Frustule‐related gene transcription and the influence of diatom community composition on silica precipitation in an iron‐limited environment

Abstract

A microcosm study in iron-limited waters of the northeast subarctic Pacific Ocean was conducted to examine how iron availability affects the frustule-related response of individual diatoms and thus the total quantity of silica precipitated by the community. New silica precipitated per cell was estimated using the fluorescent cell stain 2-(4-pyridyl)-5{[4-dimethylaminoethyl-aminocarbamoyl)-methoxy]phenyl}oxazole (PDMPO). Differences in new silica precipitation within a particular genus before and after iron enrichment were small compared to differences among genera, indicating that the quantity of total silica precipitated is particularly sensitive to community composition. Transcriptional patterns of genes encoding silicon transporters, aminopropyltransferases, chitin synthases, and a protein with uncharacterized function were measured in natural populations to identify indicators of the frustule-related responses of different genera to iron limitation. Transcripts associated with silicon transporters were the most readily detectable in three metatranscriptome datasets and were capable of resolving species composition shifts and physiological responses. Silicon transporter transcripts from a distinct phylogenetic clade were most abundant in the iron-limited community, and transcripts from a separate clade were more abundant in the community that bloomed after iron enrichment. Transcripts of the gene present in the ironlimited community were also more abundant in iron-limited laboratory cultures of Pseudo-nitzschia multiseries, suggesting that this gene plays a role in silicon uptake during iron limitation. The responses of individual cells, as detected in this study, determine how the community influences silicon cycling in iron-limited environments.

Silicic acid supplied to coastal diatom communities influences cellular silicification and the potential export of carbon

“…4). The populations detected by this method have been previously shown to contain only silicifying phytoplankton (Durkin et al 2012).…”

“…The total translated sequence lengths were between 37 and 505 amino acids and spanned different regions of the aligned sequences. The translated sequences of Minutocellus were most closely related to SIT clades b and c of a previously constructed SIT phylogenetic tree (Durkin et al 2012). The translated sequences of Cylindrotheca were most closely related to clades a and b, Thalassiosira sequences were most closely related to clades e and b, and Odontella sequences were most closely related to clades a, b, c, and d. The placement location of each transcript fragment on the phylogenetic tree had a posterior probability (pp) .…”

“…These data sets were used to identify the SIT genes encoded by each isolate. A hidden Markov model profile was constructed based on an alignment of amino acid sequences from previously identified silicon transporters (Durkin et al 2012) and the software HMMer (www.hmmer.org) was used to identify SIT sequences in each transcriptome. Sequences were placed on a phylogenetic tree (Durkin et al 2012) using pplacer software (Matsen et al 2010) to identify the phylogenetic clade of each sequence.…”

“…A hidden Markov model profile was constructed based on an alignment of amino acid sequences from previously identified silicon transporters (Durkin et al 2012) and the software HMMer (www.hmmer.org) was used to identify SIT sequences in each transcriptome. Sequences were placed on a phylogenetic tree (Durkin et al 2012) using pplacer software (Matsen et al 2010) to identify the phylogenetic clade of each sequence. Actin gene sequences were similarly identified using a reference alignment of translated actin gene sequences identified in the genomes of Fragilariopsis cylindrus (protein ID 222562), Pseudo-nitzscha multiseries (protein ID 22272), and Thalassiosira pseudonana (protein ID 269504; http://genome.jgi-psf.org).…”

“…All diatoms studied to date possess multiple SIT genes, and often these gene copies have diverged into separate clades of the gene family (Thamatrakoln et al 2006;Durkin et al 2012). The diverged SIT genes are transcribed differently from one another across the cell cycle (Thamatrakoln and Hildebrand 2007) and when cells are silicon starved, iron starved, or iron limited (Allen et al 2008;Mock et al 2008;Durkin et al 2012).…”