News, Events and Happenings
PhD Graduate student Junyao Gu produced podcast on our group’s efforts to develop marine microalgae as a sustainable platform for fuel, feed and food has just been released. Her from current and former students and researchers on the group’s efforts and how their participation helped shape their career trajectory.
https://sites.nicholas.duke.edu/seastheday/2022/11/02/episode-24-algae-biofuel-the-future/
By mid-century, society will need to significantly intensify the output of its food production system while simultaneously reducing that system’s detrimental impacts on climate, land use, freshwater resources, and biodiversity. This will require finding alternatives to carbon emissions-intensive agriculture, which provides the backbone of today’s global food production system. Here, we explore the hypothesis that marine algae-based aquaculture can help close the projected gap in society’s future nutritional demands while simultaneously improving environmental sustainability. Food production from marine algae-based aquaculture has the potential to contribute more than the total global protein demand projected for 2050, which ranges from 263.8 Mt/yr to 286.5 Mt/yr. It also offers important nutritional and environmental sustainability advantages relative to terrestrial agriculture. Marine algae can provide a better source of high-quality nutritional protein, essential amino acids, and other micronutrients relative to terrestrial plants. In addition, because marine algae do not require soil, irrigation, and the open application of fertilizer, their cultivation does not need to compete with agriculture for arable land and freshwater nor does it lead to fertilizer runoff and downstream eutrophication. Furthermore, by reducing agriculture’s demand for arable land and freshwater, marine algae-based aquaculture can reduce the pressure for deforestation, potentially leading to globally significant reductions in carbon emissions and biodiversity loss.
Accurate and robust retrieval of ocean color from remote sensing enables critical observations of aquatic natural systems, from open ocean biological oceanography, coastal biodiversity, and water quality for human health. In the last decade, studies have increasingly highlighted the important role of small-scale processes in coastal and marine ecology and biogeochemistry, but observation and modeling at these scales remains technologically limited. Unoccupied aircraft systems (UAS, aka drones) can rapidly sample large areas with high spatial and temporal resolution; but the challenge of accurately retrieving ocean color, particularly with common wide field-of-view multispectral imagers, has limited the adoption of this technology. As UAS endurance, autonomy, and sensor capabilities continue to increase, so does this technology’s potential to observe the ocean at fine scales, but only if proper protocols are followed. The present study provides a guide for achieving (1) ideal viewing geometry of UAS-borne ocean color sensors, (2) techniques for the removal of sun glint and reflected skylight to derive water-leaving radiances, (3) characterization of uncertainty in these measurements, and (4) converting water-leaving radiances to remote-sensing reflectance for analytic end products such as chlorophyll a estimates. Documented open-source code facilitates replication of this emerging technique. Using this methodology, we briefly describing fine-scale variability of the Gulf Stream front off North Carolina alongside synoptic satellite data and in situ measurements for comparison. These results demonstrate how UAS-based ocean color measurements complement and enhance conventional ocean observations and modeling to resolve fine-scale variability and close the lacuna between satellite and in situ methods.
The Johnson Lab was selected for a Spark Award for pilot demonstration of carbon capture/storage technology based on ABECCS (Algae with BioEnergy Carbon Capture and Storage). As atmospheric carbon dioxide concentrations continue to rise there are substantial negative impacts to the environment and societies across the globe. Beyond just reducing future emissions, Intergovernmental Panel on Climate Change (IPCC) projections demonstrate that active carbon dioxide removal technologies will be needed to maintain climate within tolerable levels (+2°C). With their fast growth and utilization of atmospheric/oceanic carbon dioxide, microalgae offer a potential solution to this grand societal challenge. This project will demonstrate at pilot scale a combined system that utilizes waste forest products (bark/sawdust) to generate CO2 that is transformed and integrated using calcium carbonate, which in turn will be used to efficiently grow algae for the production valuable bioproducts while durably sequestering carbon. A preliminary analysis of the combined process shows it to be carbon negative and economically viable.
Disturbances, here defined as events that directly alter microbial community composition, are commonly studied in host-associated and engineered systems. In spite of global change both altering environmental averages and increasing extreme events, there has been relatively little research into the causes, persistence and population-level impacts of disturbance in the dynamic coastal ocean. Here, we utilize 3 years of observations from a coastal time series to identify disturbances based on the largest week-over-week changes in the microbiome (i.e. identifying disturbance as events that alter the community composition). In general, these microbiome disturbances were not clearly linked to specific environmental factors and responsive taxa largely differed, aside from SAR11, which generally declined. However, several disturbance metagenomes identified increased phage-associated genes, suggesting that unexplained community shifts might be caused by increased mortality. Furthermore, a category 1 hurricane, the only event that would likely be classified a priori as an environmental disturbance, was not an outlier in microbiome composition, but did enhance a bloom in seasonally abundant phytoplankton. Thus, as extreme environmental changes intensify, assumptions of what constitutes a disturbance should be re-examined in the context of ecological history and microbiome responses.
While planktonic microbes play key roles in the coastal oceans, our understanding of heterotrophic microeukaryotes’ ecology, particularly their spatiotemporal patterns, drivers, and functions, remains incomplete. In this study, we focus on a ubiquitous marine fungus-like protistan group, the Labyrinthulomycetes, whose biomass can exceed that of bacterioplankton in coastal oceans but whose ecology is largely unknown. Using quantitative PCR and amplicon sequencing of their 18S rRNA genes, we examine their community variation in repeated five-station transects across the nearshore-to-offshore surface waters of North Carolina, United States. Their total 18S rRNA gene abundance and phylotype richness decrease significantly from the resource-rich nearshore to the oligotrophic offshore waters, but their Pielou’s community evenness appears to increase offshore. Similar to the bacteria and fungi, the Labyrinthulomycete communities are significantly structured by distance from shore, water temperature, and other environmental factors, suggesting potential niche partitioning. Nevertheless, only several Labyrinthulomycete phylotypes, which belong to aplanochytrids, thraustochytrids, or unclassified Labyrinthulomycetes, are prevalent and correlated with cohesive bacterial communities, while more phylotypes are patchy and often co-occur with fungi. Overall, these results complement previous time-series observations that resolve the Labyrinthulomycetes as persistent and short-blooming ecotypes with distinct seasonal preferences, further revealing their partitioning spatial patterns and multifaceted roles in coastal marine microbial food webs.
The biological pump plays a vital role in exporting organic particles into the deep ocean for long-term carbon sequestration. However, much remains unknown about some of its key microbial players. In this study, Labyrinthulomycetes protists (LP) were used to understand the significance of heterotrophic microeukaryotes in the transport of particulate organic matter from the surface to the dark ocean. Unlike the sharp vertical decrease of prokaryotic biomass, the LP biomass only slightly decreased with depth and eventually exceeded prokaryotic biomass in the bathypelagic layer. Sequencing identified high diversity of the LP communities with a dominance of Aplanochytrium at all depths. Notably, ASVs that were observed in the surface layer comprised ~20% of ASVs and ~60% of sequences in each of the deeper (including bathypelagic) layers, suggesting potential vertical export of the LP populations to the deep ocean. Further analyses of the vertical patterns of the 50 most abundant ASVs revealed niche partitioning of LP phylotypes in the pelagic ocean, including those that could decompose organic detritus and/or facilitate the formation of fast-sinking particles. Overall, this study presents several lines of evidence that the LP can be an important component of the biological pump through their multiple ecotypes in the pelagic ocean.
Bai M, Xie N, He Y, Li J, Collier JL, Hunt DE, Johnson ZI, Jiao N, Wang G (2022). Vertical community patterns of Labyrinthulomycetes protists reveal their potential importance in the oceanic biological pump. Environ Microbiol 24: 1703-1713. https://doi.org/10.1111/1462-2920.15709
Using a commercially scalable system designed for processing thousands of liters a day, here we evaluated the factors that affected the performance, energy consumption and capital/operating costs of both flocculation-based and filtration-based algal harvesting systems over a 16 month period. Coagulation efficiency was the primary driver of harvest efficiency in the flocculation-based method, while cell lysis was important for the filtration-based method. Culture (algae) age differentially influenced harvest efficiency through changes in cell fragility and stickiness. The average energy consumption of the flocculation-based method was 0.389 kWh/m3, while that for the filtration-based method was 4.343 kWh/m3. The average harvesting cost of the filtration-based method was 5.35 $/m3, while for flocculation-based method it was 4.52 $/m3. The concentration factor of filtration-based and flocculation-based method were 770–1086 and 407–448, respectively. For both harvesting methods, labor costs dominated and ranged from 55.84%–67.94% of total cost. Further system automation is a potential method to lower the harvesting cost. The filtration-based harvesting method could produce a better quality of algal biomass with higher concentration factors and less ash content, but needed more energy input, as compared with a flocculation-based method. This study highlights the importance of algal culture status to successful harvesting, and it also provides insight into developing more efficient harvesting technology with lower energy and capital cost.
The Galápagos Archipelago lies within the Eastern Equatorial Pacific Ocean at the convergence of major ocean currents that are subject to changes in circulation. The nutrient-rich Equatorial Undercurrent upwells from the west onto the Galápagos platform, stimulating primary production, but this source of deep water weakens during El Niño events. Based on measurements from repeat cruises, the 2015/16 El Niño was associated with declines in phytoplankton biomass at most sites throughout the archipelago and reduced utilization of nitrate, particularly in large-sized phytoplankton in the western region. Protistan assemblages were identified by sequencing the V4 region of the 18S rRNA gene. Dinoflagellates, chlorophytes and diatoms dominated most sites. Shifts in dinoflagellate communities were most apparent between the years; parasitic dinoflagellates, Syndiniales, were highly detected during the El Niño (2015) while the dinoflagellate genus, Gyrodinium, increased at many sites during the neutral period (2016). Variations in protistan communities were most strongly correlated with changes in subthermocline water density. These findings indicate that marine protistan communities in this region are regimented by deep water mass sources and thus could be profoundly affected by altered ocean circulation.
In memory of Joe Bonaventura, a long time faculty member at the Duke Marine Laboratory and inspiration to so many, a crab pot Christmas Tree (a distinct eastern NC tradition) was decorated by the Johnson Lab and shown as part of the Crystal Coast Hospice 2021 Gingerbread Festival. The tree featured ornaments and other items inspired by Joe B’s life and research. It was transported by boat on the R/V Kirby-Smith for display at the Crystal Coast Civic Center. Joe was an eager and engaged friend and colleague to many and he will be missed deeply. Sara, Junyao and Lauren lead the entry.
As part of the Duke University Marine Laboratory produced “Seas the Day” podcast series, Junyao lead the latest episode “Navigating the Choppy Waters of the US PhD Application Process” In this episode, she interviewed five PhD students and the doctoral program coordinator, to learn about the biggest challenges of applying PhD, reasons to do it, tips for those wishing to apply, as well as some systemic inequalities inherent in the process and how to potentially overcome them. Congratulations Junyao!
Dr. Johnson received the Algae Biomass Organization Mid-Career Excellence Award – For excellence in scholarly achievements and a record of productive, independent, and impactful peer-reviewed research and creative scholarship activities
“Dr. Johnson has made vast contributions to the peer-reviewed literature in areas associated with microalgae cultivation, oceanography, molecular ecology, and microbiology genetics. He has served as PI for three consortia funded by the U.S. DOE, including the Marine Algae Industrialization Consortium (MAGIC) and two derivative projects of the MAGIC consortium that are focused on cultivating algae using calcium carbonate and atmospheric CO2, respectively. In addition, Dr. Johnson’s lab has conducted a range of basic science research associated with marine microbes, as detailed in the vast number of his peer-reviewed publications, including several publications in Science, Nature, and PNAS. In addition to research, Dr. Johnson teaches many classes in molecular biology and marine science, such as Aquaculture in the Environment, Biological Oceanography, and Analysis of Ocean Ecosystems, to name a few.”
The Algae Biomass Organization is the non-profit trade association and unified voice of the algae industry. Working on behalf of all sectors, the ABO advocates for algae-advancing policy and funding, serves as a hub for innovation and networking, and drives demand for “made with algae” products and services.
Algae Biomass Organization Announces 2021 Algae Industry Awards
Expanding markets for microalgae and macroalgae products have led to increased development of commercial farming operations. While microalgae and macroalgae, or seaweed, have historically been harvested in many parts of the globe, more recent developments seek to improve productivity, decrease production costs, increase scale, and mitigate environmental impacts of cultivation. This review describes current progress and proposes future directions in the commercial scale farming of microalgae and seaweeds.
The biological pump plays a vital role in exporting organic particles into the deep ocean for long-term carbon sequestration. However, much remains unknown about some of its key microbial players. In this study, Labyrinthulomycetes protists (LP) were used to understand the significance of heterotrophic microeukaryotes in the transport of particulate organic matter from the surface to the dark ocean. Unlike the sharp vertical decrease of prokaryotic biomass, the LP biomass only slightly decreased with depth and eventually exceeded prokaryotic biomass in the bathypelagic layer. Sequencing identified high diversity of the LP communities with a dominance of Aplanochytrium at all depths. Notably, ASVs that were observed in the surface layer comprised ~20% of ASVs and ~60% of sequences in each of the deeper (including bathypelagic) layers, suggesting potential vertical export of the LP populations to the deep ocean. Further analyses of the vertical patterns of the 50 most abundant ASVs revealed niche partitioning of LP phylotypes in the pelagic ocean, including those that could decompose organic detritus and/or facilitate the formation of fast-sinking particles. Overall, this study presents several lines of evidence that the LP can be an important component of the biological pump through their multiple ecotypes in the pelagic ocean.
This study determined effects of full-fatted (C046, 41% crude protein) and lipid extracted (LEA, 39% crude protein) microalgae Desmodesmus sp. on growth performance, gut health, and excreta hydrothermal liquefaction of broiler chickens. Two experiments were conducted by feeding day-old Cornish male chicks: 1) a corn-soybean meal basal diet (control) 2) control +5% C046, or 3) control +5% LEA for 2 weeks. Growth performance was measured weekly in both experiments. Blood, liver, and duodenum samples of chickens were collected for biochemical analyses, and excreta samples were collected for hydrothermal liquefaction (300 °C, 60 min) at the end of Experiment 2. Compared with the control, supplemental dietary C046 and LEA enhanced average daily gain (13% to 40%, p < 0.05) in both experiments, and improved feed efficiency (15% and 11%, p < 0.01) in Experiment 2. The C046 and LEA diets enhanced the duodenum (19% to –2 fold, p < 0.05), but decreased the liver (17 to 78%, p < 0.05) mRNA abundances of interleukins-1, 6 and 8 and (or) tumor necrosis factor-α, respectively, compared with the controls. Meanwhile, the two types of biomass enhanced the protein amounts of claudin-1 in the duodenum (5–34%, p < 0.05) than the controls. Hydrothermal liquefaction of the excreta derived from the three diets showed no major differences in total bio-crude oil (average of 23%), hydrochar yield (average of 12%), or elemental compositions. However, the heating values of the resultant two bio-crude oils from the microalgae-fed chicken excreta (average of 34 MJ/kg) were 16% greater than those from the control chickens (29 MJ/kg). In conclusion, supplementing the full- and de-fatted Desmodesmus sp. microalgal biomass in the starter diets for broiler chickens produced largely similar improvements of growth performance, gut health, and excreta-derived oil quality.
The database on ocean primary productivity comprises over two decades (1985–2008) of data that the authors have participated in collecting, using the assimilation of inorganic 14C through photosynthesis, in incubations carried out in situ. The dataset is perhaps unique in that it uses, overwhelmingly, consistent methodology while covering a wide geographic range. Ancillary data are included. Using the database, it is hoped that investigators can test for the relationships among the environmental drivers for ocean productivity, the meaning of the 14C method in terms of phytoplankton physiology and the dynamics in the water column, and as a resource for further development of productivity algorithms using satellite ocean color imagery.
While disappointingly not algae related….unless it is….Lauren was a winner at the 2020 DUML pumpkin carving competition. Well done!
Heterotrophic microbes play a key role in remineralizing organic material in the coastal ocean. While there is a significant body of literature examining heterotrophic bacterioplankton and phytoplankton communities, much less is known about the diversity, dynamics, and ecology of eukaryotic heterotrophs. Here we focus on the Labyrinthulomycetes, a fungus-like protistan group whose biomass can exceed that of the bacterioplankton in coastal waters. We examined their diversity and community structure in a weekly temperate coastal ocean time series. Their seasonal community patterns were related to temperature, insolation, dissolved inorganic carbon, fungal abundance, ammonia, chlorophyll a, pH, and other environmental variables. Similar to the bacterioplankton, annual community patterns of the Labyrinthulomycetes were dominated by a few persistent taxa with summer or winter preferences. However, like the patterns of fungi at this site, the majority of the Labyrinthulomycetes phylotypes occurred mostly as short, reoccurring, season-specific blooms. Furthermore, some of specific phylotypes of Labyrinthulomycetes displayed time-lagged correlations or co-occurrences with bacterial, algal, or fungal phylotypes, suggesting their potentially multifaceted involvement in the marine food webs. Overall, this study reports niche partitioning between closely-related Labyrinthulomycetes and identifies distinct ecotypes and temporal patterns compared to bacterioplankton and fungi.
Economical production of algal commodities (food, feed, and fuels) requires reusing cultivation water to reduce operating costs. While some algae strains show growth inhibition in reused water, other strains appear unaffected. Reusing water to grow different strains (i.e., crop rotation) could potentially improve overall biomass production compared to water reuse with the same strain by reducing accumulation of strain-specific waste products, limiting carryover of population-specific pathogens such as viruses, and introducing bacteria that degrade residual organic matter. Here, batch culture experiments tested the effects of reused cultivation water from the self-inhibiting diatom Staurosira sp. C323 on the diatom Navicula sp. SFP and green alga Chlorella sp. D046, as well as their microbiomes. Navicula sp. and Chlorella sp. grew well in Staurosira sp. reused water, indicating that previously observed self-inhibition was likely specific to this Staurosira strain. While algal microbiomes were not significantly different between controls and reused water treatments, specific bacteria taxa were differentially abundant in reused treatments, suggesting that some taxa responded to compounds remaining in the reused water. Results suggest that algae growth responses in reused water may depend largely on strain-specific factors, and that crop rotation can support biomass production.
Ambient conditions shape microbiome responses to both short- and long-duration environment changes through processes including physiological acclimation, compositional shifts, and evolution. Thus, we predict that microbial communities inhabiting locations with larger diel, episodic, and annual variability in temperature and pH should be less sensitive to shifts in these climate-change factors. To test this hypothesis, we compared responses of surface ocean microbes from more variable (nearshore) and more constant (offshore) sites to short-term factorial warming (+3 °C) and/or acidification (pH −0.3). In all cases, warming alone significantly altered microbial community composition, while acidification had a minor influence. Compared with nearshore microbes, warmed offshore microbiomes exhibited larger changes in community composition, phylotype abundances, respiration rates, and metatranscriptomes, suggesting increased sensitivity of microbes from the less-variable environment. Moreover, while warming increased respiration rates, offshore metatranscriptomes yielded evidence of thermal stress responses in protein synthesis, heat shock proteins, and regulation. Future oceans with warmer waters may enhance overall metabolic and biogeochemical rates, but they will host altered microbial communities, especially in relatively thermally stable regions of the oceans.
A substantial body of research now exists demonstrating sensitivities of marine organisms to ocean acidification (OA) in laboratory settings. However, corresponding in situ observations of marine species or ecosystem changes that can be unequivocally attributed to anthropogenic OA are limited. Challenges remain in detecting and attributing OA effects in nature, in part because multiple environmental changes are co-occurring with OA, all of which have the potential to influence marine ecosystem responses. Furthermore, the change in ocean pH since the industrial revolution is small relative to the natural variability within many systems, making it difficult to detect, and in some cases, has yet to cross physiological thresholds. The small number of studies that clearly document OA impacts in nature cannot be interpreted as a lack of larger-scale attributable impacts at the present time or in the future but highlights the need for innovative research approaches and analyses. We summarize the general findings in four relatively well-studied marine groups (seagrasses, pteropods, oysters, and coral reefs) and integrate overarching themes to highlight the challenges involved in detecting and attributing the effects of OA in natural environments. We then discuss four potential strategies to better evaluate and attribute OA impacts on species and ecosystems. First, we highlight the need for work quantifying the anthropogenic input of CO2 in coastal and open-ocean waters to understand how this increase in CO2 interacts with other physical and chemical factors to drive organismal conditions. Second, understanding OA-induced changes in population-level demography, potentially increased sensitivities in certain life stages, and how these effects scale to ecosystem-level processes (e.g. community metabolism) will improve our ability to attribute impacts to OA among co-varying parameters. Third, there is a great need to understand the potential modulation of OA impacts through the interplay of ecology and evolution (eco–evo dynamics). Lastly, further research efforts designed to detect, quantify, and project the effects of OA on marine organisms and ecosystems utilizing a comparative approach with long-term data sets will also provide critical information for informing the management of marine ecosystems.
Coastal acidification in southeastern U.S. estuaries and coastal waters is influenced by biological activity, run-off from the land, and increasing carbon dioxide in the atmosphere. Acidification can negatively impact coastal resources such as shellfish, finfish, and coral reefs, and the communities that rely on them. Organismal responses for species located in the U.S. Southeast document large negative impacts of acidification, especially in larval stages. For example, the toxicity of pesticides increases under acidified conditions and the combination of acidification and low oxygen has profoundly negative influences on genes regulating oxygen consumption. In corals, the rate of calcification decreases with acidification and processes such as wound recovery, reproduction, and recruitment are negatively impacted. Minimizing the changes in global ocean chemistry will ultimately depend on the reduction of carbon dioxide emissions, but adaptation to these changes and mitigation of the local stressors that exacerbate global acidification can be addressed locally. The evolution of our knowledge of acidification, from basic understanding of the problem to the emergence of applied research and monitoring, has been facilitated by the development of regional Coastal Acidification Networks (CANs) across the United States. This synthesis is a product of the Southeast Coastal and Ocean Acidification Network (SOCAN). SOCAN was established to better understand acidification in the coastal waters of the U.S. Southeast and to foster communication among scientists, resource managers, businesses, and governments in the region. Here we review acidification issues in the U.S. Southeast, including the regional mechanisms of acidification and their potential impacts on biological resources and coastal communities. We recommend research and monitoring priorities and discuss the role SOCAN has in advancing acidification research and mitigation of and adaptation to these changes.
The Pivers Island Coastal Observatory turned 10-years old today! What started out as an undergraduate summer project focused on nearshore ocean acidification, has blossomed into a comprehensive microbial and biogeochemical time-series with more than 1000 time points (and still going) and with extensions to the open ocean. We look forward to another decade of contributions to microbial oceanography using PICO as a sentinel of local and global change.
Microalgae hold great promise as environmentally sustainable sources of food, animal feed, and fuel. However, large amounts of water are used during microalgae cultivation and this negatively impacts economic viability and environmental sustainability. Reusing cultivation water can reduce the direct impacts of water usage and also reduce nutrient requirements and algal wastewater treatment. However, studies have shown that algae growth in reused water can be compromised, unaffected, or sometimes enhanced compared to controls. This review examines recent studies on water reuse to qualitatively understand these varied effects. Growth inhibitors and stimulators in reused water and their underlying mechanisms are discussed, as well as recent pre-treatment technologies and factors affecting the quality of reused water, such as microalgae taxa, culture conditions, and harvesting methods, are considered. A scheme is proposed for water reuse and harvesting methods based on the desired algal end products. Taking these findings together, here we provide recommendations for further research directions as well as new insights into designing and integrating a cultivation strategy with a harvesting platform to reuse water for more efficient microalgae cultivation.
The Pivers Island Coastal Observatory (PICO) sampled its 1000th time point today. The time-series, was started in 2010 by a Duke undergraduate (Christina C.) interested in the temporal variability of ocean acidification. Ten years later, the time-series has generated a rich, publically available dataset to examine the physical, chemical and biological variability associated with regular processes (e.g. seasons and tides) and episodic events (e.g. hurricanes). Over 50 trainees, undergraduates, graduate students, PIs and other scientists have been part of the sampling. Fittingly, today’s sampling was carried out by Sara Blinebry who has sampled PICO the most over the course of the ten years. Congratulations to all and looking forward to another 1000 time-points!
Keep up! 🙂
The Duke Marine Lab’s Biological Oceanography 2020 class was held aboard the new Duke University research vessel R/V Shearwater. The 77′ power catamaran is a all purpose research vessel with a cruising speed of >20 knots and better than 1000 miles radius. The research vessel had three crew along with the ten members for the inaugural at-sea class. The adventure started in Miami, FL and cruised around Florida visiting Key West, Dry Tortugas and Fort Myers among other locations before returning to Miami via the gulf stream. With a fully functional CTD equipped rosette, along with on-board sampling capabilities, the class carried out numerous onsite depth profiles and underway samplings to characterize biological variability (and its chemical and physical drivers) in this region of the Atlantic Ocean. A trove of data was brought home where everyone had a chance to analyze and interpret as part of broader oceanographic processes. In spite of (or perhaps because of) the close-quarters, everyone had an amazing time and earned their ranks as the pioneering research and educational expedition aboard this amazing vessel. We greatly look forward to more adventures in the future.
Led by Sara, Courtney and Jess, the marine microbe group tree was the ‘crowd favorite’ at this year’s Gingerbread Festival Crab Pot Christmas Tree decorating contest. The tree, themed Sparkling Science in the Deep Blue Sea, was loaded with ornaments that highlight the various types of marine science research and education that occur at the Duke Marine Lab. Perhaps the highlight of the decorations was the moving bubble/water stream that encircled the tree. Further adding to the excitement was the the tree was transported to the venue via boat. Congratulations to Team Microbe!
The decarbonization of agriculture faces many challenges and has received a level of attention insufficient to abate the worst effects of climate change and ensure a sustainable bioeconomy. Agricultural emissions are caused both by fossil-intensive fertilizer use and land-use change, which in turn are driven in part by increasing demand for dietary protein. To address this challenge, we present a synergistic system in which organic waste-derived biogas (a mixture of methane and carbon dioxide) is converted to dietary protein and ammonia fertilizer. This system produces low-carbon fertilizer inputs alongside high-quality protein, addressing the primary drivers of agricultural emissions. If the proposed system were implemented across the United States utilizing readily available organic waste from municipal wastewater, landfills, animal manure, and commercial operations, we estimate 30% of dietary protein intake and 127% of ammonia usage could be displaced while reducing land use, water consumption, and greenhouse gas emissions.
The marine microbe group held a going away part for Ningdong (Daniel) Xie, a visiting Chinese scholar from Tianjin University, China. While here, Daniel studied marine protists, focusing on Labyrinthulomycetes and Fungi, in our coastal waters. Using the PICO time-series and PICO-LOVE transect he found surprising patterns in the abundance and diversity of these important organisms. Some of the papers he published are here (with more to come!) We’ll miss you!
The Johnson Lab hosted several presentations and demonstrations as part of DUML Open House 2019. The exhibits focused on the diversity and role of algae / phytoplankton in the coastal ocean as well as the biotechnological applications of algae for sustainable food, feed and fuels. Hundreds of visitors were able to see first hand how algae is grown and to view both cultured and natural plankton samples. Lots of fun!
Read more about the DUML 2019 Open House here in an article by recent Johnson Lab PhD Sarah Loftus.
Recent studies have focused on linking marine microbial communities with environmental factors, yet relatively little is known about the drivers of microbial community patterns across the complex gradients from the nearshore to open ocean. Here, we examine microbial dynamics in 15 five‐station transects beginning at the estuarine Piver’s Island Coastal Observatory (PICO) time‐series site and continuing 87 km across the continental shelf to the oligotrophic waters of the Sargasso Sea. 16S rRNA gene libraries reveal strong clustering by sampling site with distinct nearshore, continental shelf, and offshore oceanic communities. Water temperature and distance from shore (which serves as a proxy for gradients in factors such as productivity, terrestrial input, and nutrients) both most influence community composition. However, at the phylotype level, modeling shows the distribution of some taxa is linked to temperature, others to distance from shore and some by both factors, highlighting that taxa with distinct environmental preferences underlie apparent clustering by station. Thus, continental margins contain microbial communities that are distinct from those of either the nearshore or offshore environments and contain mixtures of phylotypes with nearshore or offshore preferences rather than those unique to the shelf environment.
The Pivers Island Coastal Observatory (PICO) weekly (and sometimes more) time-series turned nine today. Started in 2010 as an undergraduate independent student project focusing on ocean acidification, the coastal time-series has matured into a long term coastal sentinel, observing seasonal, yearly and interannual changes in the physics, chemistry and biology of the coastal marine environment with weekly sampling. Additional offshore longitudinal sampling (PICO-LOVE) provides spatial context. Data is available through BCO-DMO. Happy Birthday and hooray for PICO!
Drs. Lu and Johnson both presented at IABBB 2019 meeting in Boulder CO.
Implementation of UV-based advanced oxidation processes in algal medium reuse
Z. Lu, W. Wang, J. Sha, X. Zhang, P. Sun, Q. Hu
Algae show great potential as sustainable feedstock for numerous bioproducts. However, large volume of water consumption during algal biomass production make the culture media recycling is a necessity due to economic and environmental concern. To avoid the negative effect of enriched organic matters in the harvested culture media, pre-treatment prior to medium replenishment and reuse is required. In this study, degradation of algenitic organic matters (AOM) in the culture media by UV-based photolysis processes (i.e., direct UV, UV/peroxydisulfate (PDS), UV/H2O2 and UV/NH2Cl) was explored. The results showed that UV, UV/ PDS, UV/H2O2 and UV/NH2Cl caused a decrease of SUVA for 29.9%, 35.4%, 40.45% and 22.6%, respectively, though the organic matter was almost not mineralized. Fluorescence excitation-emission matrix combined with parallel factor analysis indicated that UV/ PDS and UV/H2O2 degraded 47.26%-56.31% of the fluvic-like and humic-like fractions in AOM. Powder activated carbon absorption and growth evaluation for the AOPs-treated media indicated that UV/ PDS and UV/H2O2 processes not only could remove the growth inhibitors in the media, but also were beneficial to the algae growth. These results suggested that UV/PDS and UV/H2O2 could effectively degradation the hydrophobic components in AOM and converted the growth inhibition fraction of AOM in the recycled media into nutrient source for algal growth. Unlike the general application of UV-based AOP in the wastewater treatment, this study provided an innovative idea about how to pre-treat AOM in the media recycling: utilization rather than removal, which was a more sustainable and environment-friendly technology.
Algae production from the Marine Algae Industrialization Consortium (MAGIC)
Z. Johnson
Duke University, USA
Introduction: The Marine Algae Industrialization Consortium (MAGIC) is a group of academic and private institutions that together seek to advance the large scale use of marine algae for the sustainable production of food, feed and fuel. Our team is an integrated pipeline from algae strain selection to production, separation, product assessment and economic and life cycle analyses. Here we present results and interpretation from the outdoor cultivation and harvesting of several top candidate strains. Methods: Numerous taxonomically diverse strains of marine microalgae were grown in outdoor raceway ponds across an annual cycle to investigate factors that lead to enhanced production and recovery of algae biomass for downstream applications. These marine microalgae were grown in a hybrid PBR – raceway pond system that experienced natural environmental variability and thus the range of values recovered represent a real world assessment of production. Results: We show that there is a dramatic variability in the productivity across taxa, environmental conditions, and pond operational parameters with some combinations leading to substantial improvements over ‘standard’ conditions in overall biomass yields. Discussion: These results demonstrate the variability across strains/conditions and the importance of using industrially relevant conditions when design testing infrastructure and operational conditions. The best combinations suggest areas that may be further optimized for future increases in algae productivity. Finally, the biomass generated has excellent biochemical characteristics that support an improved economic assessment of the use of marine algae for the sustainable production of fuel, feed and food.
Reusing growth medium (water supplemented with nutrients) for microalgae cultivation is required for economical and environmentally sustainable production of algae bioproducts (fuels, feed, and food). However, reused medium often contains microbes and dissolved organic matter that may affect algae growth. While the accumulation of dissolved organic carbon (DOC) in reused medium has been demonstrated, it is unclear whether DOC concentrations affect algae growth or subsequent rates of algal DOC release. To address these questions, lab-scale experiments were conducted with three marine microalgae strains, Navicula sp. SFP, Staurosira sp. C323, and Chlorella sp. D046, grown in medium reused up to four times. Navicula sp. and Chlorella sp. grew similarly in reused medium as in fresh medium, while Staurosira sp. became completely inhibited in reused medium. Across the three algae, there was no broad trend between initial DOC concentration in reused medium and algae growth response. Navicula sp. released less DOC overall in reused medium than in fresh medium, but DOC release rates did not decrease proportionally with increased DOC concentrations. Net DOC accumulation was much lower than gross DOC released by Navicula sp. and Staurosira sp., indicating the majority of released DOC was degraded. Additionally, biodegradation experiments with reused media showed no further net decrease in DOC, suggesting the accumulated DOC was recalcitrant to the associated bacteria. Overall, these results suggest that taxa-specific factors may be responsible for algae growth response in reused medium, and that DOC release and accumulation are insensitive to prior cultivation rounds. Choosing an algae strain that is uninhibited by accumulated DOC is therefore critical to ensure successful water reuse in the algae industry.
PhD student Sarah Loftus attended the 2019 ASLO Aquatic Sciences Meeting in San Juan, Puerto Rico. ASLO’s mission is to “foster a diverse, international scientific community that creates, integrates and communicates knowledge across the full spectrum of aquatic sciences, advances public awareness and education about aquatic resources and research, and promotes scientific stewardship of aquatic resources for the public interest.” Loftus presented her PhD research in the special session on Phytoplankton-Bacteria Interactions, with a talk titled “Effects of DOC pools on phytoplankton growth and bacteria communities.” She was also selected to participate in ASLO’s Journalist for a Day program, which involves writing an article about research presented at the conference. Articles from this program will be published in the August issue of the Limnology & Oceanography Bulletin.
Subsurface chlorophyll maximum layers (SCMLs) are nearly ubiquitous in stratified water columns and exist at horizontal scales ranging from the submesoscale to the extent of oligotrophic gyres. These layers of heightened chlorophyll and/or phytoplankton concentrations are generally thought to be a consequence of a balance between light energy from above and a limiting nutrient flux from below, typically nitrate (NO3). Here we present multiple lines of evidence demonstrating that iron (Fe) limits or with light colimits phytoplankton communities in SCMLs along a primary productivity gradient from coastal to oligotrophic offshore waters in the southern California Current ecosystem. SCML phytoplankton responded markedly to added Fe or Fe/light in experimental incubations and transcripts of diatom and picoeukaryote Fe stress genes were strikingly abundant in SCML metatranscriptomes. Using a biogeochemical proxy with data from a 40-y time series, we find that diatoms growing in California Current SCMLs are persistently Fe deficient during the spring and summer growing season. We also find that the spatial extent of Fe deficiency within California Current SCMLs has significantly increased over the last 25 y in line with a regional climate index. Finally, we show that diatom Fe deficiency may be common in the subsurface of major upwelling zones worldwide. Our results have important implications for our understanding of the biogeochemical consequences of marine SCML formation and maintenance.
Salmon
id feeds can be formulated with high quality microalgae to maintain sustainability in the aquaculture industry. But, the suitability of different microalgae species as potential feed ingredients needs to be documented to enable ready acceptance by the farming industry. The aim of the present study is to investigate the potential of the microalga Scenedesmus sp. as a major ingredient in low fishmeal feeds of Atlantic salmon. Three feeds were formulated with Scenedesmus/fishmeal, at inclusion levels of 0/10, 10/5 and 20/2.5% (CT, SCE 10 and SCE 20, respectively); to investigate the effect of the ingredient on the weight gain, growth rate, feed conversion ratio, nutrient retention and chemical composition and nutrient digestibility in Atlantic salmon. In addition, the physical characteristics of feeds were investigated to assess the impact of the alga-incorporation on the quality of the feeds. Fish (initial average weight of 229 g) in 6 replicate tanks were fed one of the experimental feeds for 65 days. The results showed that fish fed SCE 20 had significantly lower weight gain, specific growth rate, thermal growth coefficient and feed conversion ratio than the CT group, which did not receive the microalga. Furthermore, the condition factor and protein efficiency ratio of the microalga-fed groups were lower than the CT group. Hepatosomatic and viscerosomatic indices of the groups did not differ significantly. Ash and protein content of whole fish fed SCE 20 were significantly higher, but dry matter, lipid, and energy of this group were lower than either the CT or the SCE 10 group. Retention of lipid and energy of all groups differed significantly, while that of protein was significantly different in the Scenedesmus-fed groups. Compared to the CT feed, digestibility of dry matter, protein, and energy in the algal feeds were significantly reduced. The highest fat leakage observed for the feed devoid of the alga and the hardness of the SCE 20 feed points to the better physical stability of the alga-containing feeds. Higher contents of n-3 fatty acids and PUFAs were found in the whole body of fish fed SCE 10. In conclusion, Scenedesmus sp. can be incorporated in low fishmeal diets for Atlantic salmon, at inclusion levels below 10%.
The Second State of the Carbon Cycle Report (SOCCR2) was released by the U.S. Global Change Research Program (USGCRP) via https://carbon2018.globalchange.gov on Friday, November 23, 2018. With over 200 contributing experts including PI Johnson, this interagency Highly Influential Scientific Assessment was led by the Carbon Cycle Interagency Working Group (CCIWG) and U.S. Carbon Cycle Science Program under USGCRP auspices. SOCCR2 is an authoritative decadal assessment of carbon cycle science across North America, developed by over 200 experts from the U.S., Canadian and Mexican governments, national laboratories, universities, private sector, and research institutions. SOCCR2 is a Sustained Assessment Product of the U.S. Global Change Research Program.
USGCRP, 2018: Second State of the Carbon Cycle Report (SOCCR2): A Sustained Assessment Report. [Cavallaro, N., G. Shrestha, R. Birdsey, M. A. Mayes, R. G. Najjar, S. C. Reed, P. Romero-Lankao, and Z. Zhu (eds.)]. U.S. Global Change Research Program, Washington, DC, USA, 878 pp., https://doi.org/10.7930/SOCCR2.2018.
Peggy Mullin, visiting UNC student who is working with the Johnson Lab on modeling outdoor large scale algae growth, successfully defended her undergraduate honor’s thesis. The thesis, “Development of a laboratory metric to predict large scale algae productivity” uses small scale, rapid laboratory measurements in conjunction with environmental data and mathematical modeling to predict outdoor algae production. This work is an important step towards the broader implementation of the use of marine algae for the sustainable production of food, feed and fuel. Congratulations Peggy!
PhD graduate student Sarah Loftus was the top prize winner of the biology section at the Algae Biomass Summit. The Summit is the algae industry’s premier event, where leading producers of algae products go to network with industry suppliers and technology providers, where project developers converse with utility executives, and where researchers and technology developers rub elbows with venture capitalists. Ms. Loftus presented on recycled water use for industrial applications of algae. Congratulations!
Recycled algae cultivation water steadily accumulates dissolved organic carbon
Summary: Reusing cultivation water is required for economical and environmentally sustainable production of algal biofuels and co-products. However, recycled water contains compounds released by algae that can affect their growth. Previous studies have measured dissolved organic carbon (DOC) accumulation in recycled water, yet none have determined if recycled water affects DOC release or if DOC concentrations predict growth success in recycled water. Here, lab-scale water recycling experiments showed that different algae responded uniquely to recycled growth medium, but growth responses did not correlate with DOC concentration. DOC release rates were lower on average in recycled medium, although there was no trend of decreasing release rates across multiple water reuses. Accumulated DOC in recycled water was also not degraded, so at least a portion may be recalcitrant (i.e., non-biodegradable). Results can inform algae selection and cultivation decisions to maximize both the quality of recycled water and the carbon retained in algae biomass.
There is a growing awareness of the ecological and biogeochemical importance of fungi in coastal marine systems, while highly diverse fungi have been discovered in these marine systems, still little is known about their seasonality and associated drivers in coastal waters. Here, we examined fungal communities over three years of weekly samples at a dynamic, temperate coastal site (Piver’s Island Coastal Observatory (PICO), Beaufort NC USA). Fungal 18S rRNA gene abundance, OTU richness and Shannon’s diversity exhibited prominent seasonality. Fungi 18S rRNA gene copies peak in abundance during the summer and fall, with positive correlations with chlorophyll a, SiO4 and oxygen saturation. Diversity (measured using Internal Transcribed Spacer: ITS libraries) was highest during winter and lowest during summer; it was linked to temperature, pH, chlorophyll a, insolation, salinity, and DIC. Fungal community ITS libraries were dominated throughout the year by Ascomycota with contributions from Basidiomycota, Chytridiomycota and Mucoromycotina, with seasonal patterns linked to water temperature, light, and the carbonate system. Network analysis revealed that while co-occurrence and exclusion existed within fungal network, exclusion dominated the fungi and phytoplankton network, in contrast with reported pathogenic and nutritional interactions between marine phytoplankton and fungi. Compared with the seasonality of bacterial community in the same samples, the timing, extent and associated environmental variables for fungi community are unique. These results highlighted the fungal seasonal dynamics in coastal water and improve our understanding of the ecology of planktonic fungi.ImportanceCoastal fungal dynamics were long assumed to be due to terrestrial inputs; here, a high-resolution time-series, reveals strong, repeating annual patterns linked to in situ environmental conditions, arguing for a resident coastal fungal community shaped by environmental factors. These seasonal patterns do, however, differ from those observed in the bacterioplankton at the same site: e.g., fungal diversity peaks in winter whereas bacterial diversity maxima occur in the spring and fall. While dynamics of these communities are linked to water temperature and insolation, fungi are also influenced by the carbonate system (pH and DIC). As both fungi and heterotrophic bacteria are thought to be key organic material metabolizers, differences in their environmental drivers may offer clues as to which group dominates secondary production at this dynamic site. Overall, this study suggests the unique ecological roles of mycoplankton and their potentially broad niche complementarities to other microbial groups in the coastal ocean.
The unicellular Labyrinthulomycete protists have long been considered to play a significant role in ocean carbon cycling. However, their distribution and biogeochemical function remain poorly understood. We present a large‐scale study of their spatiotemporal abundance and diversity in the coastal waters of Bohai Sea using flow cytometry and high‐throughput sequencing. These protists display niche preferences and episodic higher biomass than that of bacterioplankton with much phylogenetic diversity (> 4000 OTUs) ever reported. They were ubiquitous with a typical abundance range of 100–1000 cells ml−1 and biomass range of 0.06–574.59 μg C L−1. The observed spatiotemporal abundance variations support the current ‘left‐over scavengers’ nutritional model and highlight these protists as a significant component of the marine microbial loop. The higher average abundance and phylogenetic diversity in the nearshore compared with those in the offshore reveal their predominant role in the terrigenous matter decomposition. Furthermore, the differential relationship of the protist genera to environmental conditions together with their co‐occurrence network suggests their unique substrate preferences and niche partitioning. With few subnetworks and possible keystone species, their network topology indicates community resilience and high connectance level of few operational taxonomic units (OTUs). We demonstrate the significant contribution of these protists to the secondary production and nutrient cycling in the coastal waters. As secondary producers, their role will become more important with increasingly coastal eutrophication.
The annual Duke Marine Lab Open House had exceptional attendance this year as it coincided with alumni weekend and a visit from Duke University President Vincent Price. Johnson Lab members hosted two stations at Open House on the sunny July afternoon. One station showcased the open raceway ponds, a feature of the DOE-funded large-scale algae cultivation project. Visitors were even invited to enter a rubber duck race, cheering for their small plastic toy as it rounded the bend of the raceway pond. Another station taught visitors about the diversity and lifestyles of the algae we research in lab. President Price even peered into a microscope to watch Tetraselmis cells whip around using their tail-like flagella. More photos from the weekend can be viewed on Duke’s Nicholas School news page.
First year PhD student Laura Givens receive an IBIEM Graduate Trainee award. IBIEM (Integrative Bioinformatics for Investigating and Engineering Microbiomes) is an interdisciplinary graduate training program between Duke University and North Carolina A&T State University which brings together scientists from various fields with an interest in microbiome research. IBIEM trainees participate in the Boot Camp, Collaborative Science Practica, and an Interactive seminar Course and other informal interactions to be exposed to multiple levels of interdisciplinary experiences to enable them to address issues of quantitative biology in the context of varying industrial sectors. Congratulations Laura!
The Pivers Island Coastal Observatory (PICO) weekly (and sometimes more) time-series turned eight today. Started in 2010 as an undergraduate independent student project focusing on ocean acidification, the coastal time-series has matured into a long term coastal sentinel, observing seasonal, yearly and interannual changes in the physics, chemistry and biology of the coastal marine environment with weekly sampling. Additional offshore longitudinal sampling (PICO-LOVE) provides spatial context. Data is available through BCO-DMO. Happy Birthday and hooray for PICO!
Volunteers from over a dozen regional institutions welcomed over 160 middle school girls to the event this Saturday. GEST’s mission is to provide hands-on STEM opportunities and female STEM role models to girls in eastern NC. PhD students Courtney Swink and Sarah Loftus were on the GEST planning team, which organized this collaborative outreach event in which girls rotated through different STEM activities and a panel discussion. Courtney Swink led one of the twelve STEM activities. She explained the concept of algae cultivation for biofuels and other products, had girls set up their own algae cultures, and described the outdoor cultivation ponds with a tour.
Ph.D. student Courtney traveled to Washington, D.C. to volunteer at the USA Science & Engineering Festival on Saturday, April 6th. This free 2 day event was held at the Walter E. Washington Convention Center and had over 3,000 exhibitors and 350,000 visitors! The mission of this festival is to stimulate interest in the nation’s youth in science, technology, engineering and math (STEM) related fields.
As a student member of ASLO (Association for the Sciences of Limnology and Oceanography), Courtney participated as a volunteer for the CASS (Consortium of Aquatic Science Societies) booth which shared activities and information about aquatic sciences for all age levels. Students were taught about the different morphologic adaptations of all types of plankton and asked to build their own plankton models to “race” to see who’s creation would sink the slowest. Students also learned about turbidity and how to use a secchi disk. The CASS booth alone interacted with ~3,300 young students, parents and teachers! Many students left the booth with a better understanding of what plankton look like and why they are important in the environment.
Second year PhD student Courtney Swink was awarded a NSF Graduate Research Fellowship Program Fellowship. Her selection as an NSF Graduate Fellowship awardee is a significant accomplishment and was based on her demonstrated potential to contribute to strengthening the vitality of the U.S. science and engineering enterprise. Courtney is researching microbial communities associated with large, industrial scale marine microalgae ponds.
Bioenergy Carbon Capture and Storage (BECCS) has been proposed to reduce atmospheric CO2 concentrations, but concerns remain about competition for arable land and freshwater. The synergistic integration of algae production, which does not require arable land or freshwater, with BECCS (called “ABECCS”) can reduce CO2 emissions without competing with agriculture. This study presents a techno-economic and life-cycle assessment for co-locating a 121-ha algae facility with a 2,680-ha eucalyptus forest for BECCS. The eucalyptus biomass fuels combined heat and power generation (CHP) with subsequent amine based carbon capture and storage (CCS). A portion of the captured CO2 is used for growing algae and the remainder is sequestered. Biomass combustion supplies CO2, heat, and electricity, thus increasing the range of sites suitable for algae cultivation. Economic, energetic, and environmental impacts are considered. The system yields as much protein as soybeans while generating 61.5 TJ of electricity and sequestering 29,600 t of CO2 per year. More energy is generated than consumed and the freshwater footprint is roughly equal to that for soybeans. Financial break-even is achieved for product value combinations ranging from 1) algal biomass sold for $1,780/t without a carbon credit to 2) algal biomass sold for $100/t with a carbon credit of $396/t. Sensitivity analysis shows significant reductions to the cost of carbon sequestration are possible. The ABECCS system represents a unique technology for negative emissions without reducing protein production or increasing water demand, and should therefore be included in the suite of technologies being considered to address global sustainability.