About

Dr. Zackary Johnson is an Associate Professor whose research group focuses on studying the abundance, diversity, and activity of marine microbes, with a particular emphasis on Prochlorococcus, the most abundant phytoplankton in the open ocean. His group leads the Marine AlGae Industrialization Consortium (MAGIC), which is dedicated to developing microalgae as an economical and reduced carbon source of biofuel, feeds, and other products. Through this work, Dr. Johnson contributes to advancing the understanding of marine microbial ecology and the potential of microalgae in sustainable bioenergy and bioproducts.

Research topics

• Environmental science
• Ecology
• Biology
• Fishery
• Oceanography
• Biochemical engineering
• Environmental protection
• Engineering
• Geology
• Agroforestry
• Environmental engineering
• Waste management

Selected publications

• Validation of a modified Landry-Hassett dilution technique to quantify the growth and mortality rates of subpopulations of planktonic microbes

  Frontiers in Marine Science · 2026-01-26

  articleOpen accessSenior authorCorresponding

  Due to their importance in global ocean ecology and biogeochemistry, much is known about the abundance and diversity of marine microbes and this data informs our studies of microbial genetic variability and niche partitioning. However, much less is known about marine microbes’ vital rates, including phylogenetically-resolved intrinsic growth and mortality. Here, we use cyanobacteria to validate a recently-developed, sequence-based modification of the Landry-Hassett Dilution (LHD) technique, which simultaneously assesses the growth and grazer-induced mortality of microbial subpopulations. Using laboratory cultures, we show that most approaches for quantifying cyanobacterial intrinsic growth yield similar results, providing a foundation for methods comparisons in complex communities. We then leverage these findings to validate the modified LHD approach by sampling from a highly-dynamic, coastal marine ecosystem. We find that the LHD 16S rRNA gene-based method returns the same intrinsic growth as other biomass estimates. Further, field sampling yields distinct intrinsic growth among closely-related lineages of both cyano- and heterotrophic bacteria. While grazer-mediated mortality was less variable, we did observe distinct mortality rates within the broader microbiome, supporting the importance of examining vital rates in subpopulations. This validated methodology (and initial field findings) opens the door to answer fundamental ecological and biogeochemical questions about the microbial oceanography of spatially and temporally-variable coastal and open ocean ecosystems.

  PublisherOA PDFDOI

• The Piver’s Island Coastal Observatory – a decade of weekly+ observations reveal the press and pulse of a changing temperate coastal marine system

  Frontiers in Marine Science · 2025-04-03 · 1 citations

  articleOpen access1st authorCorresponding

  Historically, oceanographic time-series have focused on long-term measurements of large open ocean gyres; yet, the coastal oceans, with their high productivity, tidal impacts, human feedbacks, and land-sea coupling, represent critical regions for predicting ocean dynamics and biogeochemistry under global change. The Piver’s Island Coastal Observatory (PICO) time-series, located in the second largest estuarine system on the US East Coast (Albemarle-Pamlico Sound), comprises more than a decade of weekly (or more frequent) measurements of core physical, chemical, and biological oceanographic variables. PICO provides insight into a coastal, mesotrophic ecosystem in an ecologically-diverse and biochemically-active region impacted by global change. Here, we report on a decade of observations focusing on pulse and press ecosystem changes. We observe strong mean annual cycles in environmental variables including temperature (10.1-28.9°C), pH (7.89-8.12), dissolved inorganic carbon (DIC: 1965 – 2088 µM), chlorophyll (2.54-5.77 mg Chl m -3 ), upon which are layered episodic disturbances (e.g., tropical cyclones) that dramatically and persistently (>1 month) impact this ecosystem. Among other variables, long term trends in pH (-0.004 ± 0.001 y -1 ; p<0.01), DIC (-9.8 ± 1.5 µM y -1 ; p<0.01) and chlorophyll (-0.17 ± 0.02 µg L -1 y -1 ; p<0.01) are exceeding those observed in the open ocean, suggesting an ecosystem in flux. These analyses provide a benchmark for future studies of the impact of changing climate and oceanographic climatology; further research will use this long-term research to developed targeted sampling and experimental manipulations to better understand ecosystem structure and function.

  PublisherDOI

• Drivers of Marine Phytoplankton Diversity and Connectivity in the Galápagos Archipelago Spanning an <scp>ENSO</scp> Cycle

  Environmental Microbiology · 2025-07-01

  article

  The Galápagos Islands are a biodiversity hotspot, largely due to the Equatorial Undercurrent (EUC) which supplies nutrient-rich waters to the euphotic zone and supports enhanced levels of primary productivity performed by phytoplankton. Understanding phytoplankton responses to changing environmental conditions is crucial for regional conservation and management efforts. Research cruises conducted between 2014 and 2022, spanning a major El Niño event in 2015 and a La Niña event in 2022, observed varying oceanic conditions and diverse phytoplankton community composition. At most EUC-influenced stations, larger-sized phytoplankton groups (≥ 5 μm) were dominant while warmer, oligotrophic sites favoured smaller-sized phytoplankton groups (< 5 μm). Predictably, nutrient supply was suppressed during the El Niño event associated with the weakening of the EUC and deepening of the thermocline. Counterintuitively, nutrient levels were not significantly enhanced during the La Niña event likely because increased stratification between the mixed and deep water layers reduced entrainment, particularly at Eastern stations. Protist community composition was evaluated using 18S rRNA gene metabarcoding; the majority of detected OTUs were associated with upwelling conditions prevalent around the archipelago. Taxonomic variability reflected heterogeneous environmental conditions generated by the convergence of multiple ocean currents. These results highlight the dynamic interplay of physical and biological factors shaping primary productivity in the Galápagos marine ecosystem.

  PublisherDOI

• Integrating microbial communities into algal biotechnology: a pathway to enhanced commercialization

  Frontiers in Microbiology · 2025-04-01 · 10 citations

  reviewOpen accessSenior authorCorresponding

  Microalgae are increasingly recognized for their potential in wastewater treatment and the sustainable production of feedstock for fuel, feed, food, and other bioproducts. Like conventional agricultural systems, algal cultivation involves complex microbial communities. However, despite their pivotal role in cultivation outcomes, especially at the commodity-scale, the critical interactions between microalgae and their microbiomes are often overlooked. Here we synthesize current knowledge on the taxonomic diversity, ecological roles, and biotechnological potential of algal microbiomes, with a focus on their interactions with algal hosts through nutrient exchange, growth modulation, pathogen defense, and environmental conditioning. We also examine how environmental factors such as nutrient availability, salinity, and temperature influence these interactions. Advances in microbiome engineering, including synthetic biology and ecological approaches, offer opportunities to enhance beneficial algal-microbiome interactions, thereby improving growth, resilience, and yield. These advancements could lead to more sustainable and economically viable microalgae cultivation, with far-reaching implications for environmental management and biotechnological innovation. By addressing key economic and environmental barriers, microbiome engineering holds transformative potential to revolutionize large-scale algae cultivation and provide sustainable solutions to global challenges.

  PublisherOA PDFDOI

• Oysters as microbial engineers govern planktonic viral and microbial dynamics

  Research Square · 2025-12-23

  preprintOpen access
  PublisherOA PDFDOI

• Supranutrition of n-3 Polyunsaturated Fatty Acids and 25-Hydroxyvitamin D3 Affects Intestinal Structure and Function of Broiler Chickens

  Journal of Nutrition · 2025-11-24

  articleOpen access
  PublisherOA PDFDOI

• Enhanced Tolerance to Antifungals as a General Feature of Rho− Mutants in Yeast Species: Implications to Positive Selection of Respiratory Deficiency

  Microorganisms · 2025-01-07

  articleOpen access1st author

  Although the mitochondrial genome is an attribute of all eukaryotes, some yeast species (called petite-positive) can replicate without mitochondrial DNA (mtDNA). Strains without mtDNA (known as rho− mutants or petite mutants) are respiration-deficient and require fermentable carbon sources (such as glucose) for their metabolism. However, they are compromised in many aspects of fitness and competitiveness. Nevertheless, a few research groups have reported that some petite mutants of Candida glabrata and Saccharomyces cerevisiae manifested higher levels of tolerance to the antifungal fluconazole than their wild-type (WT) counterparts. In this study, we show that elevated tolerance to two or three out of four tested antifungals is a generic feature of at least five petite-positive species of yeasts including C. glabrata (higher tolerance of petites to clotrimazole and miconazole), S. bayanus (tolerance to clotrimazole, fluconazole, and miconazole), S. cerevisiae (tolerance to clotrimazole and fluconazole), S. paradoxus (tolerance to clotrimazole, fluconazole, and miconazole), and S. pastorianus (tolerance to clotrimazole and fluconazole). Comparing the levels of tolerance to the antifungals in WT and petite mutants was based on measuring the diameters of the zones of inhibition (ZOIs) using disc diffusion assays. The mode of inhibition in the majority of WT strains by all antifungals was fungicidal; most of the rho− mutants manifested fungistatic inhibition. We observed partial (not complete) inhibition in WT, with four different types of ZOI patterns that were species- and antifungal-specific. The partial inhibition was characterised by the presence of antifungal-tolerant colonies within ZOI areas. The inability of these colonies selected from ZOIs to grow on glycerol, as a single source of carbon, proved that they were rho− mutants spontaneously generated in the WT populations. The results on the elevated tolerance of petite strains to antifungals are discussed in terms of the prospective positive selection of respiratory-deficient mutants and the various implications of such selection.

  PublisherOA PDFDOI

• Carbon utilization efficiency in marine algae biofuel production systems through loss minimization and carbonate chemistry modification

  2025-06-30

  reportOpen access

  Final technical report for US Department of Energy Award DE-EE0008518 "Carbon utilization efficiency in marine algae biofuel production systems through loss minimization and carbonate chemistry modification"

  PublisherOA PDFDOI

• Marine Algae Industrialization Consortium (MAGIC): Combining biofuel and high-value bioproducts to meet the RFS

  2024-05-08

  reportOpen access1st authorCorresponding

  The Marine Algae Industrialization Consortium (MAGIC) was formed to address pressing challenges in the commercialization of microalgae as a source of biofuel. The “Marine Algae Industrialization Consortium (MAGIC): Combining biofuel and high-value bioproducts to meet the RFS” project formally addressed two US Department of Energy Bioenergy Technologies Office (BETO) goals: (1) Model the sustainable supply of 1 million metric tonnes ash free dry weight (AFDW) cultivated algal biomass and (2) Demonstrate valuable co-products produced along with biofuel intermediates to increase value of algal biomass by 30%. To achieve these goals, the project demonstrated and validated high-value co-products to drive down the cost of biofuel by increasing the value of algae “co-products” towards increasing the selling price of total algae biomass as one of the key drivers of economics and adoption. This was accomplished through five core, interdependent tasks including: (1) strain selection to identify and deliver strains for mass culture, (2) mass culture using a hybrid cultivation system and following key operating parameters for downstream applications to provide algae feedstock, (3) recovery and conversion to evaluate two alternative methods to separate dry algae biomass into oil and residuals for downstream testing, (4) product assessment to determine biofuel, aquafeed or poultry feed product efficacy using algae biomass fractions as well as to provide critical performance data for valuation and (5) commercialization to use technoeconomic and life cycle assessments (TEA/LCA) as iterative design and assessment tools including consideration of target markets, competitors, and distribution channels to guide product assessment, development and valuation. A total of 46 peer-review publications, many open-access, provide detail of much of the work carried out and the results of the tasks. Additional reports and presentations provide other technical and public engagement material. At a high level, using a variety of approaches, more than 1000 marine microalgae strains were evaluated to ultimately identify the seven winners that were down-selected to be grown in mass culture. Strain selection demonstrated that there were no ‘super strains’ and that each candidate had strengths and limitations for specific products, growth conditions or operational considerations. Mass culture growth of these seven strains at >5000 L / 29 m2 scale found that four them were suitable for product assessment. More than 250 kg of biomass was produced across hundreds of pond runs along with thousands of cultivation entries on the growth and biomass characteristics as well as environmental parameters. In the process, dozens of standard operating procedures were generated as was custom software to process and analyze cultivation data. Recovery and conversion of algae biomass demonstrated that a hexane solvent based extraction protocol was most effective at recovering oil (biocrude) from algae and four strains were processed to produce oil and lipid extracted algae (residuals) for downstream testing. Membrane-based oil separation was less successful, but may still be applicable to other commercial applications in the future. Product testing demonstrated that algae biocrude is of high quality and hydrotreating generated numerous fractions of high quality composition for fuel and lubricate based applications. Aquafeed studies performed at a variety of scales showed that both whole and defatted (lipid extracted algae) microalgae were suitable as a feed ingredient, but that the specifics of the fed animal and biochemical composition of the algae are critical factors when determining formulation. Similarly, poultry studies on whole and defatted microalgae generally showed positive outcomes on animal growth and health, with some microalgae providing enhanced nutritional composition of the animal product. Economic and life cycle assessments covered a wide range of possible commercialization and sustainability scenarios. Replacement value, improved product value added, consumer values marketing added valuation and improved animal health were considered as alternatives for microalgae valuation. Using the open pond system, algae productivity was identified as the key driver of commercialization economics, but combination of co-products (e.g. animal feed) with biofuel production substantially increased the total selling price of algae. Modeled microalgae selling price exceeded $1500/tonne and could generate competitive biofuel selling prices below $5 gallon gas equivalents using realistic algal productivities. Short (process scale) and longer (decadal trends) sustainability assessments show that marine microalgae can enhance the sustainability of energy production and lead to other realized benefits in water, fertilizer and land use for other sectors (e.g. agriculture). This project successfully demonstrated all of the components of an end-to-end process from mass microalgae cultivation and dewatering, to recovery and conversion of algae biomass components, to final product demonstration and process valuation; the combined results provide a framework for future commercialization of algae based biofuels.

  PublisherOA PDFDOI

• OPLS5: Addition of Polarizability and Improved Treatment of Metals

  ChemRxiv · 2024-08-13 · 18 citations

  preprintOpen access

  We report on the development and validation of the OPLS5 force field. OPLS5 further extends the accuracy of our previous model (OPLS4) with the addition of explicit polarization to improve model accuracy for molecular ions and cation-pi interactions. OPLS5 also includes advances to the functional form for metals achieving significant improvements across benchmarks assessing the structure and energetics of metal-organic complexes. Together these advances lead to improved accuracy on our protein-ligand binding benchmarks.

  PublisherOA PDFDOI

Recent grants

• MRI-R2: Acquisition of a High-Speed Sorting Flow Cytometer for Multi-User Environmental Microbiology Research

  NSF · $473k · 2010–2012

• Collaborative Research: Seasonal and decadal changes in temperature drive Prochlorococcus ecotype distribution patterns

  NSF · $601k · 2010–2015

• Collaborative Research: Ecotypic Diversity and Adaptation of Prochlorococcus in the Stratified, High Temperature Waters of the Western Pacific Warm Pool

  NSF · $397k · 2006–2010

• Collaborative Research: Iron-light Co-limitation in the Deep Chlorophyll Maximum of Stratified Oceanic Regimes

  NSF · $126k · 2006–2010

• Collaborative Research: Ocean Acidification: microbes as sentinels of adaptive responses to multiple stressors: contrasting estuarine and open ocean environments

  NSF · $798k · 2015–2019

Frequent coauthors

• Mark Huntley

  Luxel (United States)

  77 shared

• Dana E. Hunt

  University of South Carolina Beaufort

  63 shared

• Erik R. Zinser

  University of Tennessee at Knoxville

  50 shared

• Arjun Hausner

  Cornell University

  49 shared

• Charles S. Greene

  Cornell University

  49 shared

• Celina Scott-Buechler

  49 shared

• Sallie W. Chisholm

  Massachusetts Institute of Technology

  39 shared

• Susan L Brown

  37 shared

Labs

• Johnson LabPI