Metaproteomic analysis decodes trophic interactions of microorganisms in the dark ocean.

Proteins in the open ocean represent a significant source of organic matter, and their profiles reflect the metabolic activities of marine microorganisms. Here, by analyzing metaproteomic samples collected from the Pacific, Atlantic and Southern Ocean, we reveal size-fractionated patterns of the structure and function of the marine microbiota protein pool in the water column, particularly in the dark ocean (>200 m). Zooplankton proteins contributed three times more than algal proteins to the deep-sea community metaproteome. Gammaproteobacteria exhibited high metabolic activity in the deep-sea, contributing up to 30% of bacterial proteins. Close virus-host interactions of this taxon might explain the dominance of gammaproteobacterial proteins in the dissolved fraction. A high urease expression in nitrifiers suggested links between their dark carbon fixation and zooplankton urea production. In summary, our results uncover the taxonomic contribution of the microbiota to the oceanic protein pool, revealing protein fluxes from particles to the dissolved organic matter pool.

Substrate uptake patterns shape niche separation in marine prokaryotic microbiome.

Marine heterotrophic prokaryotes primarily take up ambient substrates using transporters. The patterns of transporters targeting particular substrates shape the ecological role of heterotrophic prokaryotes in marine organic matter cycles. Here, we report a size-fractionated pattern in the expression of prokaryotic transporters throughout the oceanic water column due to taxonomic variations, revealed by a multi-"omics" approach targeting ATP-binding cassette (ABC) transporters and TonB-dependent transporters (TBDTs). Substrate specificity analyses showed that marine SAR11, Rhodobacterales, and Oceanospirillales use ABC transporters to take up organic nitrogenous compounds in the free-living fraction, while Alteromonadales, Bacteroidetes, and Sphingomonadales use TBDTs for carbon-rich organic matter and metal chelates on particles. The expression of transporter proteins also supports distinct lifestyles of deep-sea prokaryotes. Our results suggest that transporter divergency in organic matter assimilation reflects a pronounced niche separation in the prokaryote-mediated organic matter cycles.

Marine Polymer-Gels' Relevance in the Atmosphere as Aerosols and CCN.

Marine polymer gels play a critical role in regulating ocean basin scale biogeochemical dynamics. This brief review introduces the crucial role of marine gels as a source of aerosol particles and cloud condensation nuclei (CCN) in cloud formation processes, emphasizing Arctic marine microgels. We review the gel's composition and relation to aerosols, their emergent properties, and physico-chemical processes that explain their change in size spectra, specifically in relation to aerosols and CCN. Understanding organic aerosols and CCN in this context provides clear benefits to quantifying the role of marine nanogel/microgel in microphysical processes leading to cloud formation. This review emphasizes the DOC-marine gel/aerosolized gel-cloud link, critical to developing accurate climate models.

Dissolved Organic Matter in the Global Ocean: A Primer.

Marine dissolved organic matter (DOM) holds ~660 billion metric tons of carbon, making it one of Earth's major carbon reservoirs that is exchangeable with the atmosphere on annual to millennial time scales. The global ocean scale dynamics of the pool have become better illuminated over the past few decades, and those are very briefly described here. What is still far from understood is the dynamical control on this pool at the molecular level; in the case of this Special Issue, the role of microgels is poorly known. This manuscript provides the global context of a large pool of marine DOM upon which those missing insights can be built.

Contrasting heat stress response patterns of coral holobionts across the Red Sea suggest distinct mechanisms of thermal tolerance.

Corals from the northern Red Sea, in particular the Gulf of Aqaba (GoA), have exceptionally high bleaching thresholds approaching >5℃ above their maximum monthly mean (MMM) temperatures. These elevated thresholds are thought to be due to historical selection, as corals passed through the warmer Southern Red Sea during recolonization from the Arabian Sea. To test this hypothesis, we determined thermal tolerance thresholds of GoA versus central Red Sea (CRS) Stylophora pistillata corals using multi-temperature acute thermal stress assays to determine thermal thresholds. Relative thermal thresholds of GoA and CRS corals were indeed similar and exceptionally high (~7℃ above MMM). However, absolute thermal thresholds of CRS corals were on average 3℃ above those of GoA corals. To explore the molecular underpinnings, we determined gene expression and microbiome response of the coral holobiont. Transcriptomic responses differed markedly, with a strong response to the thermal stress in GoA corals and their symbiotic algae versus a remarkably muted response in CRS colonies. Concomitant to this, coral and algal genes showed temperature-induced expression in GoA corals, while exhibiting fixed high expression (front-loading) in CRS corals. Bacterial community composition of GoA corals changed dramatically under heat stress, whereas CRS corals displayed stable assemblages. We interpret the response of GoA corals as that of a resilient population approaching a tipping point in contrast to a pattern of consistently elevated thermal resistance in CRS corals that cannot further attune. Such response differences suggest distinct thermal tolerance mechanisms that may affect the response of coral populations to ocean warming.

Fe limitation decreases transcriptional regulation over the diel cycle in the model diatom Thalassiosira pseudonana.

Iron (Fe) is an important growth factor for diatoms and its availability is further restricted by changes in the carbonate chemistry of seawater. We investigated the physiological attributes and transcriptional profiles of the diatom Thalassiosira pseudonana grown on a day: night cycle under different CO2/pH and iron concentrations, that in combination generated available iron (Fe') concentrations of 1160, 233, 58 and 12 pM. We found the light-dark conditions to be the main driver of transcriptional patterns, followed by Fe' concentration and CO2 availability, respectively. At the highest Fe' (1160 pM), 55% of the transcribed genes were differentially expressed between day and night, whereas at the lowest Fe' (12 pM), only 28% of the transcribed genes displayed comparable patterns. While Fe limitation disrupts the diel expression patterns for genes in most central metabolism pathways, the diel expression of light- signaling molecules and glycolytic genes was relatively robust in response to reduced Fe'. Moreover, we identified a non-canonical splicing of transcripts encoding triose-phosphate isomerase, a key-enzyme of glycolysis, generating transcript isoforms that would encode proteins with and without an active site. Transcripts that encoded an active enzyme maintained a diel expression at low Fe', while transcripts that encoded the non-active enzyme lost the diel expression. This work illustrates the interplay between nutrient limitation and transcriptional regulation over the diel cycle. Considering that future ocean conditions will reduce the availability of Fe in many parts of the oceans, our work identifies some of the regulatory mechanisms that may shape future ecological communities.

Systems biology approaches towards predictive microbial ecology.

Through complex interspecies interactions, microbial processes drive nutrient cycling and biogeochemistry. However, we still struggle to predict specifically which organisms, communities and biotic and abiotic processes are determining ecosystem function and how environmental changes will alter their roles and stability. While the tools to create such a predictive microbial ecology capability exist, cross-disciplinary integration of high-resolution field measurements, detailed laboratory studies and computation is essential. In this perspective, we emphasize the importance of pursuing a multiscale, systems approach to iteratively link ecological processes measured in the field to testable hypotheses that drive high-throughput laboratory experimentation. Mechanistic understanding of microbial processes gained in controlled lab systems will lead to the development of theory that can be tested back in the field. Using N2 O production as an example, we review the current status of field and laboratory research and layout a plausible path to the kind of integration that is needed to enable prediction of how N-cycling microbial communities will respond to environmental changes. We advocate for the development of realistic and predictive gene regulatory network models for environmental responses that extend from single-cell resolution to ecosystems, which is essential to understand how microbial communities involved in N2 O production and consumption will respond to future environmental conditions.

Ocean acidification conditions increase resilience of marine diatoms.

The fate of diatoms in future acidified oceans could have dramatic implications on marine ecosystems, because they account for ~40% of marine primary production. Here, we quantify resilience of Thalassiosira pseudonana in mid-20th century (300 ppm CO2) and future (1000 ppm CO2) conditions that cause ocean acidification, using a stress test that probes its ability to recover from incrementally higher amount of low-dose ultraviolet A (UVA) and B (UVB) radiation and re-initiate growth in day-night cycles, limited by nitrogen. While all cultures eventually collapse, those growing at 300 ppm CO2 succumb sooner. The underlying mechanism for collapse appears to be a system failure resulting from "loss of relational resilience," that is, inability to adopt physiological states matched to N-availability and phase of the diurnal cycle. Importantly, under elevated CO2 conditions diatoms sustain relational resilience over a longer timeframe, demonstrating increased resilience to future acidified ocean conditions. This stress test framework can be extended to evaluate and predict how various climate change associated stressors may impact microbial community resilience.

Pan-transcriptomic analysis identifies coordinated and orthologous functional modules in the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum.

Diatoms are important primary producers in the ocean that thrive in diverse and dynamic environments. Their survival and success over changing conditions depend on the complex coordination of gene regulatory processes. Here we present an integrated analysis of all publicly available microarray data for the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum. This resource includes shared expression patterns, gene functions, and cis-regulatory DNA sequence motifs in each species that are statistically coordinated over many experiments. These data illustrate the coordination of transcriptional responses in diatoms over changing environmental conditions. Responses to silicic acid depletion segregate into multiple distinctly regulated groups of genes, regulation by heat shock transcription factors (HSFs) is implicated in the response to nitrate stress, and distinctly coordinated carbon concentrating, CO2 and pH-related responses are apparent. Fundamental features of diatom physiology are similarly coordinated between two distantly related diatom species, including the regulation of photosynthesis, cellular growth functions and lipid metabolism. These integrated data and analyses can be explored publicly (http://networks.systemsbiology.net/diatom-portal/).

Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii.

BACKGROUND: Algae accumulate lipids to endure different kinds of environmental stresses including macronutrient starvation. Although this response has been extensively studied, an in depth understanding of the transcriptional regulatory network (TRN) that controls the transition into lipid accumulation remains elusive. In this study, we used a systems biology approach to elucidate the transcriptional program that coordinates the nitrogen starvation-induced metabolic readjustments that drive lipid accumulation in Chlamydomonas reinhardtii. RESULTS: We demonstrate that nitrogen starvation triggered differential regulation of 2147 transcripts, which were co-regulated in 215 distinct modules and temporally ordered as 31 transcriptional waves. An early-stage response was triggered within 12 min that initiated growth arrest through activation of key signaling pathways, while simultaneously preparing the intracellular environment for later stages by modulating transport processes and ubiquitin-mediated protein degradation. Subsequently, central metabolism and carbon fixation were remodeled to trigger the accumulation of triacylglycerols. Further analysis revealed that these waves of genome-wide transcriptional events were coordinated by a regulatory program orchestrated by at least 17 transcriptional regulators, many of which had not been previously implicated in this process. We demonstrate that the TRN coordinates transcriptional downregulation of 57 metabolic enzymes across a period of nearly 4 h to drive an increase in lipid content per unit biomass. Notably, this TRN appears to also drive lipid accumulation during sulfur starvation, while phosphorus starvation induces a different regulatory program. The TRN model described here is available as a community-wide web-resource at http://networks.systemsbiology.net/chlamy-portal. CONCLUSIONS: In this work, we have uncovered a comprehensive mechanistic model of the TRN controlling the transition from N starvation to lipid accumulation. The program coordinates sequentially ordered transcriptional waves that simultaneously arrest growth and lead to lipid accumulation. This study has generated predictive tools that will aid in devising strategies for the rational manipulation of regulatory and metabolic networks for better biofuel and biomass production.

Modeling the evolution of C4 photosynthesis.

The prediction and verification of adaptive trajectories on macroevolutionary timescales have rarely been achieved for complex biological systems. Employing a model linking biological information at multiple scales, Heckmann et al. simulate likely sequences of evolutionary changes from C3 to C4 photosynthesis biochemistry.

A role for programmed cell death in the microbial loop.

The microbial loop is the conventional model by which nutrients and minerals are recycled in aquatic eco-systems. Biochemical pathways in different organisms become metabolically inter-connected such that nutrients are utilized, processed, released and re-utilized by others. The result is that unrelated individuals end up impacting each others' fitness directly through their metabolic activities. This study focused on the impact of programmed cell death (PCD) on a population's growth as well as its role in the exchange of carbon between two naturally co-occurring halophilic organisms. Flow cytometric, biochemical, ¹4C radioisotope tracing assays, and global transcriptomic analyses show that organic algal photosynthate released by Dunalliela salina cells undergoing PCD complements the nutritional needs of other non-PCD D. salina cells. This occurs in vitro in a carbon limited environment and enhances the growth of the population. In addition, a co-occurring heterotroph Halobacterium salinarum re-mineralizes the carbon providing elemental nutrients for the mixoheterotrophic chlorophyte. The significance of this is uncertain and the archaeon can also subsist entirely on the lysate of apoptotic algae. PCD is now well established in unicellular organisms; however its ecological relevance has been difficult to decipher. In this study we found that PCD in D. salina causes the release of organic nutrients such as glycerol, which can be used by others in the population as well as a co-occurring halophilic archaeon. H. salinarum also re-mineralizes the dissolved material promoting algal growth. PCD in D. salina was the mechanism for the flow of dissolved photosynthate between unrelated organisms. Ironically, programmed death plays a central role in an organism's own population growth and in the exchange of nutrients in the microbial loop.

Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana.

Marine diatoms are important primary producers that thrive in diverse and dynamic environments. They do so, in theory, by sensing changing conditions and adapting their physiology accordingly. Using the model species Thalassiosira pseudonana, we conducted a detailed physiological and transcriptomic survey to measure the recurrent transcriptional changes that characterize typical diatom growth in batch culture. Roughly 40% of the transcriptome varied significantly and recurrently, reflecting large, reproducible cell-state transitions between four principal states: (i) "dawn," following 12 h of darkness; (ii) "dusk," following 12 h of light; (iii) exponential growth and nutrient repletion; and (iv) stationary phase and nutrient depletion. Increases in expression of thousands of genes at the end of the reoccurring dark periods (dawn), including those involved in photosynthesis (e.g., ribulose-1,5-bisphosphate carboxylase oxygenase genes rbcS and rbcL), imply large-scale anticipatory circadian mechanisms at the level of gene regulation. Repeated shifts in the transcript levels of hundreds of genes encoding sensory, signaling, and regulatory functions accompanied the four cell-state transitions, providing a preliminary map of the highly coordinated gene regulatory program under varying conditions. Several putative light sensing and signaling proteins were associated with recurrent diel transitions, suggesting that these genes may be involved in light-sensitive and circadian regulation of cell state. These results begin to explain, in comprehensive detail, how the diatom gene regulatory program operates under varying environmental conditions. Detailed knowledge of this dynamic molecular process will be invaluable for new hypothesis generation and the interpretation of genetic, environmental, and metatranscriptomic data from field studies.

A NAD(P) reductase like protein is the salicylic acid receptor in the appendix of the Sauromatum guttatum inflorescence.

The mode of action of the thermogenic inducers (salicylic acid, aspirin, and 2,6-dihydroxybenzoic acid) in the appendix of the Sauromatum guttatum inflorescence is poorly understood. Using ESI-MS and light scattering analysis, we have demonstrated that NAD(P) reductase like protein (RL) is the salicylic acid receptor in the Sauromatum appendix. RL was self-assembled in water into a large unit with a hydrodynamic diameter of 800 nm. In the presence of 1 pM salicylic acid, RL exhibited discontinuous and reversible volume phase transitions. The volume phase changed from 800 to 300 nm diameter and vice versa. RL stayed at each volume phase for ~4-5 min with a fast relaxation time between the 2 phases. ESI-MS analysis of RL extracted from appendices treated with salicylic acid, aspirin, and 2,6-DHBA at a micromolar range demonstrated that these compounds are capable of inducing graded conformational changes that are concentration-dependent. A strong correlation between RL conformations and heat-production induced by salicylic acid was also observed. These preliminary findings reveal structural and conformational roles for RL by which plants regulate their temperature and synchronize their time keeping mechanisms.

Marine microgels as a source of cloud condensation nuclei in the high Arctic.

Marine microgels play an important role in regulating ocean basin-scale biogeochemical dynamics. In this paper, we demonstrate that, in the high Arctic, marine gels with unique physicochemical characteristics originate in the organic material produced by ice algae and/or phytoplankton in the surface water. The polymers in this dissolved organic pool assembled faster and with higher microgel yields than at other latitudes. The reversible phase transitions shown by these Arctic marine gels, as a function of pH, dimethylsulfide, and dimethylsulfoniopropionate concentrations, stimulate the gels to attain sizes below 1 µm in diameter. These marine gels were identified with an antibody probe specific toward material from the surface waters, sized, and quantified in airborne aerosol, fog, and cloud water, strongly suggesting that they dominate the available cloud condensation nuclei number population in the high Arctic (north of 80°N) during the summer season. Knowledge about emergent properties of marine gels provides important new insights into the processes controlling cloud formation and radiative forcing, and links the biology at the ocean surface with cloud properties and climate over the central Arctic Ocean and, probably, all oceans.

DIMETHYLSULFONIOPROPIONATE STORAGE IN PHAEOCYSTIS (PRYMNESIOPHYCEAE) SECRETORY VESICLES(1).

Despite the global importance of dimethylsulfoniopropionate (DMSP)/dimethyl sulfide (DMS) and their role in climate regulation, little is known about the mechanisms of their production and storage in Phaeocystis sp., a major contributor of DMS in polar areas. Phaeocystis secretes polymer microgels, by regulated exocytosis, remaining in condensed phase while stored in secretory vesicles (Chin et al. 2004). In secretory cells, vesicles also store small molecules, which are released during exocytosis. Here, we demonstrated that DMSP and DMS were stored in the secretory vesicles of Phaeocystis antarctica G. Karst. They were trapped within a polyanionic gel matrix, which prevented an accurate measurement of their concentration in the absence of a chelating agent such as EDTA. Understanding the production and the export mechanisms of DMSP and DMS into seawater is important because of the impact the cellular and extracellular pools of these highly relevant biogeochemical metabolites have on the environment. The pool of total DMSP in the presence of Phaeocystis may be underestimated by as much as half. Obtaining accurate budget measurements is the first step toward gaining a better understanding of key issues related to the DMS ocean-air interaction and the effect of phytoplankton DMS production on climate change.

Marine biopolymer self-assembly: implications for carbon cycling in the ocean.

Dissolved organic matter is the largest reservoir of reduced carbon in the ocean and is primarily composed of small biopolymers. It is a critical substrate for the microbial community and plays a pivotal role in global carbon cycling.

Secretion in unicellular marine phytoplankton: demonstration of regulated exocytosis in Phaeocystis globosa.

Almost half of the global photosynthetic activity is carried out in the ocean. During blooms, Phaeocystis can fix CO(2) at rates up to 40 g C m(-2) month(-1). Most of this carbon is released as polysaccharides. However, the cellular mechanism whereby this huge amount of organic material is exported into the seawater remains unknown. A vaguely defined process of "exudation" is believed responsible for the release of these biopolymers. Here we report the first demonstration that Phaeocystis globosa does not "exude", but secretes microscopic gels. Secretion is stimulated by blue light (lambda = 470+/-20 nm), and it is transduced by a characteristic intracellular Ca(2+) signal that precedes degranulation. The polysaccharides that form the matrix of these gels remain in condensed phase while stored in secretory vesicles. Upon exocytosis, the exopolymer matrix undergoes a characteristic phase transition accompanied by extensive swelling resulting in the formation of microscopic hydrated gels. Owing to their tangled topology, once released into the seawater, the polymers that make these gels can reptate (axially diffuse), interpenetrate neighboring gels, and anneal them together forming massive mucilage accumulations that are characteristic of Phaeocystis blooms. These gel masses can supply a rich source of microbial substrates, disperse in the seawater, and/or eventually sediment to the ocean floor.