Effects of nutrient enrichment on surface microbial community gene expression in the oligotrophic North Pacific Subtropical Gyre

Marine microbial communities are critical for biogeochemical cycles and the productivity of ocean ecosystems. Primary productivity, at the base of marine food webs, is constrained by nutrient availability in the surface ocean, and nutrient advection from deeper waters can fuel photosynthesis. In this study, we compared the transcriptional responses by surface microbial communities after experimental deep water mixing to the transcriptional patterns of in situ microbial communities collected with high-resolution automated sampling during a bloom in the North Pacific Subtropical Gyre. Transcriptional responses were assayed with the MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories) marine environmental microarray, which targets all three domains of life and viruses. The experiments showed that mixing of deep and surface waters substantially affects the transcription of photosystem and nutrient response genes among photosynthetic taxa within 24 hours, and that there are specific responses associated with the addition of deep water containing particles (organisms and detritus) compared to filtered deep water. In situ gene transcription was most similar to that in surface water experiments with deep water additions, showing that in situ populations were affected by mixing of nutrients at the six sampling sites. Together, these results show the value of targeted metatranscriptomes for assessing the physiological status of complex microbial communities. Transcription by surface water and deep water microbial communities was assessed for samples collected during the BioLINCS cruise from 6-21 September 2011 in the North Pacific Subtropical Gyre (NPSG). In situ surface samples (24 m) were collected with an Environmental Sample Processer (ESP) each morning (5:00-6:00) and evening (17:00). As the ESP drifted along the boundary of two anticyclonic eddies from 14-16 September, large increases in nutrient concentrations were observed at the surface, possibly indicating vertical advection of deep, nutrient-rich water. To study the surface community transcriptional response to this hypothesized advection event, morning and evening ESP samples from 14, 15, and 16 September (six ESP samples in total) were assayed with the MicroTOOLs microarray v2.0 (GPL24371). Additionally, the surface community response to nutrient increases was assesed with MicroTOOLs in a mixing experiment (simulated advection). The mixing experiment used surface (25 m) and, by comparison, deep (130 m) water that was collected on 12 September and observed to have, respectively, low and high nutrient concentrations (typical of the NPSG in the late summer). In order to distinguish the effects of nutrient changes versus biological interactions between surface and deep communities, the mixing experiment used both filtered and unfiltered water as follows (see Fig. 2 in our publication): Surf_FDW = unfiltered surface water (16 L) mixed with filtered deep water (4 L), to assess effects of nutrients alone on the surface community (by comparison to control Surf_Cnt); Deep_FSW = unfiltered deep water (4 L) mixed with filtered surface water (16 L), to assess effects of surface conditions on the deep community (by comparison to control Deep_Cnt); Surf_UDW = unfiltered surface and unfiltered deep water (16 L and 4 L, respectively), to assess biological effects (by comparison to Surf_FDW). Control samples mixed filtered and unfiltered water from the same depth: Surf_Cnt = unfiltered (16 L) and filtered (4 L) surface water; Deep_Cnt = unfiltered (4 L) and filtered (16 L) deep water. Ten mixing experiment samples (5 types x 2 replicates) were assayed with MicroTOOLs. [variable] other: in situ sample: ESP_Sep14_500_id_2012, ESP_Sep15_1700_id_2041, ESP_Sep14_1700_id_2061, ESP_Sep15_500_id_3045, ESP_Sep16_500_id_3052, ESP_Sep16_1700_id_3053 [variable] other: mixing experiment sample: Surf_FDW_id_52602, Surf_FDW_id_52603, Surf_Cnt_id_52604, Surf_Cnt_id_52605, Deep_FSW_id_52606, Deep_FSW_id_52607, Deep_Cnt_id_52608, Deep_Cnt_id_52609, Surf_UDW_id_52610, Surf_UDW_id_52611