Associated Bacteria Affect Sexual Reproduction by Altering Gene Expression and Metabolic Processes in a Biofilm Inhabiting Diatom

Abstract

Diatoms are unicellular algae with a fundamental role in global biogeochemical cycles as major primary producers at the base of aquatic food webs. In recent years, chemical communication between diatoms and associated bacteria has emerged as a key factor in diatom ecology, spurred by conceptual and technological advancements to study the mechanisms underlying these interactions. Here, we use a combination of physiological, transcriptomic, and metabolomic approaches to study the influence of naturally co-existing bacteria, Maribacter sp. and Roseovarius sp., on the sexual reproduction of the biofilm inhabiting marine pennate diatom Seminavis robusta . While Maribacter sp. severely reduces the reproductive success of S. robusta cultures, Roseovarius sp. slightly enhances it. Contrary to our expectation, we demonstrate that the effect of the bacterial exudates is not caused by altered cell-cycle regulation prior to the switch to meiosis. Instead, Maribacter sp. exudates cause a reduced production of diproline, the sexual attraction pheromone of S. robusta . Transcriptomic analyses show that this is likely an indirect consequence of altered intracellular metabolic fluxes in the diatom, especially those related to amino acid biosynthesis, oxidative stress response, and biosynthesis of defense molecules. This study provides the first insights into the influence of bacteria on diatom sexual reproduction and adds a new dimension to the complexity of a still understudied phenomenon in natural diatom populations.

Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatomSeminavis robusta

“…In this study, we generated a new time-series dataset to investigate the response of dark-synchronized MT+ cultures to SIP-(6 time points, 0-9h, Figure 2A) and to compare expression patterns with two existing datasets on the response of MT-to SIP+ (5 time points, 0-10h, Figure 2B) 17,19 . For each dataset, three replicates are available for both control and SIP treated conditions at every time point.…”

“…Overall, most genes are significant in only a single time point (5% OFDR, Figure 2D). Combined, on a 5% overall FDR (OFDR) level, 4037 genes are DE in response to SIP treatment for MT+, while 5486 genes are found to be DE in MT-in the first three hours 17 and 6079 genes after 10h 19 .…”

“…RNA-seq data generated in this study representing the response of MT+ to SIP-was complemented with existing data on the response of MT-to SIP+. The experimental setup for the two MT-RNA-seq datasets are described in their respective publications 17,19 . For the novel MT+ dataset, we harvested control cultures in the dark (time point 0h) and further harvested dark-synchronized cultures consisting of three control replicates and three SIP-treated replicates at five time points: 15min, 1h, 3h, 6h and 9h.…”

“…All three RNA-seq datasets were mapped with Salmon v0.9.1 20 to the S. robusta gene models v1.0 from Cirri et al 19 (available at https://bioinformatics.psb.ugent.be/gdb/seminavis/Version1.0; mapping rates shown in Supplementary Figure 1) and a conventional differential expression (DE) analysis was performed using negative binomial models implemented in the edgeR package 21 . Details about the model, design matrix and contrasts of interest are described in Supplementary Methods.…”

TheSeminavis robustagenome provides insights into the evolutionary adaptations of benthic diatoms

“…The family that shows the highest pleiotropic signal is involved in cyclic guanosine monophosphate (cGMP) biosynthesis, which was shown to play a key role during the onset of sexual reproduction in S. robusta [16] as well as Pseudo-nitzschia multistriata [23]. A recent study suggests that this signaling pathway might also be involved in the response to bacteria [24]. Our results corroborate these functions, but also indicate that the cGMP-related signaling may have a much broader role than previously thought, showing significant upregulation in a wide-range of abiotic stresses ( Figure 3B).…”