Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics

Abstract

Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking, because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements showed that the harmful alga Aureococcus anophagefferens outcompeted co-occurring phytoplankton in estuaries with elevated levels of dissolved organic matter and turbidity and low levels of dissolved inorganic nitrogen. We subsequently sequenced the genome of A. anophagefferens and compared its gene complement with those of six competing phytoplankton species identified through metaproteomics. Using an ecogenomic approach, we specifically focused on gene sets that may facilitate dominance within the environmental conditions present during blooms. A. anophagefferens possesses a larger genome (56 Mbp) and has more genes involved in light harvesting, organic carbon and nitrogen use, and encoding selenium- and metal-requiring enzymes than competing phytoplankton. Genes for the synthesis of microbial deterrents likely permit the proliferation of this species, with reduced mortality losses during blooms. Collectively, these findings suggest that anthropogenic activities resulting in elevated levels of turbidity, organic matter, and metals have opened a niche within coastal ecosystems that ideally suits the unique genetic capacity of A. anophagefferens and thus, has facilitated the proliferation of this and potentially other HABs.

A family of diatom-like silicon transporters in the siliceous loricate choanoflagellates

“…The convergent evolution of SITs in loricate choanoflagellates and siliceous stramenopiles would require not only parallel evolution of multiple SIT-specific features, but also the loss of all related or ancestral genes in all other opisthokonts and non-siliceous stramenopiles. The taxonomic coverage of available sequence data [55,56] makes such a conclusion highly unlikely.…”

Agrigenomics for Microalgal Biofuel Production: An Overview of Various Bioinformatics Resources and Recent Studies to Link OMICS to Bioenergy and Bioeconomy

“…To date, the whole genome sequences of more than ten microalgae have been generated (Guarnieri et al, 2011;Liu and Benning, 2012;) (Table 1). These includes the Cyanidioschyzon merolae 10D (Matsuzaki et al, 2004), Phaeodactylum tricornutum CCP1055/1 , Thalassiosira pseudonana CCMP1335 (Armbrust et al, 2004), Guillardia theta CCMP2712 (Curtis et al, 2012), Chlamydomonas reinhardtii CC-503 (Merchant et al, 2007), Ostreococcus tauri OTH95 (Derelle et al, 2006), Ostreococcus lucimarinus CCE9901 (Palenik et al, 2007), two strains of Micromonas pusilla, RCC299 and CCMP1545 (Worden et al, 2009), Bathycoccus prasinos RCC1105 (Moreau et al, 2012), Volvox carteri UTEX2908 (Prochnik et al, 2010), Chlorella vulgaris NC64A (Blanc et al, 2010), Coccomyxa subellipsoidea C-169 (Blanc et al, 2012), Ectocarpus siliculosus EC32 (Cock et al, 2010), Aureococcus anophagefferens CCMP1984 (Gobler et al, 2011), Nannochloropsis gaditana (Radakovits et al, 2012), and Bigelowiella natans CCMP2755 (Curtis et al, 2012). Other algal genomes in the sequencing pipeline are Ostreococcus sp RCC809, Botryococcus braunii Berkeley strain, Dunaliella salina CCAP19/18, Galdieria sulphuraria, Chondrus crispus, Fragilariopsis cylindrus CCMP1102, Pseudo-nitzchia multiseries CLN-47, Emiliana huxleyi CCMP1516 (Radakovits et al, 2010;Tirichine and Bowler, 2011).…”

Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton

“…The genetic repertoire of N and P transporters shows evidence of gene duplication, differential loss, and horizontal gene transfer (HGT) in phytoplankton genomes as well as contrasting gene expression levels (5)(6)(7)(8)(9), suggesting that the evolution of these genes has been driven by adaptation to environmental limitation. Ammonium (NH + 4 ) and nitrate (NO − 3 ) are commonly available N sources for marine phytoplankton (10,11) and, as such, the gene repertoires of cyanobacterial and eukaryotic phytoplankton are configured toward utilization of these two forms of inorganic N sources (12).…”