MODELING THE RELEASE OF DISSOLVED ORGANIC MATTER BY PHYTOPLANKTON(1)

Environmental Factors Modulate Saxitoxins (STXs) Production in Toxic Dinoflagellate Alexandrium: An Updated Review of STXs and Synthesis Gene Aspects

The marine dinoflagellate Alexandrium is known to form harmful algal blooms (HABs) and produces saxitoxin (STX) and its derivatives (STXs) that cause paralytic shellfish poisoning (PSP) in humans. Cell growth and cellular metabolism are affected by environmental conditions, including nutrients, temperature, light, and the salinity of aquatic systems. Abiotic factors not only engage in photosynthesis, but also modulate the production of toxic secondary metabolites, such as STXs, in dinoflagellates. STXs production is influenced by a variety of abiotic factors; however, the relationship between the regulation of these abiotic variables and STXs accumulation seems not to be consistent, and sometimes it is controversial. Few studies have suggested that abiotic factors may influence toxicity and STXs-biosynthesis gene (sxt) regulation in toxic Alexandrium, particularly in A. catenella, A. minutum, and A. pacificum. Hence, in this review, we focused on STXs production in toxic Alexandrium with respect to the major abiotic factors, such as temperature, salinity, nutrients, and light intensity. This review informs future research on more sxt genes involved in STXs production in relation to the abiotic factors in toxic dinoflagellates.

Metabolic Phenotyping of Marine Heterotrophs on Refactored Media Reveals Diverse Metabolic Adaptations and Lifestyle Strategies

Microbial communities, through their metabolism, drive carbon cycling in marine environments. These complex communities are composed of many different microorganisms including heterotrophic bacteria, each with its own nutritional needs and metabolic capabilities. Yet, models of ecosystem processes typically treat heterotrophic bacteria as a “black box,” which does not resolve metabolic heterogeneity nor address ecologically important processes such as the successive modification of different types of organic matter. Here we directly address the heterogeneity of metabolism by characterizing the carbon source utilization preferences of 63 heterotrophic bacteria representative of several major marine clades. By systematically growing these bacteria on 10 media containing specific subsets of carbon sources found in marine biomass, we obtained a phenotypic fingerprint that we used to explore the relationship between metabolic preferences and phylogenetic or genomic features. At the class level, these bacteria display broadly conserved patterns of preference for different carbon sources. Despite these broad taxonomic trends, growth profiles correlate poorly with phylogenetic distance or genome-wide gene content. However, metabolic preferences are strongly predicted by a handful of key enzymes that preferentially belong to a few enriched metabolic pathways, such as those involved in glyoxylate metabolism and biofilm formation. We find that enriched pathways point to enzymes directly involved in the metabolism of the corresponding carbon source and suggest potential associations between metabolic preferences and other ecologically relevant traits. The availability of systematic phenotypes across multiple synthetic media constitutes a valuable resource for future quantitative modeling efforts and systematic studies of interspecies interactions.

IMPORTANCE Half of the Earth’s annual primary production is carried out by phytoplankton in the surface ocean. However, this metabolic activity is heavily impacted by heterotrophic bacteria, which dominate the transformation of organic matter released from phytoplankton. Here, we characterize the diversity of metabolic preferences across many representative heterotrophs by systematically growing them on different fractions of dissolved organic carbon. Our analysis suggests that different clades of bacteria have substantially distinct preferences for specific carbon sources, in a way that cannot be simply mapped onto phylogeny. These preferences are associated with the presence of specific genes and pathways, reflecting an association between metabolic capabilities and ecological lifestyles. In addition to helping understand the importance of heterotrophs under different conditions, the phenotypic fingerprint we obtained can help build higher resolution quantitative models of global microbial activity and biogeochemical cycles in the oceans.

Microbial metabolites in the marine carbon cycle

One-quarter of photosynthesis-derived carbon on Earth rapidly cycles through a set of short-lived seawater metabolites that are generated from the activities of marine phytoplankton, bacteria, grazers and viruses. Here we discuss the sources of microbial metabolites in the surface ocean, their roles in ecology and biogeochemistry, and approaches that can be used to analyse them from chemistry, biology, modelling and data science. Although microbial-derived metabolites account for only a minor fraction of the total reservoir of marine dissolved organic carbon, their flux and fate underpins the central role of the ocean in sustaining life on Earth.

Scaling down the microbial loop: data-driven modelling of growth interactions in a diatom-bacterium co-culture

An intricate set of interactions characterizes marine ecosystems. One of the most important is represented by the microbial loop, which includes the exchange of dissolved organic matter (DOM) from phototrophic organisms to heterotrophic bacteria. Here, it can be used as the major carbon and energy source. This interaction is one of the foundations of the entire ocean food-web. The carbon fixed by phytoplankton can be redirected to bacteria in two main ways; either (i) bacteria feed on dead phytoplankton cells or (ii) DOM is actively released by phytoplankton (a process resulting in up to 50% of the fixed carbon leaving the cell). Here, we have set up a co-culture of the diatom Phaeodactylum tricornutum and the chemoheterotrophic bacterium Pseudoalteromonas haloplanktis TAC125 and used this system to study the interactions between these two representatives of the microbial loop. We show that the bacterium can thrive on diatom-derived carbon and that this growth can be sustained by both diatom dead cells and diatom-released compounds. These observations were formalized in a network of putative interactions between P. tricornutum and P. haloplanktis and implemented in a model that reproduces the observed co-culture dynamics, revealing an overall accuracy of our hypotheses in explaining the experimental data.

Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy

The communities of bacteria that assemble around marine microphytoplankton are predictably dominated by Rhodobacterales, Flavobacteriales, and families within the Gammaproteobacteria. Yet whether this consistent ecological pattern reflects the result of resource-based niche partitioning or resource competition requires better knowledge of the metabolites linking microbial autotrophs and heterotrophs in the surface ocean. We characterized molecules targeted for uptake by three heterotrophic bacteria individually co-cultured with a marine diatom using two strategies that vetted the exometabolite pool for biological relevance by means of bacterial activity assays: expression of diagnostic genes and net drawdown of exometabolites, the latter detected with mass spectrometry and nuclear magnetic resonance using novel sample preparation approaches. Of the more than 36 organic molecules with evidence of bacterial uptake, 53% contained nitrogen (including nucleosides and amino acids), 11% were organic sulfur compounds (including dihydroxypropanesulfonate and dimethysulfoniopropionate), and 28% were components of polysaccharides (including chrysolaminarin, chitin, and alginate). Overlap in phytoplankton-derived metabolite use by bacteria in the absence of competition was low, and only guanosine, proline, and N-acetyl-D-glucosamine were predicted to be used by all three. Exometabolite uptake pattern points to a key role for ecological resource partitioning in the assembly marine bacterial communities transforming recent photosynthate.

Quantifying nutrient throughput and DOM production by algae in continuous culture

Freshwater and marine algae can balance nutrient demand and availability by regulating uptake, accumulation and exudation. To obtain insight into these processes under nitrogen (N) and phosphorus (P) limitation, we reanalyze published data from continuous cultures of the chlorophyte Selenastrum minutum. Based on mass budgets, we argue that much of the non-limiting N and P had passed through the organisms and was present as dissolved organic phosphorus or nitrogen (DOP or DON). We construct a model that describes the production of biomass and dissolved organic matter (DOM) as a function of the growth rate. A fit of this model against the chemostat data suggests a high turnover of the non-limiting N and P: at the highest growth rates, N and P atoms spent on average only about 3 h inside an organism, before they were exuded as DON and DOP, respectively. This DOM exudation can explain the observed trends in the algal stoichiometric ratios as a function of the dilution rate. We discuss independent evidence from isotope experiments for this apparently wasteful behavior and we suggest experiments to quantify and characterize DON and DOP exudation further.

Ecological drivers of bacterial community assembly in synthetic phycospheres

In the nutrient-rich region surrounding marine phytoplankton cells, heterotrophic bacterioplankton transform a major fraction of recently fixed carbon through the uptake and catabolism of phytoplankton metabolites. We sought to understand the rules by which marine bacterial communities assemble in these nutrient-enhanced phycospheres, specifically addressing the role of host resources in driving community coalescence. Synthetic systems with varying combinations of known exometabolites of marine phytoplankton were inoculated with seawater bacterial assemblages, and communities were transferred daily to mimic the average duration of natural phycospheres. We found that bacterial community assembly was predictable from linear combinations of the taxa maintained on each individual metabolite in the mixture, weighted for the growth each supported. Deviations from this simple additive resource model were observed but also attributed to resource-based factors via enhanced bacterial growth when host metabolites were available concurrently. The ability of photosynthetic hosts to shape bacterial associates through excreted metabolites represents a mechanism by which microbiomes with beneficial effects on host growth could be recruited. In the surface ocean, resource-based assembly of host-associated communities may underpin the evolution and maintenance of microbial interactions and determine the fate of a substantial portion of Earth's primary production.

Sulfur metabolites in the pelagic ocean

Marine microorganisms play crucial roles in Earth's element cycles through the production and consumption of organic matter. One of the elements whose fate is governed by microbial activities is sulfur, an essential constituent of biomass and a crucial player in climate processes. With sulfur already being well studied in the ocean in its inorganic forms, organic sulfur compounds are emerging as important chemical links between marine phytoplankton and bacteria. The high concentration of inorganic sulfur in seawater, which can readily be reduced by phytoplankton, provides a freely available source of sulfur for biomolecule synthesis. Mechanisms such as exudation and cell lysis release these phytoplankton-derived sulfur metabolites into seawater, from which they are rapidly assimilated by marine bacteria and archaea. Energy-limited bacteria use scavenged sulfur metabolites as substrates or for the synthesis of vitamins, cofactors, signalling compounds and antibiotics. In this Review, we examine the current knowledge of sulfur metabolites released into and taken up from the marine dissolved organic matter pool by microorganisms, and the ecological links facilitated by their diversity in structures, oxidation states and chemistry.

Ammonia-oxidizing archaea release a suite of organic compounds potentially fueling prokaryotic heterotrophy in the ocean

Ammonia‐oxidizing archaea (AOA) constitute a considerable fraction of microbial biomass in the global ocean, comprising 20%–40% of the ocean's prokaryotic plankton. However, it remains enigmatic to what extent these chemolithoautotrophic archaea release dissolved organic carbon (DOC). A combination of targeted and untargeted metabolomics was used to characterize the exometabolomes of three model AOA strains of the Nitrosopumilus genus. Our results indicate that marine AOA exude a suite of organic compounds with potentially varying reactivities, dominated by nitrogen‐containing compounds. A significant fraction of the released dissolved organic matter (DOM) consists of labile compounds, which typically limit prokaryotic heterotrophic activity in open ocean waters, including amino acids, thymidine and B vitamins. Amino acid release rates corresponded with ammonia oxidation activity and the three Nitrosopumilus strains predominantly released hydrophobic amino acids, potentially as a result of passive diffusion. Despite the low contribution of DOC released by AOA (~0.08%–1.05%) to the heterotrophic prokaryotic carbon demand, the release of physiologically relevant metabolites could be crucial for microbes that are auxotrophic for some of these compounds, including members of the globally abundant and ubiquitous SAR11 clade.

Physiology limits commercially viable photoautotrophic production of microalgal biofuels

Algal biofuels have been offered as an alternative to fossil fuels, based on claims that microalgae can provide a highly productive source of compounds as feedstocks for sustainable transport fuels. Life cycle analyses identify algal productivity as a critical factor affecting commercial and environmental viability. Here, we use mechanistic modelling of the biological processes driving microalgal growth to explore optimal production scenarios in an industrial setting, enabling us to quantify limits to algal biofuels potential. We demonstrate how physiological and operational trade-offs combine to restrict the potential for solar-powered algal-biodiesel production in open ponds to a ceiling of ca. 8000 L ha^-1 year^-1. For industrial-scale operations, practical considerations limit production to ca. 6000 L ha^-1 year^-1. According to published economic models and life cycle analyses, such production rates cannot support long-term viable commercialisation of solar-powered cultivation of natural microalgae strains exclusively as feedstock for biofuels. The commercial viability of microalgal biofuels depends critically upon limitations in microalgal physiology (primarily in rates of C-fixation); we discuss the scope for addressing this bottleneck concluding that even deployment of genetically modified microalgae with radically enhanced characteristics would leave a very significant logistical if not financial burden.

Dynamic exchanges between DOM and POM pools in coastal and inland aquatic ecosystems: A review

Dynamic exchanges between dissolved organic matter (DOM) and particulate organic matter (POM) plays a critical role in organic carbon cycling in coastal and inland aquatic ecosystems, interactions with aquatic organisms, mobility and bioavailability of pollutants, among many other ecological and geochemical phenomena. Although DOM-POM exchange processes have been widely studied from different aspects, little to no effort has been made to date to provide a comprehensive, mechanistic, and micro-spatial schema for understanding various exchange processes occurring in different aquatic ecosystems in a unified way. The phenomena occurring between DOM and POM were explained here with the homogeneous and heterogeneous mechanisms. In the homogeneous mechanism, the participating components are only organic matter (OM) constituents themselves with aggregation and dissolution involved, whereas OM is associated with other components such as minerals and particulate colloids in the heterogeneous counterpart. Besides the generally concerned processes of aggregation/dissolution and adsorption/desorption, other ecological factors such as sunlight and organisms can also participate in DOM-POM exchanges through altering the chemical nature of OM. Despite the limitation of current analytical technologies, many unknown and/or unquantified processes need to be identified to unravel the complicated exchanges of OM between its dissolved and particulate states. Based on the review of several previous mathematical models, we proposed a unified conceptual model to describe all major dynamic exchange mechanisms on the basis of exergy theory. More knowledge of dynamic DOM-POM exchanges is warranted to overcome the potential problems arising from a simple division of OM into dissolved versus particulate states and to further develop more sophisticated mathematic models.

Potentiodynamic study of Al-Mg alloy with superhydrophobic coating in photobiologically active/not active natural seawater

Superhydrophobic coating technology is regarded as an attractive possibility for the protection of materials in a sea environment. DC techniques are a useful tool to characterize metals' behavior in seawater in the presence/absence of coatings and/or corrosion inhibitors. In this work, investigations concerning Al-5%Mg alloy with and without a sprayed superhydrophobic coating were carried out with potentiodynamic scans in photobiologically active and not active seawater (3 weeks of immersion). In not photobiologically active seawater, the presence of the superhydrophobic coating did not prevent pitting corrosion. With time, the coating underwent local exfoliations, but intact areas still preserved superhydrophobicity. In photobiologically active seawater, on samples without the superhydrophobic coating (controls) pitting was inhibited, probably due to the adsorption of organic compounds produced by the photobiological activity. After 3 weeks of immersion, the surface of the coating became hydrophilic due to diatom coverage. As suggested by intermediate observations, the surface below the diatom layer is suspected of having lost its superhydrophobicity due to early stages of biofouling processes (organic molecule adsorption and diatom attachment/gliding). Polarization curves also revealed that the metal below the coating underwent corrosion inhibiting phenomena as observed in controls, likely due to the permeation of organic molecules through the coating. Hence, the initial biofouling stages (days) occurring in photobiologically active seawater can both accelerate the loss of superhydrophobicity of coatings and promote corrosion inhibition on the underlying metal. Finally, time durability of superhydrophobic surfaces in real seawater still remains the main challenge for applications, where the early stages of immersion are demonstrated to be of crucial importance.

Transparent exopolymer particle production and aggregation by a marine planktonic diatom (Thalassiosira weissflogii) at different growth rates

Transparent exopolymer particles (TEP) play an important role in the ocean carbon cycle as they are sticky and affect particle aggregation and the biological carbon pump. We investigated the effect of growth rate on TEP production in nitrogen limited semi-continuous cultures of the diatom Thalassiosira weissflogii (Grunow) G. Fryxell & Hasle. Steady-state diatom concentrations and other indicators of biomass (chl a, and total carbohydrate) were inversely related to growth rate, while individual cell volume increased with growth rate. There was no change in total TEP area with growth rate; however, individual TEP were larger at high growth rates and the number of individual TEP particles was lower. TEP concentration per cell was higher at higher growth rates. SYTOX Green staining showed that <5% of the diatom population had permeable cell membranes, with the proportion increasing at low growth rates. However, TEP production rates were greater at high growth rates, refuting our hypothesis that TEP formation is dependent on dying cells with compromised cell membranes in a diatom population. Measurements of particle size distribution in the cultures using laser scattering showed that they were most aggregated at high growth rates. These results indicate a coupling between TEP production and growth rate in diatoms under N limitation, with fast growing T. weissflogii producing more TEP and aggregates.

In silico optimization for production of biomass and biofuel feedstocks from microalgae

Optimization of the production rate of biomass rich in N (e.g. for protein) or C (e.g. for biofuels) is key to making algae-based technology commercially viable. Creating the appropriate conditions to achieve this is a challenge; operational permutations are extensive, while geographical variations localise effective methods of cultivation when utilising natural illumination. As an aid to identifying suitable operational envelopes, a mechanistic acclimative model of microalgae growth is used for the first time to simulate production in virtual systems over a broad latitudinal range. Optimization of production is achieved through selection of strain characteristics, system optical depth, nutrient supply, and dilution regimes for different geographic and seasonal illumination profiles. Results reveal contrasting requirements for optimising biomass vs biofuels production. Trade-offs between maximising areal and volumetric production while conserving resources, plus hydrodynamic limits on reactor design, lead to quantifiable constraints for optimal operational permutations. Simulations show how selection of strains with a high maximum growth rate, U_m , remains the prime factor enabling high productivity. Use of an f/2 growth medium with a culture dilution rate set at ~25 % of U_m delivers sufficient nutrition for optimal biomass production. Further, sensitivity to the balance between areal and volumetric productivity leads to a well-defined critical depth at ~0.1 m at which areal biofuel production peaks with use of a low concentration f/4 growth medium combined with a dilution rate ~15 % of U_m . Such analyses, and developments thereof, will aid in developing a decision support tool to enable more productive methods of cultivation.

Monster potential meets potential monster: pros and cons of deploying genetically modified microalgae for biofuels production

Biofuels production from microalgae attracts much attention but remains an unproven technology. We explore routes to enhance production through modifications to a range of generic microalgal physiological characteristics. Our analysis shows that biofuels production may be enhanced ca fivefold through genetic modification (GM) of factors affecting growth rate, respiration, photoacclimation, photosynthesis efficiency and the minimum cell quotas for nitrogen and phosphorous (N : C and P : C). However, simulations indicate that the ideal GM microalgae for commercial deployment could, on escape to the environment, become a harmful algal bloom species par excellence, with attendant risks to ecosystems and livelihoods. In large measure, this is because an organism able to produce carbohydrate and/or lipid at high rates, providing stock metabolites for biofuels production, will also be able to attain a stoichiometric composition that will be far from optimal as food for the support of zooplankton growth. This composition could suppress or even halt the grazing activity that would otherwise control the microalgal growth in nature. In consequence, we recommend that the genetic manipulation of microalgae, with inherent consequences on a scale comparable to geoengineering, should be considered under strict international regulation.

Accumulation characteristics of soluble algal products (SAP) by a freshwater microalga Scenedesmus sp. LX1 during batch cultivation for biofuel production

Algae cultivation is the essential basis for microalgal biofuel production. Soluble algal products (SAP) are significant obstacle to large-scale, high-cell-density cultivation processes. SAP accumulation during batch cultivation of Scenedesmus sp. LX1 (a unique strain accumulating lipid substantially while growing fast under low-nutrient conditions) with different initial nitrogen concentrations (7.4-34.0mgNL(-1)) was investigated. The SAP content varied in the range of 3.4-17.4mgDOCL(-1) at stationary phase, with average yield per cell of 0.5-2.5pgDOCcell(-1). High SAP accumulation up to 15.2-17.4mgDOCL(-1) were observed with initial nitrogen above 20.2mgNL(-1). The maximum SAP production rate per unit culture volume (r(SAP)) was 2.6mgDOC(Ld)(-1) and that per cell (ν(SAP)) was 1.5pgDOC(celld)(-1). The r(SAP) increased with cell growth rate and decreased with cell density linearly. The SAP accumulation was majorly due to the release of growth-associated products.

The globally distributed genus Alexandrium: multifaceted roles in marine ecosystems and impacts on human health

The dinoflagellate genus Alexandrium is one of the major harmful algal bloom (HAB) genera with respect to the diversity, magnitude and consequences of blooms. The ability of Alexandrium to colonize multiple habitats and to persist over large regions through time is testimony to the adaptability and resilience of this group of species. Three different families of toxins, as well as an as yet incompletely characterized suite of allelochemicals are produced among Alexandrium species. Nutritional strategies are equally diverse, including the ability to utilize a range of inorganic and organic nutrient sources, and feeding by ingestion of other organisms. Many Alexandrium species have complex life histories that include sexuality and often, but not always, cyst formation, which is characteristic of a meroplanktonic life strategy and offers considerable ecological advantages. Due to the public health and ecosystem impacts of Alexandrium blooms, the genus has been extensively studied, and there exists a broad knowledge base that ranges from taxonomy and phylogeny through genomics and toxin biosynthesis to bloom dynamics and modeling. Here we present a review of the genus Alexandrium, focusing on the major toxic and otherwise harmful species.

Effects of gamma-sterilization on DOC, uranium and arsenic remobilization from organic and microbial rich stream sediments

Organic-rich sediments are known to be effective accumulators for uranium and arsenic. Much is known about the capacity for metal or metalloid fixation by microbes and organic compounds as well as inorganic sediment particles. Experiments investigating the effect of microbes on the process of metal fixation in sediments require sterilized sediments as control treatment which is often realized by gamma-sterilization. Only few studies show that gamma-sterilization has an effect on the remobilization of metal and metalloids and on their physico-chemical properties. These studies deal with sediments with negligible organic content whereas almost nothing is known about organic-rich sediments including a probably high microbial activity. In view of this, we investigated the effect of gamma-sterilization of organic-rich sediments on uranium and arsenic fixation and release. After ten days within an exposure experiment we found a significant higher remobilization of uranium and arsenic in sterile compared to unsterile treatments. In line with these findings the content of dissolved organic carbon (DOC), manganese, and iron increased to even significantly higher concentration in the sterile compared to unsterile treatment. Gamma-sterilization seems to change the physico-chemical properties of organic-rich sediments. Microbial activity is effectively eliminated. From increased DOC concentrations in overlaying water it is concluded that microbes are eventually killed with leaching of cellular compounds in the overlaying water. This decreases the adsorption capacity of the sediment and leads to enhanced uranium and arsenic remobilization.