News, Events and Happenings
Happy holidays from the Johnson Lab! Hope plankton brings you something good this year. (Plankton converts to coal in ~300 million years.)
Microbial science at Duke is taking a major step forward with the launch of the Duke Microbiome Center (DMC), which is intended to address growing scientific interest in the roles microbial communities play in human health, the environment and biotechnology. The new center expands on the mission of the five-year-old Duke Center for Genomics of Microbial Systems (GeMS) by going beyond genomic analysis of microorganisms. See related article at Duke Today.
Marine aggregates play a critical role in the biological pump, both as a dominant component of carbon flux and as hotspots for organic matter remineralization by microbial communities. In this study, we used laboratory experiments to investigate how aggregate thin layers, such as those commonly found in the coastal ocean, affect the distribution of bacteria and their activity. Diatom aggregates were added to a stratified water column, forming layers within which both microbial concentration and extracellular enzyme activity were substantially increased relative to background levels. Importantly, this enhancement of bacterial concentration and activity persisted long after the marine snow aggregates settled through the tank—that is, 10 times longer than the duration of the aggregate layer at the density interface. Thus, these small-scale microbial interactions within aggregate layers leave behind considerable “carbon processing footprints” in the water column that may affect biogeochemical cycles at much larger temporal and spatial scales.
Prairie JC, Ziervogel K, Camassa R, McLaughlin RM, White BL, Johnson ZI, Arnosti C Ephemeral aggregate layers in the water column leave lasting footprints in the carbon cycle. Limnology and Oceanography Letters. DOI: 10.1002/lol2.10053
Prochlorococcus, the smallest and most abundant phytoplankter in the ocean, is highly sensitive to hydrogen peroxide (HOOH), and co-occurring heterotrophs such as Alteromonas facilitate the growth of Prochlorococcus by scavenging HOOH. Temperature is also a major influence on Prochlorococcus abundance and distribution in the ocean, and studies in other photosynthetic organisms have shown that HOOH and temperature extremes can act together as synergistic stressors. To address potential synergistic effects of temperature and HOOH on Prochlorococcus growth, high- and low-temperature adapted representative strains were cultured at ecologically relevant concentrations under a range of HOOH concentrations and temperatures. Higher concentrations of HOOH severely diminished the permissive temperature range for growth of both Prochlorococcus strains. At the permissive temperatures, the growth rates of both Prochlorococcus strains decreased as a function of HOOH, and cold temperature increased susceptibility of photosystem II to HOOH-mediated damage. Serving as a proxy for the natural community, co-cultured heterotrophic bacteria increased the Prochlorococcus growth rate under these temperatures, and expanded the permissive range of temperature for growth. These studies indicate that in the ocean, the cross-protective function of the microbial community may confer a fitness increase for Prochlorococcus at its temperature extremes, especially near the ocean surface where oxidative stress is highest. This interaction may play a substantial role in defining the realized thermal niche and habitat range of Prochlorococcus with respect to latitude.
Ma L, Calfee BC, Morris JJ, Johnson ZI, Zinser ER (2017). Degradation of hydrogen peroxide at the ocean/’s surface: the influence of the microbial community on the realized thermal niche of Prochlorococcus. ISME J. http://doi.org/10.1038/ismej.2017.182
Associate Professor Zackary Johnson presented on the trends and patterns of coastal and ocean acidification in coastal North Carolina at the Southeastern Ocean and Coastal Acidification Network NC Stakeholder meeting. The presentation was titled, ‘Variability of the carbonate system (including acidity) in a dynamic coastal NC system’. Ocean and coastal acidification are changing the chemistry of seawater with potential effects for economically important marine life and coastal communities. Runoff pollution, land-use change, and a vibrant shellfish industry render North Carolina among the most socioeconomically vulnerable states to future acidification impacts, but an understanding of these changes can provide the tools necessary for coastal industries and ecosystems to mitigate and adapt to these changes.
Dr. Zhiying “Bruce” Lu joined the Johnson Lab as a postdoctoral research associate and funded by the China Research Council. Dr. Lu’s research focuses on using recycled medium (used water) for growing microalgae as a source of food and fuel. At the Johnson Lab he will work as part of the MAGIC team, to cultivate algae at large scale for sustainable food and fuel production.
Five large scale ponds, three ~1000L and two ~4500L , have been installed and are growing microalgae as part of the Marine Algae Industrialization Consortium (MAGIC). The ponds will grow ~10 strains of microalgae to compare their growth characteristics, algae biochemical signatures, and product suitability across a range of potential applications.
The North Pacific Ocean (between approximately 0°N and 50°N) contains the largest continuous ecosystem on Earth. This region plays a vital role in the cycling of globally important nutrients as well as carbon. Although the microbial communities in this region have been assessed, the dynamics of viruses (abundances and production rates) remains understudied. To address this gap, scientific cruises during the winter and summer seasons (2013) covered the North Pacific basin to determine factors that may drive virus abundances and production rates. Along with information on virus particle abundance and production, we collected a spectrum of oceanographic metrics as well as information on microbial diversity. The data suggest that both biotic and abiotic factors affect the distribution of virus particles. Factors influencing virus dynamics did not vary greatly between seasons, although the abundance of viruses was almost an order of magnitude greater in the summer. When considered in the context of microbial community structure, our observations suggest that members of the bacterial phyla Proteobacteria, Planctomycetes, and Bacteroidetes were correlated to both virus abundances and virus production rates: these phyla have been shown to be enriched in particle associated communities. The findings suggest that environmental factors influence virus community functions (e.g., virion particle degradation) and that particle-associated communities may be important drivers of virus activity.
Gainer PJ, Pound HL, Larkin AA, LeCleir GR, DeBruyn JM, Zinser ER, Johnson ZI, Wilhelm SW (2017). Contrasting seasonal drivers of virus abundance and production in the North Pacific Ocean. PLOS ONE 12: e0184371. DOI: 10.1371/journal.pone.0184371
In this study, we investigated the environmental impacts of scallop culture on two coastal estuaries adjacent the Bohai Sea including developing a quantitative PCR assay to assess the abundance of the bacterial pathogens Escherichia coli and Vibrio parahaemolyticus. Scallop culture resulted in a significant reduction of nitrogen, Chlorophyll a, and phosphorous levels in seawater during summer. The abundance of bacteria including V. parahaemolyticus varied significantly across estuaries and breeding seasons and was influenced by nitrate as well as nutrient ratios (Si/DIN, N/P). Bacterioplankton diversity varied across the two estuaries and seasons, and was dominated by Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes. Overall, this study suggests a significant influence of scallop culture on the ecology of adjacent estuaries and offers a sensitive tool for monitoring scallop contamination.
He Y, Sen B, Shang J, He Y, Xie N, Zhang Y, Johnson ZI and Wang G. (2017) Seasonal influence of scallop culture on nutrient flux, bacterial pathogens and bacterioplankton diversity across estuaries off the Bohai Sea Coast of Northern China. Marine Pollution Bulletin. DOI: 10.1016/j.marpolbul.2017.07.062
In spite of challenging weather, the Duke Marine Lab hosted about 500 visitors for it’s 2017 Open House extravaganza. The Marine Microbe Group presented 3 exhibits including examples of ocean acidification, phytoplankton/algae in the coastal ocean and a demonstrating the large scale of production of microalgae for food and fuel. Lots of good questions and participation and looking forward to showing off even more next year.
The Duke Marine Lab joined the Beaufort NC July 4th parade to promote it’s upcoming open house. Lead by REU student Ford Fishman, the R/V Richard Barber was paraded through the streets to cheering residents and visitors alike!
ZIJ presented on the diversity and activity of Prochlorococcus at the OCB2017 summer meeting at WHOI in Woods Hole, MA. The presentation, “Ribosomal RNA and DNA (23S) of Prochlorococcus reveal variable activity and abundance relationships across taxonomic ranks” was based on a study with lead author and former student Alyse Larkin, now at UCI. The work highlights how the fine taxonomic scale of Prochlorococcus has unexpected patterns in activity and suggests population ecological differentiation, regulation and biogeochemistry that are still poorly understood for this keystone microbe.
Abstract: Phytoplankton communities in oligotrophic temperate and tropical oceans are numerically dominated by Prochlorococcus sp., a genetically diverse and biogeochemically important marine cyanobacterium. The phylogenetic clades and subgroups of Prochlorococcus exhibit niche partitioning based on light, temperature and other resources in the ocean, but it is unknown how these clades/ecotypes differ in their in situ activity across large spatiotemporal environmental gradients. Here using relative 23S rRNA:rDNA ratios as a proxy for specific activity, we examine high light (HL) adapted Prochlorococcus across environmental gradients in the surface North Pacific Ocean to (1) determine the coupling between activity and abundance across taxonomic ranks and (2) examine the specific activity among closely related operational taxonomic units (OTUs). We show that activity and abundance are highly correlated for all 97% similarity OTUs of Prochlorococcus across all sites in the surface ocean. However, finer molecular scale resolution (oligotyping) shows significantly more variability in rRNA:rDNA ratios and reveals differing trends among closely related OTUs including different patterns between high and low abundance oligotypes. These results suggest that HL Prochlorococcus populations respond quickly to (a)biotic changes and the mechanisms that lead to uncoupling between activity and abundance (e.g. density dependent processes) are less important for this community at course molecule scales. These findings also suggest that relative Prochlorococcus population abundances at a given location can serve as a proxy for activity, providing an important tool for ecosystem model development. However, uncoupling at fine molecular scales suggests population differentiation and mechanisms of regulation that are still poorly understood, but important for understanding their relative role to biogeochemical cycles.
Alyse Larkin & Zackary Johnson OCB217
Thraustochytrids are unicellular fungi-like (heterotrophic) marine protists and have long been considered to play an important role in the biogeochemical cycles of the coastal oceans. However, the significance of their ecological functions and diversity in marine ecosystems remain largely unknown. In this report, we examined the spatial and temporal variations of planktonic thraustochytrids, their relationship with other environmental factors, and their diversity in the subtropical coastal waters of China. The abundance of planktonic thraustochytrids ranged from 2.56 × 105 to 17.57 × 105 cells L−1 with highest abundance detected in polluted coastal water and the Spring (March) season. Thraustochytrids biomass was greater than bacterial biomass in most of seawater samples, ranging from 32.29 to 359.51% that of bacterioplankton. The abundance of thraustochytrids appeared to be largely related to that of bacterioplankton and chemical oxygen demand (COD) in water columns. High-throughput sequencing analyses revealed a total of 105 OTUs (97% similarity), which were members of genera Thraustochytrium, Aplanochytrium, Oblongichytrium, Ulkenia, Labyrinthula and undescribed novel phylotypes. Results of this study indicated unprecedented high diversity of labyrinthulomycetes as well as the presence of novel labyrinthulomycetes and thraustochytrids lineage, and also provided new information on the significant role of thraustochytrids in microbial food webs in a coastal marine ecosystem.
Liu Y, Singh P, Liang Y, Li J, Xie N, Song Z, Daroch M, Leng K, Johnson ZI, Wang G (2017). Abundance and Molecular Diversity of Thraustochytrids in Coastal Waters of Southern China FEMS Microbiol Ecology. DOI: 10.1093/femsec/fix070
Trace metals and B-vitamins play critical roles in regulating marine phytoplankton growth and composition. While some microorganisms are capable of producing certain B-vitamins, others cannot synthesize them and depend on an exogenous supply. Therefore, external factors influencing vitamin synthesis, such as micronutrient concentrations, alter the extent to which B-vitamins are available to auxotrophs in surface waters. We examined iron, B7 (biotin) and B12 (cobalamin) dynamics in diatoms through laboratory culture experiments and within natural diatom assemblages present along an iron gradient in the Northeast Pacific Ocean. In laboratory cultures of the diatom Pseudo-nitzschia granii, biotin synthase (BIOB) expression decreased 2-fold under iron limitation, suggesting iron status may affect B7 production in diatoms. Additionally in laboratory cultures of the diatom Grammonema cf. islandica, which contains a B12-independent methionine synthase (METE), a 15-fold increase in the expression of METE was observed when grown in the absence of B12 with no significant influence of iron status, suggesting METE expression can be driven by B12 status alone. Iron and B-vitamin amendment experiments with natural diatom assemblages in iron-limited waters of the Northeast Pacific Ocean provide evidence for vitamin-associated molecular responses that suggest elevated B7 biosynthesis and the emergence of B12 limitation following iron addition. Furthermore B-vitamin gene modules comprised of partial and/or complete B-vitamin biosynthetic pathways in diatoms increased in response to iron addition, including genes potentially involved in the processing of B12 intermediates. Our results indicate that vitamins may play an important role in regulating phytoplankton growth and composition in this region, particularly following natural iron addition events.
Cohen NR, Ellis K, Burns WG, Lampe RH, Schuback N, Johnson Z, Sañudo-Wilhelmy S, Marchett A (2017). Iron and vitamin interactions in marine diatom isolates and natural assemblages of the Northeast Pacific Ocean. Limnology & Oceanography DOI: 10.1002/lno.10552
On Saturday, April 1st, 135 middle school girls visited the Duke Marine Lab to take part in hands-on activities in the fields of microbiology, remote sensing, geographic information systems, environmental engineering, developmental biology, marine science, physics, and more. The goal of GEST is to expose girls to STEM opportunities and role models in eastern North Carolina.
Activities were led by local researchers and educators with a passion for outreach. Volunteers came from a wide range of institutions and organizations, including Duke, UNC, NC State, NOAA, the NC Coastal Federation, Ocracoke School, and Marine Corps Air Station Cherry Point. PhD student and Johnson Lab member Sarah Loftus is a co-founder of GEST and worked on the planning team to organize the event. PhD student Courtney Swink was an activity leader, conducting an experiment with algae cultures and teaching the girls about biofuel applications. Girls were inquisitive and curious, and Courtney’s activity received some high praise in the event survey. We’re already looking forward to hosting GEST again next year.
Current high costs of commercial-scale algal biofuel production prevent the widespread use of this renewable fuel source. One cost-saving approach is the reuse of algae cultivation water after biomass harvesting, which reduces water pumping and treatment costs. However, dissolved compounds, cell debris, and microorganisms remaining in the water could affect subsequent algae generations. Previous studies demonstrate a variety of effects of recycled medium on algae growth, yet their results have not been collectively analyzed. Here we integrate data across 86 studies to determine the relative importance of different factors influencing algae growth in recycled medium. We found that algae taxa can have the greatest influence, while the harvesting method is less influential on growth outcomes. This meta-analysis identifies favorable taxa and thus provides a tool for algae cultivation decision-making when medium reuse is an important driver. Results can also aid in estimating relative algae yield and growth rates for technoeconomic assessments that incorporate water recycling.
Supplementary Information includes full dataset.
The fluorescent stain Nile Red has been used extensively for the quantification of lipids in phytoplankton, including microalgae, because it preferentially stains neutral lipids and it is economical and sensitive to use for screening purposes. Although its basic application has not changed for several decades, recent improvements have been made to improve its utility across applications. Here we describe additional refinements in its application and interpretation as a high-throughput method for the rapid quantification of neutral lipids in liquid cultures of marine phytoplankton. Specifically we address (1) interspecies comparisons, (2) fluorescence excitation and emission wavelengths, and (3) the time course of the Nile Red signal in the context of using bulk or cell-specific fluorescence to quantify neutral lipids of live or preserved cells. We show that with proper caution in its interpretation across species and physiological states the quantity of lipid in hundreds of small volume samples can be reliably assessed daily using a refined Nile Red protocol.
Johnson ZI, Bidigare RR, Blinebry SK, Brown SL, Cullen JJ, Loftus SE, Redalje DG, Swink C, Van Mooy BAS. Screening for lipids from marine microalgae using Nile Red (2017) in Handbook of Hydrocarbon and Lipid Microbiology Series. Consequences of Microbial Interactions with Hydrocarbons, Oils and Lipids: Production of Fuels and Chemicals Springer. DOI: 10.1007/978-3-319-31421-1_382-1
Sarah and Courtney travelled to Durham on Saturday, February 25th to lead activities at the annual FEMMES Capstone event on main campus. FEMMES (Females Excelling More in Math, Engineering, and Science) is an undergraduate-led organization that seeks to provide STEM opportunities and role models to local female students. Hundreds of 4th-6th graders attended the event and each participated in 4 various STEM activities led by Duke researchers.
Thirty girls participated in Sarah and Courtney’s activities throughout the day. After learning about algae growth requirements and applications of algae, they designed and set up an experiment to test how different light levels affect algae growth. Sarah and Courtney brought the “results” previously grown in our lab, and girls measured and graphed the turbidity of the algae cultures. They enjoyed using laboratory tools and seeing if the results matched their hypotheses. Some even left thinking that “algae are cool,” which means mission accomplished!
Marine microbes exhibit seasonal cycles in community composition, yet the key drivers of these patterns and microbial population fidelity to specific environmental conditions remain to be determined. To begin addressing these questions, we characterized microbial dynamics weekly for 3 years at a temperate, coastal site with dramatic environmental seasonality. This high-resolution time series reveals that changes in microbial community composition are not continuous; over the duration of the time series, the community instead resolves into distinct summer and winter profiles with rapid spring and fall transitions between these states. Here, we show that these community shifts involve switching between closely related strains that exhibit either summer or winter preferences. Moreover, taxa repeat this process annually in both this and another temperate coastal time series, suggesting that this phenomenon may be widespread in marine ecosystems. To address potential biogeochemical impacts of these community changes, PICRUSt-based metagenomes predict seasonality in transporters, photosynthetic proteins, peptidases and carbohydrate metabolic pathways in spite of closely related summer- and winter-associated taxa. Thus, even small temperature shifts, such as those predicted by climate change models, could affect both the structure and function of marine ecosystems.
Ward CD, Yung C-M, Davis KM, Blinebry SK, Williams TC, Johnson ZI, Hunt DE (2017). Annual community patterns are driven by seasonal switching between closely related marine bacteria. ISME J. DOI: 10.1038/ismej.2017.4
Prof. Claudia Benitez-Nelson of the University of South Carolina visited the Duke Marine Lab and gave a stirring seminar on harmful algal blooms off of California. Claudia’s talk, “Neurotoxins and the Environment. Understanding the Production, Cycling and Fate of Domoic Acid Along the California Coast” was a fantastic mixture of oceanography and environmental monitoring, all in the context of environmental change and management. Can’t wait to have her come back and hear more about her exciting research!
The microbe team welcomed two new students, Elsa (Jia Li) and Norah (Xue Rui), two visiting undergraduates to the group. They are joining the lab for 5 months to complete their undergraduate honors dissertations at Tianjin University, China. Both are working on the molecular diversity of microbes, in the context of environmental variability. Elsa is focusing on the cyanobacteria of the North Pacific, while Norah is working with cyanobacterial communities from the PICO project. Welcome!
The Pivers Island Coastal Observatory (PICO) closed 2016 by reaching a major milestone – the 750th time point! Started in mid-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. Congratulations team PICO!
Climate, energy, and food security are three of the greatest challenges society faces this century. Solutions for mitigating the effects of climate change often conflict with solutions for ensuring society’s future energy and food requirements. For example, BioEnergy with Carbon Capture and Storage (BECCS) has been proposed as an important method for achieving negative CO2 emissions later this century while simultaneously producing renewable energy on a global scale. However, BECCS has many negative environmental consequences for land, nutrient, and water use as well as biodiversity and food production. In contrast, large-scale industrial cultivation of marine microalgae can provide society with a more environmentally favorable approach for meeting the climate goals agreed to at the 2015 Paris Climate Conference, producing the liquid hydrocarbon fuels required by the global transportation sector, and supplying much of the protein necessary to feed a global population approaching 10 billion people.
Greene, C.H., M.E. Huntley, I. Archibald, L.N. Gerber, D.L. Sills, J. Granados, J.W. Tester, C.M. Beal, M.J. Walsh, R.R. Bidigare, S.L. Brown, W.P. Cochlan, Z.I. Johnson, X.G. Lei, S.C. Machesky, D.G. Redalje, R.E. Richardson, V. Kiron, and V. Corless. 2016. Marine microalgae: Climate, energy, and food security from the sea. Oceanography 29(4), https://doi.org/10.5670/oceanog.2016.91.
Approximately 100 sixth graders from Morehead City visited the Marine Laboratory to learn about marine science and experience a college campus. Six learning stations covered different aspects of marine science from fisheries to marine mammals to remote sensing. The Sarah Loftus, Courtney Swink and Bailey Slagle of the Marine Microbe Group described the importance of algae (phytoplankton) for natural ecosystems as well as the current research in the group to develop algae as a sustainable source of food and fuel. Students made media, started cultures and even tasted some algae cookies. Yum!
The goals of ensuring energy, water, food, and climate security can often conflict. Microalgae (algae) are being pursued as a feedstock for both food and fuels—primarily due to algae’s high areal yield and ability to grow on non-arable land, thus avoiding common bioenergy-food tradeoffs. However, algal cultivation requires significant energy inputs that may limit potential emission reductions. We examine the tradeoffs associated with producing fuel and food from algae at the energy–food–water–climate nexus. We use the GCAM integrated assessment model to demonstrate that algal food production can promote reductions in land-use change emissions through the offset of conventional agriculture. However, fuel production, either via co-production of algal food and fuel or complete biomass conversion to fuel, is necessary to ensure long-term emission reductions, due to the high energy costs of cultivation. Cultivation of salt–water algae for food products may lead to substantial freshwater savings; but, nutrients for algae cultivation will need to be sourced from waste streams to ensure sustainability. By reducing the land demand of food production, while simultaneously enhancing food and energy security, algae can further enable the development of terrestrial bioenergy technologies including those utilizing carbon capture and storage. Our results demonstrate that large-scale algae research and commercialization efforts should focus on developing both food and energy products to achieve environmental goals.
Walsh, M. J., Gerber Van-Doren, L., Sills, D. L., Archibald, I., Beal, C. M., Lei, X. G., Huntley, M. E., Johnson, Z. & Greene, C. H. 2016. Algal food and fuel coproduction can mitigate greenhouse gas emissions while improving land and water-use efficiency. Environmental Research Letters 11:114006.
PhD student Sarah Loftus attended the 10th annual Algae Biomass Summit in Phoenix, AZ. The summit brings together individuals from academia, industry, and government who research, lobby for, and capitalize on the products and services provided by algae, notably biofuels, food, carbon capture, wastewater treatment, and more. Sarah won first place in the Young Researcher Poster Competition, Biology Division, for her poster titled “Meta-analysis reveals influential and non-influential factors affecting algae growth in recycled cultivation water.”
Victoire Blanc-Garin visited the Johnson Lab from France for 6 weeks. While in Beaufort, her research focused on comparing the variability of outdoor cultures with those in constant conditions indoors. She showed that outdoor environmental conditions can be at times extreme, but generally the algae strains examined were able to grow as well and sometimes better outdoors. We wish her the best back in Paris and hope to work with her again in the future.
ZIJ presented at ISME16 in Montreal on the temperature regulation of Prochlorococcus photosynthesis and growth under the title, “The effect of temperature on gene expression and carbon uptake/release in diverse strains of Prochlorococcus” Its a good time to be a Microbial Ecology!
Abstract: The ecological success of the marine cyanobacteria Prochlorococcus is driven in part by its genomic diversity and the concentrations of the two dominant high light clades in the ocean have been shown to niche partition along latitudinal temperature gradients. Nevertheless, little is known about how temperature affects carbon uptake and its fate for these genetically distinct, yet closely related cyanobacteria. Here we present results from temperature acclimation experiments and show that while temperature has an expected (and differential) effect on the major clades of Prochlorococcus, the temperature response curves of carbon uptake and growth rate are uncoupled. Further, there are substantial differences among the clades in how temperature affects the partitioning of this carbon to particulate (i.e. retained) or dissolved (i.e. dissolved organic carbon release) fates. Physiology and transcript data show even more dramatic uncoupling of carbon uptake/fate growth rate (biomass accumulation or division) and regulation with different responses between the two clades. These results highlight the importance of temperature in poising the fundamental processes of Prochlorococcus photosynthesis and growth, and that the physiological and regulatory responses are different between the major genetic clades. These results also demonstrate that future climate scenarios with increased temperature may significantly alter the distribution, biogeochemical rates and role of Prochlorococcus and its clades in broader marine microbial communities through changes in cell division and carbon fate.
On Saturday, the Johnson Lab welcomed hundreds of people into the laboratory as part of the Duke Marine Lab’s annual Open House event. The Open House is an opportunity for the public to tour DUML facilities, learn about ongoing research, and view some of that research in action. Upstairs in the Pilkey Laboratory, the Johnson Lab spoke to community members about both PICO and algae biofuel projects. Research technician Sara Blinebry showed her video of the weekly PICO sampling process. She explained that these samples help us understand changes in coastal ocean acidity and seasonal changes in the marine microbial community. PhD student Courtney Swink displayed cultures of green algae and diatoms, and talked about the Johnson Lab’s role in studying algae cultivation for biofuels and co-products. PhD student Sarah Loftus then gave visitors a closer look at these cultures under the microscope and answered questions about microalgae.
Experts in the field of algal biology shared their recent successes with participants at the DOE Algal Biology Toolbox to further the community’s understanding of the current state of the art. These presentations ensure that a range of expertise is represented at the event. ZIJ presented pilot results from MAGIC- the Marine Algae Industrialization Consortium specifically focusing on LCA/TEA, cultivation strategies and initial co-product trials.
The National Ocean Science Bowl Finals were held in Morehead City, NC with many local marine scientists and marine laboratories facilitating the event. (ZIJ served as a science judge for some of the competition.) The finals had the theme,“Our Changing Ocean: Science for Strong Coastal Communities.” The National Ocean Sciences Bowl is an education competition that tests students’ knowledge of ocean-related topics, which include cross-disciplines of biology, chemistry, policy, physics, and geology. The NOSB is an interdisciplinary ocean science education program of the Consortium for Ocean Leadership based in Washington, D.C.
There is a growing recognition of marine microenvironments’ roles as reservoirs of biodiversity, sites of enhanced biological activity and in facilitating biological interactions. Here, we examine the bacterial community inhabiting free-living and particle-associated seawater microenvironments at the Pivers Island Coastal Observatory (PICO). 16S rRNA gene libraries from monthly samples (July 2013-August 2014) were used to identify microbes in four size fractions of seawater >63 μm (zooplankton and large particles), 63-5 μm (particles), 5-1 μm (small particles/dividing cells) and <1 μm (free-living prokaryotes). Analyses of microbial community composition highlight the importance of microhabitat (e.g. particle-associated versus free-living lifestyle) as communities cluster by size fraction, and microhabitat explains more community variability than measured environmental parameters including pH, particle concentration, projected daily insolation, nutrients, and temperature. While temperature is statistically associated with community changes in the <1 μm and 5-1 μm fractions, none of the measured bulk seawater environmental variables are statistically significant in larger particle-associated fractions. These results, combined with high particle-associated community variability, especially in the largest size fraction (i.e. >63 μm), suggest that particle composition, including eukaryotes and their associated microbiomes, may be an important factor in selecting for specific particle-associated bacteria.
Yung C-M, Ward CS, Davis KM, Johnson ZI, Hunt DE (2016). Diverse and temporally-variable particle-associated microbial communities are insensitive to bulk seawater environmental parameters. Applied & Environmental Microbiology. DOI: 10.1128/aem.00395-16
Foraging theory predicts the evolution of feeding behaviors that increase consumer fitness. Sponges were among the earliest metazoans on earth and developed a unique filter-feeding mechanism that does not rely on a nervous system. Once thought indiscriminate, sponges are now known to selectively consume picoplankton, but it is unclear whether this confers any benefit. Additionally, sponges consume dissolved organic carbon (DOC) and detritus, but relative preferences for these resources are unknown. We quantified suspension feeding by the giant barrel sponge Xestospongia muta on Conch Reef, Florida, to examine relationships between diet choice, food resource availability, and foraging efficiency. Sponges consistently preferred cyanobacteria over other picoplankton, which were preferred over detritus and DOC; nevertheless, the sponge diet was mostly DOC (∼70%) and detritus (∼20%). Consistent with foraging theory, less-preferred foods were discriminated against when relatively scarce, but were increasingly accepted as they became relatively more abundant. Food uptake was limited, likely by post-capture constraints, yet selective foraging enabled sponges to increase nutritional gains.
Hydrogen peroxide (HOOH) is omnipresent in natural waters. Given that sunlight is the primary source of HOOH, we investigated the relationship between time of day and microbial HOOH degradation. Genes encoding HOOH-degrading enzymes were significantly more abundant during the day in ocean metatranscriptomes. While bacterial catalase-peroxidases were the most abundant transcripts, the abundance of algal peroxidases, along with the insensitivity of HOOH degradation rates to antibiotic treatment in our incubations, suggested that eukaryotic microorganisms were also important scavengers of HOOH. Phylogenetic placement of transcripts for HOOH degrading enzymes suggested that different taxa expressed these enzymes during the day than during the night. We also measured HOOH concentrations over a 24 h period in the South Pacific, and simultaneously conducted bottle incubations to measure HOOH dark degradation rates. Fitting these data to a dynamic model confirmed that the ability of the microbial community to degrade HOOH during the day increased, with peak HOOH removal rates occurring in late afternoon coincident with the highest HOOH concentrations. Collectively, these data suggest that even in dilute HOOH environments, there is a dynamic diel response to HOOH, and that the open ocean microbial community is complicit in its cross-protection of Prochlorococcus and other HOOH-sensitive taxa.
J. Jeffrey Morris; Zackary I. Johnson; Steven W. Wilhelm; Erik R. Zinser
Journal of Plankton Research 2016; doi: 10.1093/plankt/fbw016
Lots of good stuff at the TOS/ALSO/AGU Ocean Sciences Meeting in New Orleans this year! ZIJ presented in the “Linking ‘Omics Insights to Marine Microbial Ecology and Biogeochemical Functioning” session with the following abstract:
The effect of temperature on carbon uptake and its fate in diverse strains of Prochlorococcus
The ecological success of the marine cyanobacteria Prochlorococcus is driven in part by its genomic diversity and the concentrations of the two dominant high light clades in the ocean have been shown to niche partition along latitudinal temperature gradients. Nevertheless, little is known about how temperature affects carbon uptake and its fate for these genetically distinct, yet closely related cyanobacteria. Here we present results from a series of steady state and temperature shift experiments. We show that as expected, temperature has a profound effect on carbon uptake and growth rate, but is different among the major clades of Prochlorococcus. However, the temperature response curves of carbon uptake and growth rate are uncoupled. Further, there are substantial differences among the clades in how temperature affects the partitioning of this carbon to particulate (i.e. retained) or dissolved (i.e. dissolved organic carbon release) fates. Physiology data from temperature shift experiments show even more dramatic uncoupling of carbon uptake/fate growth rate (biomass accumulation or division) and regulation often with unexpected patterns. These results highlight the importance of temperature in poising the fundamental processes of Prochlorococcus photosynthesis and growth, and that the physiological and regulatory responses are different between the major genetic clades. These results also demonstrate that climate change, via increasing temperature, may significantly alter the distribution, biogeochemical rates and role of Prochlorococcus and its clades in broader marine microbial communities through changes in cell division and carbon fate.
The distribution of major clades of Prochlorococcus tracks light, temperature and other environmental variables; yet, the drivers of genomic diversity within these ecotypes and the net effect on biodiversity of the larger community are poorly understood. We examined high light (HL) adapted Prochlorococcus communities across spatial and temporal environmental gradients in the Pacific Ocean to determine the ecological drivers of population structure and diversity across taxonomic ranks. We show that the Prochlorococcus community has the highest diversity at low latitudes, but seasonality driven by temperature, day length and nutrients adds complexity. At finer taxonomic resolution, some ‘sub-ecotype’ clades have unique, cohesive responses to environmental variables and distinct biogeographies, suggesting that presently defined ecotypes can be further partitioned into ecologically meaningful units. Intriguingly, biogeographies of the HL-I sub-ecotypes are driven by unique combinations of environmental traits, rather than through trait hierarchy, while the HL-II sub-ecotypes appear ecologically similar, thus demonstrating differences among these dominant HL ecotypes. Examining biodiversity across taxonomic ranks reveals high-resolution dynamics of Prochlorococcus evolution and ecology that are masked at phylogenetically coarse resolution. Spatial and seasonal trends of Prochlorococcus communities suggest that the future ocean may be comprised of different populations, with implications for ecosystem structure and function.
This work contributes new knowledge about the distributions of the marine cyanobacterium Prochlorococcus. Specifically, it is the first to compare basin-scale latitudinal transects for the Atlantic and Pacific Oceans; it is the first to show that the ratios of the dominant lineages (ecotypes) vary as a log-linear function with temperature; it is the first to show that despite apparent fitness differences, the dominant ecotypes do not compete to the extinction of others; and is the first to consider temporal disconnects between temperature changes and population shifts.
Chandler JW, Lin Y, Gainer PJ, Post AF, Johnson ZI, Zinser ER (2016). Variable but persistent coexistence of Prochlorococcus ecotypes along temperature gradients in the ocean’s surface mixed layer. Environmental Microbiology Reports. DOI:
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.
Our educational model aims to transcend communication barriers between disciplines and promote team science.Graduate students in microbiology, engineering and other empirical sciences will be cross trained with theorists, model builders and computational scientists. This graduate training model reflects current trends in interdisciplinary research and effectively decreases discipline-centrism while promoting interdisciplinary cultural competence.
In addition to their rigorous academic training, IBIEM trainees will also be exposed to and develop a range of soft skills as well as be engaged with the community through outreach activities aimed at promoting science and engineering to the general public. IBIEM is now accepting applications through departments of participating faculty.
ZIJ presented as part of the Southeast Ocean and Coastal Acidification Network state-of-the-science webinar series. The seminar series lays a foundation for the state of ocean acidification science in the Southeast region. The talk was titled, ‘Temporal variability of the carbonate system and the microbial community in a dynamic coastal NC system’ focused on the ocean acidification and its affects on the microbial community near Beaufort NC to the Gulf Stream. Additional information on the presentation including a video link is available from SECORA.
Sarah Loftus, PhD ecology student, wins second place in the Biology student poster competition at the Algae Biomass Summit in Washington DC. The Summit, organized by the Algae Biomass Organization, unites industry professionals from all sectors of the world’s algae utilization industries including those involved financing, algal ecology, genetic systems, carbon partitioning, engineering & analysis, biofuels, animal feeds, fertilizers, bioplastics, supplements and foods.
ZIJ also at the Summit, presented on strategies for scaling up results from laboratory research to commercial sized facilities.
The Johnson Lab welcomed ~50 scientists from universities across North Carolina to discuss ongoing and future studies in coastal marine ecology. Specifically, the NC Long-Term Marine Ecology Scoping Meeting worked towards: (1) identifying ‘Coastal’ NC assets including existing data and measurement/analyses capabilities among NC scientists, (2) refining questions, project goals and hypotheses that could be addressed by coordinated long-term ecological research and (3) creating partnerships among participants to address large scale / long term ecological questions. The meeting was kicked-off by a keynote address by Mark Ohman, principal investigator of the California Current Ecosystem LTER project who described ongoing research as part of the NSF LTER program.
ZIJ co-chaired a session on Marine Photosynthetic Bacteria and presented a paper (abstract below) on the response of Prochlorococcus to temperature change at the International Symposium on Phototrophic Prokaryotes 2015 (ISPP2015) meeting in Tübingen, Germany. The meeting highlighted the current knowledge and the most recent advances of research on phototrophic prokaryotes including the latest achievements in the genetics and physiology of these organisms, also addressing their evolution, ecology, mechanisms of interaction with the environment, and biotechnological applications.
The effect of temperature on carbon uptake and its fate in diverse strains of Prochlorococcus
Zackary Johnson, Sara Blinebry, Samantha Huff, David Hurley, Samantha Rose
The ecological success of the marine cyanobacteria Prochlorococcus is driven in part by its genomic diversity and the concentrations of the two dominant high light clades in the ocean have been shown to niche partition along latitudinal temperature gradients. Nevertheless, little is known about how temperature affects carbon uptake and its fate for these genetically distinct, yet closely related cyanobacteria. Here we present results from a series of steady state and temperature shift experiments. We show that as expected, temperature has a profound effect on carbon uptake and growth rate, but is different among the major clades of Prochlorococcus. However, the temperature response curves of carbon uptake and growth rate are uncoupled. Further, there are substantial differences among the clades in how temperature affects the partitioning of this carbon to particulate (i.e. retained) or dissolved (i.e. dissolved organic carbon release) fates. Physiology and transcript data from temperature shift experiments show even more dramatic uncoupling of carbon uptake/fate growth rate (biomass accumulation or division) and regulation often with unexpected patterns. These results highlight the importance of temperature in poising the fundamental processes of Prochlorococcus photosynthesis and growth, and that the physiological and regulatory responses are different between the major genetic clades. These results also demonstrate that climate change, via increasing temperature, may significantly alter the distribution, biogeochemical rates and role of Prochlorococcus and its clades in broader marine microbial communities through changes in cell division and carbon fate.
On Saturday, August 1, the Duke Marine Lab hosted its annual Open House extravaganza. This year’s event was exceptionally well-attended, with more than 500 curious guests coming to explore our island community, learn about the history of the Marine Lab, and delve into the exciting research going on here.
The Johnson Lab was bustling with visitors of all ages peering into microscopes, watching footage from a research cruise, admiring our ocean views, and asking our scientists lots of great questions. Sara Blinebry was featured in local news coverage of the event. We had a wonderful time and can’t wait to do it again next year!
Algal biomass can be converted to advanced biofuels that offer promising alternatives to petroleum-based diesel and jet fuels. Additionally, algae can be used to make a range of other valuable bioproducts, such as industrial chemicals, bio-based polymers, and proteins. However, barriers related to algae cultivation, harvesting, and conversion to fuels and products need to be overcome to achieve the Department of Energy’s target of $3 per gge for advanced algal biofuels by 2030. To accomplish this goal, DOE is investing in applied research and development technologies that can achieve higher yields of targeted bioproducts and biofuels from algae—increasing the overall value for algae biomass. Today the DOE announced that a Duke led Consortium (MAGIC) will receive up to $5.2 million to lead a consortium including University of Hawaii, Cornell University, Cellana and others to produce protein-based human and poultry nutritional products along with hydrotreated algal oil extract.
Grounded in a TEA/LCA framework, the MAGIC consortium will use biochemical specifications for biofuel and bioproducts (animal and human foods) provided by industrial partners to identify algae strains, growth and extraction approaches to demonstrate production and efficacy at successively larger scales to reduce uncertainty in TEA/LCA and develop a market transformation / commercialization plan to achieve the Renewable Fuels Standard.
Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.
Theoretical studies predict that competition for limited resources reduces biodiversity to the point of ecological instability, whereas strong predator/prey interactions enhance the number of coexisting species and limit fluctuations in abundances. In open ocean ecosystems, competition for low availability of essential nutrients results in relatively few abundant microbial species. The remarkable stability in overall cell abundance of the dominant photosynthetic cyanobacterium Prochlorococcus is assumed to reflect a simple food web structure strongly controlled by grazers and/or viruses. This hypothesized link between stability and ecological interactions, however, has been difficult to test with open ocean microbes because sampling methods commonly have poor temporal and spatial resolution. Here we use continuous techniques on two different winter-time cruises to show that Prochlorococcus cell production and mortality rates are tightly synchronized to the day/night cycle across the subtropical Pacific Ocean. In warmer waters, we observed harmonic oscillations in cell production and mortality rates, with a peak in mortality rate consistently occurring ∼6 h after the peak in cell production. Essentially no cell mortality was observed during daylight. Our results are best explained as a synchronized two-component trophic interaction with the per-capita rates of Prochlorococcus consumption driven either directly by the day/night cycle or indirectly by Prochlorococcus cell production. Light-driven synchrony of food web dynamics in which most of the newly produced Prochlorococcus cells are consumed each night likely enforces ecosystem stability across vast expanses of the open ocean.
Ribalet F, Swalwell JE, Clayton S, Jimenez V, Sudek S, Lin Y, Johnson ZI, Worden AZ, and Armbrust EV (2015) Light-driven synchrony of Prochlorococcus growth and mortality in the north Pacific gyre. PNAS DOI: 10.1073/pnas.1424279112