Transcriptional Patterns of Biogeochemically Relevant Marker Genes by Temperate Marine Bacteria

Abstract

Environmental microbial gene expression patterns remain largely unexplored, particularly at interannual time scales. We analyzed the variability in the expression of marker genes involved in ecologically relevant biogeochemical processes at a temperate Atlantic site over two consecutive years. Most of nifH transcripts, involved in nitrogen (N) fixation, were affiliated with the symbiotic cyanobacterium Candidatus Atelocyanobacterium thalassa, suggesting a key role as N providers in this system. The expression of nifH and amoA (i.e., marker for ammonia oxidation) showed consistent maxima in summer and autumn, respectively, suggesting a temporal succession of these important N cycling processes. The patterns of expression of genes related to the oxidation of carbon monoxide (coxL) and reduced sulfur (soxB) were different from that of amoA, indicating alternate timings for these energy conservation strategies. We detected expression of alkaline phosphatases, induced under phosphorus limitation, in agreement with the reported co-limitation by this nutrient at the study site. In contrast, low-affinity phosphate membrane transporters (pit) typically expressed under phosphorus luxury conditions, were mainly detected in post-bloom conditions. Rhodobacteraceae dominated the expression of soxB, coxL and ureases, while Pelagibacteraceae dominated the expression of proteorhodopsins. Bacteroidetes and Gammaproteobacteria were major contributors to the uptake of inorganic nutrients (pit and amt transporters). Yet, in autumn, Thauma-and Euryarchaeota unexpectedly contributed importantly to the uptake of ammonia and phosphate, respectively. We provide new hints on the active players and potential dynamics of ecologically relevant functions in situ, highlighting the potential of metatranscriptomics to provide significant input to future omics-driven marine ecosystem assessment.

Transcriptional activity differentiates families of Marine Group IIEuryarchaeotain the coastal ocean

“…Proteorhodopsin genes are highly transcribed in the photic zone of both open ocean and coastal waters (e.g., [77–79]) and our data indicate coastal Ca . Poseidoniales conform to this pattern, consistent with recent evidence from other regions [21,80,81]. High transcription of proteorhodopsin supports the photoheterotrophic lifestyle hypothesized for Ca .…”

Seasonality of biogeochemically relevant microbial genes in a coastal ocean microbiome

“…Another recent study looked at microbial trait variability using multiple metagenomic time series data (Beier et al, 2020) and found that larger metacommunity sizes translates into a higher temporal variability of gene alleles. Temporal changes in the transcription of several key biogeochemical genes were also analysed during 2 years, albeit with a small sample number (Alonso‐Sáez et al, 2020). The temporal expression patterns of several genes for energy conservation such as carbon monoxide oxidation ( coxL ), reduced sulfur ( soxB ), and the oxidation of ammonia ( amoA ) differed temporally.…”

Transcriptional activity differentiates families of Marine Group II Euryarchaeota in the coastal ocean

“…Poseidoniales conform to this pattern, consistent with recent evidence from other regions. 21 , 80 , 81 High transcription of proteorhodopsin supports the photoheterotrophic lifestyle hypothesized for Ca . Poseidoniales (see refs.…”