal of 13.69% after 21 h was obtained for Na using continuous with a slow stirring method. The highest removal related to the COD and BOD was 33.53% and 29.93% after 18 h, respectively, in continuous with the slow stirring system. TDS removal was achieved 31.44% after 24 h using the batch system. The results of these three systems were compared with each other using a one-way analysis of variance (ANOVA). There was no significant difference between them. Azolla filiculoides is an abundant plant in northern nature that a biosystem was used for optimum usage. It can be used as an efficient, inexpensive, and affordable bioadsorbent for dairy wastewater treatment. PRACTITIONER POINTS: Live Azolla filiculoides was used to remove pollutants. P, Na, BOD, COD, and TDS were removed from dairy wastewater. Batch, continuous, and continuous with the slow stirring systems were used. Live Azolla was an efficient, inexpensive, and affordable bio-adsorbent for dairy wastewater treatment.

Crowdfunding scientific research: Descriptive insights and correlates of funding success

Crowdfunding has gained traction as a mechanism to raise resources for entrepreneurial and artistic projects, yet there is little systematic evidence on the potential of crowdfunding for scientific research. We first briefly review prior research on crowdfunding and give an overview of dedicated platforms for crowdfunding research. We then analyze data from over 700 campaigns on the largest dedicated platform, Experiment.com. Our descriptive analysis provides insights regarding the creators seeking funding, the projects they are seeking funding for, and the campaigns themselves. We then examine how these characteristics relate to fundraising success. The findings highlight important differences between crowdfunding and traditional funding mechanisms for research, including high use by students and other junior investigators but also relatively small project size. Students and junior investigators are more likely to succeed than senior scientists, and women have higher success rates than men. Conventional signals of quality–including scientists’ prior publications–have little relationship with funding success, suggesting that the crowd may apply different decision criteria than traditional funding agencies. Our results highlight significant opportunities for crowdfunding in the context of science while also pointing towards unique challenges. We relate our findings to research on the economics of science and on crowdfunding, and we discuss connections with other emerging mechanisms to involve the public in scientific research.

Jasmonic and salicylic acid response in the fern Azolla filiculoides and its cyanobiont

Plants sense and respond to microbes utilizing a multilayered signalling cascade. In seed plants, the phytohormones jasmonic and salicylic acid (JA and SA) are key denominators of how plants respond to certain microbes. Their interplay is especially well-known for tipping the scales in plants' strategies of dealing with phytopathogens. In non-angiosperm lineages, the interplay is less well understood, but current data indicate that it is intertwined to a lesser extent and the canonical JA/SA antagonism appears to be absent. Here, we used the water fern Azolla filiculoides to gain insights into the fern's JA/SA signalling and the molecular communication with its unique nitrogen fixing cyanobiont Nostoc azollae, which the fern inherits both during sexual and vegetative reproduction. By mining large-scale sequencing data, we demonstrate that Azolla has most of the genetic repertoire to produce and sense JA and SA. Using qRT-PCR on the identified biosynthesis and signalling marker genes, we show that Azolla is responsive to exogenously applied SA. Furthermore, exogenous SA application influenced the abundance and gene expression of Azolla's cyanobiont. Our data provide a framework for JA/SA signalling in ferns and suggest that SA might be involved in Azolla's communication with its vertically inherited cyanobiont.

Occurrence of brassinosteroids in non-flowering land plants, liverwort, moss, lycophyte and fern

Endogenous brassinosteroids (BRs) in non-flowering land plants were analyzed. BRs were found in a liverwort (Marchantia polymorpha), a moss (Physcomitrella patens), lycophytes (Selaginella moellendorffii and S. uncinata) and 13 fern species. A biologically active BR, castasterone (CS), was identified in most of these non-flowering plants but another biologically active BR, brassinolide, was not. It may be distinctive that levels of CS in non-flowering plants were orders of magnitude lower than those in flowering plants. 22-Hydroxycampesterol and its metabolites were identified in most of the non-flowering plants suggesting that the biosynthesis of BRs via 22-hydroxylation of campesterol occurs as in flowering plants. Phylogenetic analyses indicated that M. polymorpha, P. patens and S. moellendorffii have cytochrome P450s in the CYP85 clans which harbors BR biosynthesis enzymes, although the P450 profiles are simpler as compared with Arabidopsis and rice. Furthermore, these basal land plants were found to have multiple P450s in the CYP72 clan which harbors enzymes to catabolize BRs. These findings indicate that green plants were able to synthesize and inactivate BRs from the land-transition stage.

Transcriptome sequencing reveals genome-wide variation in molecular evolutionary rate among ferns

BACKGROUND

Transcriptomics in non-model plant systems has recently reached a point where the examination of nuclear genome-wide patterns in understudied groups is an achievable reality. This progress is especially notable in evolutionary studies of ferns, for which molecular resources to date have been derived primarily from the plastid genome. Here, we utilize transcriptome data in the first genome-wide comparative study of molecular evolutionary rate in ferns. We focus on the ecologically diverse family Pteridaceae, which comprises about 10 % of fern diversity and includes the enigmatic vittarioid ferns-an epiphytic, tropical lineage known for dramatically reduced morphologies and radically elongated phylogenetic branch lengths. Using expressed sequence data for 2091 loci, we perform pairwise comparisons of molecular evolutionary rate among 12 species spanning the three largest clades in the family and ask whether previously documented heterogeneity in plastid substitution rates is reflected in their nuclear genomes. We then inquire whether variation in evolutionary rate is being shaped by genes belonging to specific functional categories and test for differential patterns of selection.

RESULTS

We find significant, genome-wide differences in evolutionary rate for vittarioid ferns relative to all other lineages within the Pteridaceae, but we recover few significant correlations between faster/slower vittarioid loci and known functional gene categories. We demonstrate that the faster rates characteristic of the vittarioid ferns are likely not driven by positive selection, nor are they unique to any particular type of nucleotide substitution.

CONCLUSIONS

Our results reinforce recently reviewed mechanisms hypothesized to shape molecular evolutionary rates in vittarioid ferns and provide novel insight into substitution rate variation both within and among fern nuclear genomes.

Evolutionary aspects of plant photoreceptors

Plant photoreceptors link environmental light cues with physiological responses, determining how individual plants complete their life cycles. Structural and functional evolution of photoreceptors has co-occurred as plants diversified and faced the challenge of new light environments, during the transition of plants to land and as substantial plant canopies evolved. Large-scale comparative sequencing projects allow us for the first time to document photoreceptor evolution in understudied clades, revealing some surprises. Here we review recent progress in evolutionary studies of three photoreceptor families: phytochromes, phototropins and neochromes.

A Guide to Scientific Crowdfunding

Crowdfunding represents an attractive new option for funding research projects, especially for students and early-career scientists or in the absence of governmental aid in some countries. The number of successful science-related crowdfunding campaigns is growing, which demonstrates the public’s willingness to support and participate in scientific projects. Putting together a crowdfunding campaign is not trivial, however, so here is a guide to help you make yours a success.

A new way of funding research has recently emerged, potentially democratizing the way science is done. This article provides a guide to increasing the odds of financing your research through crowdfunding.

An Exploration into Fern Genome Space

Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (∼0.4X to 2X) for six fern species from the Polypodiales (Ceratopteris, Pteridium, Polypodium, Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of fern genomes can provide information useful for selecting a promising candidate fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between ferns and seed plants.

Between two fern genomes

Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves.