Abstract
The Amazon River has the largest discharge of all rivers on Earth, and its complex plume system fuels a wide array of biogeochemical processes, across a large area of the western tropical North Atlantic. The plume thus stimulates microbial processes affecting carbon sequestration and nutrient cycles at a global scale. Chromosomal gene expression patterns of the 2.0 to 156 μm size-fraction eukaryotic microbial community were investigated in the Amazon River Plume, generating a robust dataset (more than 100 million mRNA sequences) that depicts the metabolic capabilities and interactions among the eukaryotic microbes. Combining classical oceanographic field measurements with metatranscriptomics yielded characterization of the hydrographic conditions simultaneous with a quantification of transcriptional activity and identity of the community. We highlight the patterns of eukaryotic gene expression for 31 biogeochemically significant gene targets hypothesized to be valuable within forecasting models. An advantage to this targeted approach is that the database of reference sequences used to identify the target genes was selectively constructed and highly curated optimizing taxonomic coverage, throughput, and the accuracy of annotations. A coastal diatom bloom highly expressed nitrate transporters and carbonic anhydrase presumably to support high growth rates and enhance uptake of low levels of dissolved nitrate and CO2. Diatom-diazotroph association (DDA: diatoms with nitrogen fixing symbionts) blooms were common when surface salinity was mesohaline and dissolved nitrate concentrations were below detection, and hence did not show evidence of nitrate utilization, suggesting they relied on ammonium transporters to aquire recently fixed nitrogen. These DDA blooms in the outer plume had rapid turnover of the photosystem D1 protein presumably caused by photodegradation under increased light penetration in clearer waters, and increased expression of silicon transporters as silicon became limiting. Expression of these genes, including carbonic anhydrase and transporters for nitrate and phosphate, were found to reflect the physiological status and biogeochemistry of river plume environments. These relatively stable patterns of eukaryotic transcript abundance occurred over modest spatiotemporal scales, with similarity observed in sample duplicates collected up to 2.45 km in space and 120 minutes in time. These results confirm the use of metatranscriptomics as a valuable tool to understand and predict microbial community function.
Highlights
The Amazon River discharges an average of 1.55 × ± 0.13 m3 s-1 at Obidos, Brazil, resulting in a thin, fresh water layer at the surface called the Amazon River plume (ARP), which varies seasonally and covers up to 1.3 × km2 of the western tropical North Atlantic Ocean [1,2,3,4]
This study demonstrates that metatranscriptomic analysis of 31 pre-selected biogeochemicallyrelevant genes allowed for a reliable analysis of eukaryotic planktonic communities and their physiological status in the ARP
Phylogenetic information from 18S rDNA enabled taxa to be assigned to the short length transcript sequences collected from these environments and transcription was related to environmental conditions, supporting that a metatranscriptomic study can be used to describe the biogeochemistry
Summary
The Amazon River discharges an average of 1.55 × ± 0.13 m3 s-1 at Obidos, Brazil, resulting in a thin, fresh water layer at the surface called the Amazon River plume (ARP), which varies seasonally and covers up to 1.3 × km of the western tropical North Atlantic Ocean [1,2,3,4]. In lower salinity waters, where dissolved nutrients such as silica, iron, nitrate and phosphate are abundant, coastal diatom communities flourish once light can penetrate the initially turbid plume [4, 6]. There are at least 4 genera of diatoms (Hemiaulus, Rhizosolenia, Chaetocerous, Guinardia) which form partnerships, or symbioses, with nitrogen fixing heterocystous cyanobacteria (Richelia intracellularis and Calothrix rhizosoleniae) and collectively these are referred to as DDAs [8]. These DDA blooms exhibit high rates of nitrogen and carbon fixation worldwide [4, 9]. When silica and phosphate are no longer available, nitrogen-fixing Trichodesmium dominate, which have been shown to regulate their buoyancy with gas vesicles to acquire phosphorus at depth [12]
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