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Whole transcriptome shotgun sequencing (RNA-seq) was used to assess the transcriptomic response of the toxic cyanobacterium Microcystis aeruginosa during growth with low levels of dissolved inorganic nitrogen (low N), low levels of dissolved inorganic phosphorus (low P), and in the presence of high levels of high molecular weight dissolved organic matter (HMWDOM). Under low N, one third of the genome was differentially expressed, with significant increases in transcripts observed among genes within the nir operon, urea transport genes (urtBCDE), and amino acid transporters while significant decreases in transcripts were observed in genes related to photosynthesis. There was also a significant decrease in the transcription of the microcystin synthetase gene set under low N and a significant decrease in microcystin content per Microcystis cell demonstrating that N supply influences cellular toxicity. Under low P, 27% of the genome was differentially expressed. The Pho regulon was induced leading to large increases in transcript levels of the alkaline phosphatase phoX, the Pst transport system (pstABC), and the sphX gene, and transcripts of multiple sulfate transporter were also significantly more abundant. While the transcriptional response to growth on HMWDOM was smaller (5-22% of genes differentially expressed), transcripts of multiple genes specifically associated with the transport and degradation of organic compounds were significantly more abundant within HMWDOM treatments and thus may be recruited by Microcystis to utilize these substrates. Collectively, these findings provide a comprehensive understanding of the nutritional physiology of this toxic, bloom-forming cyanobacterium and the role of N in controlling microcystin synthesis.

In the surface ocean, light fuels photosynthetic carbon fixation of phytoplankton, playing a critical role in ecosystem processes including carbon export to the deep sea. In oligotrophic oceans, diatom–diazotroph associations (DDAs) play a keystone role in ecosystem function because diazotrophs can provide otherwise scarce biologically available nitrogen to the diatom host, fueling growth and subsequent carbon sequestration. Despite their importance, relatively little is known about the nature of these associations in situ . Here we used metatranscriptomic sequencing of surface samples from the North Pacific Subtropical Gyre (NPSG) to reconstruct patterns of gene expression for the diazotrophic symbiont Richelia and we examined how these patterns were integrated with those of the diatom host over day–night transitions. Richelia exhibited significant diel signals for genes related to photosynthesis, N 2 fixation, and resource acquisition, among other processes. N 2 fixation genes were significantly co-expressed with host nitrogen uptake and metabolism, as well as potential genes involved in carbon transport, which may underpin the exchange of nitrogen and carbon within this association. Patterns of expression suggested cell division was integrated between the host and symbiont across the diel cycle. Collectively these data suggest that symbiont–host physiological ecology is strongly interconnected in the NPSG.

The deep sea is the largest habitat on our planet, supporting a vast diversity of organisms which have yet to be fully described. This habitat is punctuated by hydrothermal vents in which energy derived from chemosynthesis drives carbon fixation, supporting a complex and rich food web. Connectivity between vent systems remains an active area of research, with questions as to how vent-influenced microbial function and diversity persists over space and time. In particular, the role hydrothermal vent plumes play as potential highways for connectivity and biogeography is not well understood. To add to the growing body of research, this study sampled plume waters above the Moytirra hydrothermal vent field, located just north of the Azores. We examined how hydrothermal vent plume community biodiversity and metabolic activities change with distance from the vent using a combination of metabarcoding and metatranscriptomic sequencing. We detected a rich diversity of both prokaryotic and eukaryotic organisms inhabiting the plume, which remained metabolically active for kilometers from the vent source. Enriched sulfur metabolism functional signals and relative abundance of sulfur oxidizing bacteria suggest reduced sulfur compounds are a fundamental energy source within plume waters. Additionally, we observed evidence of top-down controls on primary production through both known grazers and putative viral activity. Although community-level functional signals suggest active metabolic functions for over a kilometer north or south of the vent field, these functions grew increasingly dissimilar to those observed directly above the vent site, and bacterial communities displayed indications of entering quiescent stages, likely due to decreasing resources and reduced temperatures. These data provide a first glimpse of Moytirra’s microbial biodiversity, in addition to providing a high-resolution understanding of life on the drift within a hydrothermal plume, its persistence with distance, and implications for connectivity.

Marine protected areas (MPAs) can help ensure long‐term conservation of natural resources and protect biodiversity, ecosystem services, and cultural values in the face of anthropogenic change. However, determining MPA effectiveness is often challenging due to the lack of comprehensive baseline data and/or biases associated with biodiversity survey methods. Environmental DNA (eDNA) represents a promising tool to overcome these challenges. Here, we used a suite of three metabarcoding targets—prokaryote‐specific 16S, eukaryote‐specific 18S, and vertebrate‐specific 12S—to generate baseline data of all organisms, from bacteria to whales, within Stellwagen Bank National Marine Sanctuary (SBNMS). Surface water, bottom water, and sediment from 40 sites revealed three archaeal, 46 bacterial, 22 protistan, and 17 metazoan phyla. eDNA offers insight into the spatial resolution of biodiversity within SBNMS, potentially providing a new tool which could inform management practices to protect biodiversity. For vertebrate eDNA monitoring, most species were observed in bottom water, suggesting that less extensive sampling could be sufficient if targeting overall vertebrate richness. However, the inclusion of other sample types revealed patterns in relative sequence abundance that may be indicative of habitat use, particularly for Northern sand lance, a key forage fish. Microbial, phytoplankton, and zooplankton community composition differed dramatically between sample types, requiring all three to adequately capture species richness, providing data for potential indicator species such as those that cause harmful algal blooms. While future evaluations of cost, sampling scope, frequency, and how to incorporate data into management practices are needed, this study offers important baseline information for new hypotheses testing. Three marker genes targeting prokaryotic, eukaryotic, and vertebrate diversity were used to assess biodiversity within Stellwagen Bank National Marine Sanctuary. High levels of biodiversity were seen across the sampled area, with distinct communities across surface water, bottom water, and sediment. When compared to traditional visual data, eDNA provided higher resolution habitat use data for the Northern sand lance.

Background While transcriptomics have become a valuable tool for linking physiology and ecology in aquatic microbes, the temporal dynamics of global transcriptomic patterns in Microcystis have rarely been assessed. Furthermore, while many microbial studies have explored expression of nutrient transporter genes, few studies have concurrently measured nutrient assimilation rates. Here, we considered how the global transcriptomic patterns and physiology of the cyanobacterium, Microcystis aeruginosa , changed daily as cells were grown from replete to deficient nitrogen (N) conditions and then back to replete conditions. Results During N deprivation, Microcystis downregulated genes involved in photosynthesis and respiration, carbon acquisition, lipid metabolism, and amino acid biosynthesis while upregulating genes involved in N acquisition and transport. With increasing N stress, both the strength of expression and number of genes being differentially expressed increased, until N was restored at which point these patterns reversed. Uptake of 15 N-labeled nitrate, ammonium and urea reflected differential expression of genes encoding transporters for these nutrients, with Microcystis appearing to preferentially increase transcription of ammonium and urea transporters and uptake of these compounds during N deprivation. Nitrate uptake and nitrate transporter expression were correlated for one set of transporters but not another, indicating these were high and low affinity nitrate transporters, respectively. Concentrations of microcystin per cell decreased during N deprivation and increased upon N restoration. However, the transcript abundance of genes involved in the synthesis of this compound was complex, as microcystin synthetase genes involved in peptide synthesis were downregulated under N deprivation while genes involved in tailoring and transport were upregulated, suggesting modification of the microcystin molecule under N stress as well as potential alternative functions for these genes and/or this toxin. Conclusions Collectively, this study highlights the complex choreography of gene expression, cell physiology, and toxin synthesis that dynamic N levels can elicit in this ecologically important cyanobacterium. Differing expression patterns of genes within the microcystin synthetase operon in response to changing N levels revealed the potential limitations drawing conclusions based on only one gene in this operon.

Pelagophytes are abundant picophytoplankton within open ocean ecosystems and the causative algae of harmful brown tide blooms in estuaries. The physiological capabilities facilitating the ecological success of pelagophytes in these diverse ecosystems remains poorly understood. Here, we investigated the transcriptional response of two coastal pelagophytes ( Aureococcus anophagefferens and Aureoumbra lagunensis ) and two open ocean pelagophytes ( Pelagococcus subviridis and Pelagomonas calceolata ) to conditions commonly found within the marine ecosystems where they thrive: low concentrations of nitrogen (N), phosphorus (P), or light. OrthoMCL was used to generate a total of 62,653 orthologous groups (OGs) with only a small fraction of these OGs (2,776 or 4.4%) being shared among all four pelagophytes. Of the commonly shared OGs, 8% were significantly differentially abundant under low N, P, or light with the majority associated with energy and lipid metabolism. Distinct responses among pelagophytes included increased abundance of transcripts encoding phosphate transporters ( Aureococcus ) and transcripts encoding a pyrophosphatase ( Aureococcus and Pelagomonas ) under low P, the expression of a suite of organic nitrogen-degrading enzymes under low N ( Aureoumbra and Pelagomonas ), increased abundance of transcripts encoding flavodoxins relative to ferredoxins ( Pelagomonas ) and transcripts encoding lysophospholipase ( Pelagococcus ) under low light, and both increases and decreases in abundance of transcripts encoding selenoproteins in all pelagophytes except Pelagococcus . Collectively, this study provides new information on the expressed gene compliment of these poorly characterized taxa and demonstrates that these pelagophytes possess a combination of shared and unique physiological features that likely facilitate their adaptation to distinct environmental conditions.

Sunlight is the most important environmental control on diel fluctuations in phytoplankton activity, and understanding diel microbial processes is essential to the study of oceanic biogeochemical cycles. Yet, little is known about the in situ temporal dynamics of phytoplankton metabolic activities and their coordination across different populations. We investigated diel orchestration of phytoplankton activity in photosynthesis, photoacclimation, and photoprotection by analyzing pigment and quinone distributions in combination with metatranscriptomes in surface waters of the North Pacific Subtropical Gyre (NPSG). We found diel cycles in pigment abundances resulting from the balance of their synthesis and consumption. These dynamics suggest that night represents a metabolic recovery phase, refilling cellular pigment stores, while photosystems are remodeled towards photoprotection during daytime. Transcript levels of genes involved in photosynthesis and pigment metabolism had synchronized diel expression patterns among all taxa, reflecting the driving force light imparts upon photosynthetic organisms in the ocean, while other environmental factors drive niche differentiation. For instance, observed decoupling of diel oscillations in transcripts and related pigments indicates that pigment abundances are modulated by environmental factors extending beyond gene expression/regulation reinforcing the need to combine metatranscriptomics with proteomics and metabolomics to fully understand the timing of these critical processes in situ.

Cyanobacteria blooms caused by species such as Microcystis have become commonplace in many freshwater ecosystems. Although phosphorus (P) typically limits the growth of freshwater phytoplankton populations, little is known regarding the molecular response of Microcystis to variation in P concentrations and sources. For this study, we examined genes involved in P acquisition in Microcystis including two high-affinity phosphate-binding proteins (pstS and sphX) and a putative alkaline phosphatase (phoX). Sequence analyses among ten clones of Microcystis aeruginosa and one clone of Microcystis wesenbergii indicates that these genes are present and conserved within the species, but perhaps not the genus, as phoX was not identified in M. wesenbergii. Experiments with clones of M aeruginosa indicated that expression of these three genes was strongly upregulated (50-to 400-fold) under low inorganic P conditions and that the expression of phoX was correlated with alkaline phosphatase activity (P< 0.005). In contrast, cultures grown exclusively on high levels of organic phosphorus sources (adenosine 5'-monophosphate, β-glycerol phosphate, and D-glucose-6-phosphate) or under nitrogen-limited conditions displayed neither high levels of gene expression nor alkaline phosphatase activity. Since Microcystis dominates phytoplankton assemblages in summer when levels of inorganic P (Pi) are often low and/or dominate lakes with low Pi and high organic P, our findings suggest this cyanobacterium may rely on pstS, sphX, and phoX to efficiently transport Pi and exploit organic sources of P to form blooms.

From June to August 2018, the eruption of Kīlauea volcano on the island of Hawai‘i injected millions of cubic meters of molten lava into the nutrient-poor waters of the North Pacific Subtropical Gyre. The lava-impacted seawater was characterized by high concentrations of metals and nutrients that stimulated phytoplankton growth, resulting in an extensive plume of chlorophyll a that was detectable by satellite. Chemical and molecular evidence revealed that this biological response hinged on unexpectedly high concentrations of nitrate, despite the negligible quantities of nitrogen in basaltic lava. We hypothesize that the high nitrate was caused by buoyant plumes of nutrient-rich deep waters created by the substantial input of lava into the ocean. This large-scale ocean fertilization was therefore a unique perturbation event that revealed how marine ecosystems respond to exogenous inputs of nutrients.

Diazotrophy is the most important nitrogen source in the oligotrophic surface ocean, but the organisms involved and their contributions are incompletely understood due to limited observations. Only diazotrophic organisms possess the nifH gene to reduce dinitrogen to ammonium, but their distribution and activity can only be quantified through sampling and experiments during research cruises. Some recent studies document small diatoms with symbionts able to fix nitrogen, a new source of biologically available nitrogen in addition to the well-known cyanobacterial species such as Trichodesmium or symbionts of haptophytes (UCYN-A) and diatoms (Diatom–Diazotroph Associations, or DDAs). Here, we document a very active symbiosis between small pennate diatoms such as Mastogloia and Haslea with rhizobial and cyanobacterial symbionts in waters of the Western tropical North Atlantic influenced by the Amazon River plume. We used NanoSIMS analysis of 15N2 tracer experiments to quantify high rates of nitrogen fixation in generally abundant, symbiont-bearing pennate diatoms. This newly described symbiosis may contribute a previously unquantified flux of biologically available nitrogen to oceanic systems. Pennate diatoms and their symbionts may close a key gap in our understanding of the supply of nutrients to the ocean and provide a previously unknown biological sink for carbon dioxide.