Winter mixing impacts gene expression in marine microbial populations in the Gulf of Aqaba

Abstract

In aquatic systems, changes in temperature and irradiance fundamentally characterize the water column and regulate microbial population structure and function. In systems with stable thermal stratification, the warm surface mixed layer is typically nutrient impoverished, limiting biological production. In periods of destratification, convective mixing of the water column exposes the microorganisms inhabiting these mixed systems to rapid variations in light availability and spectra. We explored the impact of winter deep-mixing (500 m deep mixed layer) on microbial communities from the surface (2.5 m) and the aphotic waters (440 m) in the Gulf of Aqaba by examining changes in both population composition and function via DNA and RNA sequencing. The greatest fraction of 16S sequences was assigned to Euryarchaeota, while metatranscriptomes were dominated by Synechococcus transcripts. Community composition was highly similar at both depths, yet transcription profiles differed. Phototrophic organisms found at the photic surface overexpressed genes related to catabolism and energy metabolism, while genes affiliated with biosynthesis were overexpressed at the aphotic depth. Similar transcriptional trends were observed in the non-photoautotrophs SAR11, Euryarchaeota, and Thaumarchaeota, with niche partitioning based on differential utilization of nitrogen and phosphorus occurring between the 2 archaeal groups. We did not detect upregulated expression of cyanobacterial genes indicative of mixotrophy or glycogen metabolism in the aphotic zone, suggesting they survive the aphotic period by utilizing photosynthates produced in the photic zone. Indications for a mixotrophic lifestyle were observed for prasinophytes, with genes related to phagocytosis overexpressed at the aphotic depth compared with the surface.

Transcriptional activity differentiates families of Marine Group IIEuryarchaeotain the coastal ocean

“…2). Previous studies noted high transcription of euryarchaeal livK and aapJ genes in the water column of the Red Sea [19,20], at the Mid-Cayman Rise [21], and throughout the Atlantic Ocean [22]. Our data suggest this activity was probably associated with Ca.…”

“…Poseidoniales transcripts can be abundant in marine metatranscriptomes, suggesting transiently high transcriptional activity [18,19]. When metatranscriptome reads from the Gulf of Aqaba were mapped to metagenomic contigs from the Mediterranean Sea, genes involved in amino acid transport, carbon metabolism, and cofactor synthesis were highly transcribed in the aggregate euryarchaeal community [20,21]. In another study, mapping deep-sea metatranscriptome reads to novel Ca .…”

Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment

“…It seems likely that these capabilities allow for better adaptation to overcome the environmental disturbances produced during winter mixing and subsequent phytoplankton blooms. Unlike what the literature has described so far, we measured a temporal persistence of some taxa previously considered sporadic or rare, such as archaea [ 22 , 29 , 48 , 49 ]. Although these taxa only recruit below the photic zone during the stratified period, members of the ammonia-oxidizing group I Thaumarchaeota and groups II and III Euryarchaeota were always found to be present in the water column.…”

Evaluating the potential of direct RNA nanopore sequencing: Metatranscriptomics highlights possible seasonal differences in a marine pelagic crustacean zooplankton community

“…Metatranscriptomics is to date already widely used to study microbial community functions, including marine bacterioplankton communities (e.g. Helbling et al, 2012;Hewson et al, 2014;Kopf et al, 2015;Miller et al, 2017;Wermheuer et al, 2014) and phytoplankton communities (e.g. Alexander et al, 2015).…”