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 iron-limited 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.